From afa02ff3fcf08faf214d311f0f5b1f7fb8123d5b Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Mon, 28 Oct 2024 09:52:14 +0000
Subject: [PATCH 01/24] remove engines parameter from process_cases and make
changes tht allow fetching all results links from remote runs
---
..._test_suite_compatibility_biosimulators.py | 2 +-
utils/__init__.py | 21 ++++++++-----------
2 files changed, 10 insertions(+), 13 deletions(-)
diff --git a/test_suite/test_test_suite_compatibility_biosimulators.py b/test_suite/test_test_suite_compatibility_biosimulators.py
index 1a1a590a..a7b790e7 100644
--- a/test_suite/test_test_suite_compatibility_biosimulators.py
+++ b/test_suite/test_test_suite_compatibility_biosimulators.py
@@ -134,7 +134,7 @@ def process_cases(args):
os.path.basename(sbml_file_path),
os.path.join(test_folder,'d1_plots_remote'),
os.path.join(test_folder,'d1_plots_local'),
- engines=engines, test_folder=test_folder)
+ test_folder=test_folder)
if __name__ == "__main__":
diff --git a/utils/__init__.py b/utils/__init__.py
index 5a232bcd..ad7cb82b 100644
--- a/utils/__init__.py
+++ b/utils/__init__.py
@@ -526,13 +526,11 @@ def run_biosimulators_remote(engine,sedml_filepath,sbml_filepath):
"email": "",
}
- res = biosimulations.submit_simulation_archive(\
+ results_urls = biosimulations.submit_simulation_archive(\
archive_file=omex_file_name,\
sim_dict=sim_dict)
-
- download_url = res["download"]
-
- return download_url
+
+ return results_urls
def get_remote_results(engine, download_link, output_dir='remote_results'):
@@ -1094,7 +1092,7 @@ def create_results_table(results, sbml_filepath, sedml_filepath, output_dir):
# Create a table of the results
results_table = pd.DataFrame.from_dict(results).T
# if list is three elements
- if results_table.shape[1] == 3:
+ if results_table.shape[1] > 2:
results_table.columns = [PASS_FAIL, ERROR, TYPE]
elif results_table.shape[1] == 2:
results_table.columns = [PASS_FAIL, ERROR]
@@ -1154,16 +1152,15 @@ def run_biosimulators_remotely(sedml_file_name,
remote_output_dir = 'remote_results'
remote_output_dir = os.path.join(test_folder, remote_output_dir)
- download_links_dict = dict()
+ results_urls = dict()
for e in ENGINES.keys():
- download_link = run_biosimulators_remote(e, sedml_file_name, sbml_file_name)
- download_links_dict[e] = download_link
+ results_urls[e] = run_biosimulators_remote(e, sedml_file_name, sbml_file_name)
extract_dir_dict = dict()
results_remote = dict()
- for e, link in download_links_dict.items():
+ for e, link in results_urls.items():
try:
- extract_dir = get_remote_results(e, link, remote_output_dir)
+ extract_dir = get_remote_results(e, link["download"], remote_output_dir)
except HTTPError as emessage:
results_remote[e] = ["FAIL", str(emessage), type(emessage).__name__]
continue
@@ -1190,7 +1187,7 @@ def run_biosimulators_remotely(sedml_file_name,
exception_type = exception['type']
else:
status = None
- results_remote[e] = [status, error_message, exception_type]
+ results_remote[e] = [status, error_message, exception_type, results_urls]
file_paths = find_files(remote_output_dir, '.pdf')
move_d1_files(file_paths, d1_plots_remote_dir)
From a6993639e4800f1957ed23c04a92d2563c4ccdfd Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Mon, 28 Oct 2024 16:38:41 +0000
Subject: [PATCH 02/24] add results_[local/remote] JSONs for easy testing and
improving of results_table creation
---
.../results_compatibility_biosimulators.md | 46 ++---
SBML/tests/results_local.json | 86 ++++++++
SBML/tests/results_local.md | 23 +++
SBML/tests/results_remote.json | 191 ++++++++++++++++++
SBML/tests/results_remote.md | 23 +++
SBML/tests/test_biosimulators_local.py | 5 +
SBML/tests/test_biosimulators_remote.py | 5 +
.../test_creation_combined_results_table.py | 16 +-
utils/__init__.py | 61 +++---
9 files changed, 401 insertions(+), 55 deletions(-)
create mode 100644 SBML/tests/results_local.json
create mode 100644 SBML/tests/results_local.md
create mode 100644 SBML/tests/results_remote.json
create mode 100644 SBML/tests/results_remote.md
diff --git a/SBML/tests/results_compatibility_biosimulators.md b/SBML/tests/results_compatibility_biosimulators.md
index 1cf019a0..1dca62c0 100644
--- a/SBML/tests/results_compatibility_biosimulators.md
+++ b/SBML/tests/results_compatibility_biosimulators.md
@@ -1,23 +1,23 @@
-| | Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | Error (R) | Error (L) | Type (R) | d1 (R) | d1 (L) |
-|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------|:------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------|
-| 0 | amici
https://docs.biosimulators.org/Biosimulators_AMICI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amicibionetgen
https://docs.biosimulators.org/Biosimulators_BioNetGen/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgenDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrorboolnet
https://docs.biosimulators.org/Biosimulators_BoolNet/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnetDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrorbrian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2Details
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```MNFE
ModuleNotFoundErrorcbmpy
https://docs.biosimulators.org/Biosimulators_CBMPy/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpyDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulationDetails
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrorcobrapy
https://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapyDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulationDetails
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrorcopasi
https://docs.biosimulators.org/Biosimulators_COPASI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasigillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2ginsim
https://docs.biosimulators.org/Biosimulators_GINsim/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsimDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrorlibsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsimmasspy
https://docs.biosimulators.org/Biosimulators_MASSpy/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspyDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrornetpyne
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyneDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```MNFE
ModuleNotFoundErrorneuron
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuronDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```MNFE
ModuleNotFoundErroropencor
https://docs.biosimulators.org/Biosimulators_OpenCOR/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencorDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```MNFE
ModuleNotFoundErrorpyneuroml
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuromlDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```MNFE
ModuleNotFoundErrorpysces
https://docs.biosimulators.org/Biosimulators_PySCeS/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pyscesDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Model at /tmp/tmp1bq_quiv/./LEMS_NML2_Ex9_FN.sbml could not be imported:
File /tmp/tmp1bq_quiv/./LEMS_NML2_Ex9_FN.sbml.xml does not existDetails
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrorrbapy
https://docs.biosimulators.org/Biosimulators_RBApy/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapyDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrorsmoldyn
https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldynDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```MNFE
ModuleNotFoundErrortellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with telluriumvcell
https://github.com/virtualcell/vcell
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcellDetails
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```xpp
https://docs.biosimulators.org/Biosimulators_XPP/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xppDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```MNFE
ModuleNotFoundErroramici
https://docs.biosimulators.org/Biosimulators_AMICI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici✅ PASS
view
download
logsbionetgen
https://docs.biosimulators.org/Biosimulators_BioNetGen/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen⚠ XFAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrorboolnet
https://docs.biosimulators.org/Biosimulators_BoolNet/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet⚠ XFAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrorbrian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2⚠ XFAIL
view
download
logsDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```MNFE
ModuleNotFoundErrorcbmpy
https://docs.biosimulators.org/Biosimulators_CBMPy/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy❌ FAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulationDetails
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrorcobrapy
https://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy❌ FAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulationDetails
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrorcopasi
https://docs.biosimulators.org/Biosimulators_COPASI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasi✅ PASS
view
download
logsgillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2✅ PASS
view
download
logsginsim
https://docs.biosimulators.org/Biosimulators_GINsim/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim⚠ XFAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrorlibsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsim✅ PASS
view
download
logsmasspy
https://docs.biosimulators.org/Biosimulators_MASSpy/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy❌ FAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrornetpyne
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne⚠ XFAIL
view
download
logsDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```MNFE
ModuleNotFoundErrorneuron
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron⚠ XFAIL
view
download
logsDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```MNFE
ModuleNotFoundErroropencor
https://docs.biosimulators.org/Biosimulators_OpenCOR/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor⚠ XFAIL
view
download
logsDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```MNFE
ModuleNotFoundErrorpyneuroml
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml⚠ XFAIL
view
download
logsDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```MNFE
ModuleNotFoundErrorpysces
https://docs.biosimulators.org/Biosimulators_PySCeS/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces❌ FAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrorrbapy
https://docs.biosimulators.org/Biosimulators_RBApy/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy⚠ XFAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrorsmoldyn
https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn⚠ XFAIL
view
download
logsDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```MNFE
ModuleNotFoundErrortellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium✅ PASS
view
download
logsvcell
https://github.com/virtualcell/vcell
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcellNone
view
download
logsDetails
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```xpp
https://docs.biosimulators.org/Biosimulators_XPP/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp⚠ XFAIL
view
download
logsDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```MNFE
ModuleNotFoundErroramici
https://docs.biosimulators.org/Biosimulators_AMICI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amicibrian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2bionetgen
https://docs.biosimulators.org/Biosimulators_BioNetGen/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgenboolnet
https://docs.biosimulators.org/Biosimulators_BoolNet/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnetcbmpy
https://docs.biosimulators.org/Biosimulators_CBMPy/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpycobrapy
https://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulationsDetails
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapycopasi
https://docs.biosimulators.org/Biosimulators_COPASI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasigillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2ginsim
https://docs.biosimulators.org/Biosimulators_GINsim/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsimlibsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsimmasspy
https://docs.biosimulators.org/Biosimulators_MASSpy/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspynetpyne
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyneneuron
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuronopencor
https://docs.biosimulators.org/Biosimulators_OpenCOR/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencorpyneuroml
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuromlpysces
https://docs.biosimulators.org/Biosimulators_PySCeS/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pyscesrbapy
https://docs.biosimulators.org/Biosimulators_RBApy/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapysmoldyn
https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyntellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with telluriumvcell
https://github.com/virtualcell/vcell
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcellxpp
https://docs.biosimulators.org/Biosimulators_XPP/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xppamici
https://docs.biosimulators.org/Biosimulators_AMICI/
✅ PASS
view
download
logs
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amicibrian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logsDetails
No module named 'libsbml'MNFE
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2bionetgen
https://docs.biosimulators.org/Biosimulators_BioNetGen/
⚠ XFAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).CAEE
CombineArchiveExecutionError
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgenboolnet
https://docs.biosimulators.org/Biosimulators_BoolNet/
⚠ XFAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).CAEE
CombineArchiveExecutionError
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnetcbmpy
https://docs.biosimulators.org/Biosimulators_CBMPy/
❌ FAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulationCAEE
CombineArchiveExecutionError
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpycobrapy
https://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations❌ FAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulationCAEE
CombineArchiveExecutionError
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapycopasi
https://docs.biosimulators.org/Biosimulators_COPASI/
✅ PASS
view
download
logs
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasigillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
✅ PASS
view
download
logs
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2ginsim
https://docs.biosimulators.org/Biosimulators_GINsim/
⚠ XFAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000CAEE
CombineArchiveExecutionError
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsimlibsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
✅ PASS
view
download
logs
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsimmasspy
https://docs.biosimulators.org/Biosimulators_MASSpy/
❌ FAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .CAEE
CombineArchiveExecutionError
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspynetpyne
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logsDetails
No module named 'libsbml'MNFE
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyneneuron
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logsDetails
No module named 'libsbml'MNFE
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuronopencor
https://docs.biosimulators.org/Biosimulators_OpenCOR/
⚠ XFAIL
view
download
logsDetails
No module named 'libsbml'MNFE
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencorpyneuroml
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logsDetails
No module named 'libsbml'MNFE
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuromlpysces
https://docs.biosimulators.org/Biosimulators_PySCeS/
❌ FAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
CAEE
CombineArchiveExecutionError
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pyscesrbapy
https://docs.biosimulators.org/Biosimulators_RBApy/
⚠ XFAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).CAEE
CombineArchiveExecutionError
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapysmoldyn
https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
⚠ XFAIL
view
download
logsDetails
No module named 'libsbml'MNFE
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyntellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
✅ PASS
view
download
logs
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with telluriumvcell
https://github.com/virtualcell/vcell
None
view
download
logs
download
logs | | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcellxpp
https://docs.biosimulators.org/Biosimulators_XPP/
⚠ XFAIL
view
download
logsDetails
No module named 'libsbml'MNFE
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp
'.join([f'{create_hyperlink(results[e][k], title=k)}' for k in results[e].keys() if k in ['view', 'download', 'logs']])
+
results_table = pd.DataFrame.from_dict(results).T
- # if list is three elements
- if results_table.shape[1] > 2:
- results_table.columns = [PASS_FAIL, ERROR, TYPE]
- elif results_table.shape[1] == 2:
- results_table.columns = [PASS_FAIL, ERROR]
+ results_table.rename(columns={"status": PASS_FAIL, "error_message": ERROR, "exception_type": TYPE}, inplace=True)
results_table.index.name = ENGINE
results_table.reset_index(inplace=True)
# Error
results_table[ERROR] = results_table.apply(lambda x: None if x[PASS_FAIL] == x[ERROR] else x[ERROR], axis=1)
- results_table[PASS_FAIL] = results_table[PASS_FAIL].replace('other', 'FAIL')
results_table[ERROR] = results_table[ERROR].apply(lambda x: ansi_to_html(x))
results_table[ERROR] = results_table[ERROR].apply(lambda x: collapsible_content(x))
@@ -1120,8 +1117,6 @@ def create_results_table(results, sbml_filepath, sedml_filepath, output_dir):
for e in ENGINES.keys():
compatibility_content = check_file_compatibility_test(e, sbml_filepath, sedml_filepath)
-
- print(e, compatibility_content[0] )
if compatibility_content[0] == 'pass':
results_table.loc[results_table[ENGINE] == e, COMPAT] = collapsible_content(compatibility_content[1], title=f'{pass_html}')
elif compatibility_content[0] == 'unsure':
@@ -1135,10 +1130,12 @@ def create_results_table(results, sbml_filepath, sedml_filepath, output_dir):
compatibility_content = check_file_compatibility_test(e, sbml_filepath, sedml_filepath)
results_table.loc[results_table[ENGINE] == e, COMPAT] = collapsible_content(compatibility_content[1], title=f'{xfail_html}')
results_table.loc[results_table[ENGINE] == e, PASS_FAIL] = f'{xfail_html}'
-
-
+
+ # for PASS_FAIL column in results_table, add collapsible content (add content from combi col if it exists) but keep titles the same as the content at the momtn
+ results_table[PASS_FAIL] = results_table.apply(lambda x: collapsible_content(x['combi'], x[PASS_FAIL]), axis=1)
+
# add status message defined in ENGINES
- results_table[ENGINE] = results_table[ENGINE].apply(lambda x: collapsible_content(f'{ENGINES[x]["url"]}
{ENGINES[x]["status"]}', x))
+ results_table[ENGINE] = results_table[ENGINE].apply(lambda x: collapsible_content(f'{ENGINES[x]["url"]}
{ENGINES[x]["status"]}', x))
return results_table
@@ -1153,13 +1150,13 @@ def run_biosimulators_remotely(sedml_file_name,
remote_output_dir = 'remote_results'
remote_output_dir = os.path.join(test_folder, remote_output_dir)
- results_urls = dict()
+ results_remote = dict()
for e in ENGINES.keys():
- results_urls[e] = run_biosimulators_remote(e, sedml_file_name, sbml_file_name)
-
+ results_remote[e] = run_biosimulators_remote(e, sedml_file_name, sbml_file_name)
+ results_remote[e]['response'] = results_remote[e]['response'].status_code
+
extract_dir_dict = dict()
- results_remote = dict()
- for e, link in results_urls.items():
+ for e, link in results_remote.items():
try:
extract_dir = get_remote_results(e, link["download"], remote_output_dir)
except HTTPError as emessage:
@@ -1188,7 +1185,9 @@ def run_biosimulators_remotely(sedml_file_name,
exception_type = exception['type']
else:
status = None
- results_remote[e] = [status, error_message, exception_type, results_urls]
+ results_remote[e]["status"] = status
+ results_remote[e]["error_message"] = error_message
+ results_remote[e]["exception_type"] = exception_type
file_paths = find_files(remote_output_dir, '.pdf')
move_d1_files(file_paths, d1_plots_remote_dir)
@@ -1213,8 +1212,7 @@ def run_biosimulators_locally(sedml_file_name,
print('Running ' + e)
local_output_dir_e = os.path.abspath(os.path.join(local_output_dir, e))
print(local_output_dir_e)
- record = run_biosimulators_docker(e, sedml_file_name, sbml_file_name, output_dir=local_output_dir_e)
- results_local[e] = record
+ results_local[e] = run_biosimulators_docker(e, sedml_file_name, sbml_file_name, output_dir=local_output_dir_e)
file_paths = find_files(local_output_dir, '.pdf')
print('file paths:', file_paths)
@@ -1227,8 +1225,6 @@ def run_biosimulators_locally(sedml_file_name,
return results_local
-
-
def create_combined_results_table(results_remote,
results_local,
sedml_file_name,
@@ -1242,7 +1238,16 @@ def create_combined_results_table(results_remote,
# Create results tables for remote and local results
results_table_remote = create_results_table(results_remote, sbml_file_name, sedml_file_name, d1_plots_remote_dir)
+ # save as md file
+ path_to_results = os.path.join(test_folder, 'results_remote.md')
+ with open(path_to_results, 'w', encoding='utf-8') as f:
+ f.write(results_table_remote.to_markdown())
+
results_table_local = create_results_table(results_local, sbml_file_name, sedml_file_name, d1_plots_local_dir)
+ # save as md file
+ path_to_results = os.path.join(test_folder, 'results_local.md')
+ with open(path_to_results, 'w', encoding='utf-8') as f:
+ f.write(results_table_local.to_markdown())
# Rename columns to distinguish between local and remote results except for Engine column
results_table_remote.columns = [f"{col}{suffix_remote}" if col != ENGINE else col for col in results_table_remote.columns]
From 830810f2eb60d765f7aa1ef110bfa03e7fecdd04 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Tue, 29 Oct 2024 10:17:32 +0000
Subject: [PATCH 03/24] add links column to results table and update
collapsible content for PASS_FAIL.
---
.../results_compatibility_biosimulators.md | 42 ++++++++---------
SBML/tests/results_local.md | 46 +++++++++----------
SBML/tests/results_remote.md | 2 +-
utils/__init__.py | 10 ++--
4 files changed, 51 insertions(+), 49 deletions(-)
diff --git a/SBML/tests/results_compatibility_biosimulators.md b/SBML/tests/results_compatibility_biosimulators.md
index 1dca62c0..4b4e77d7 100644
--- a/SBML/tests/results_compatibility_biosimulators.md
+++ b/SBML/tests/results_compatibility_biosimulators.md
@@ -1,23 +1,23 @@
| | Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | Error (R) | Error (L) | Type (R) | d1 (R) | d1 (L) |
|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------|
-| 0 | amici
https://docs.biosimulators.org/Biosimulators_AMICI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici✅ PASS
view
download
logsbionetgen
https://docs.biosimulators.org/Biosimulators_BioNetGen/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen⚠ XFAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrorboolnet
https://docs.biosimulators.org/Biosimulators_BoolNet/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet⚠ XFAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrorbrian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2⚠ XFAIL
view
download
logsDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```MNFE
ModuleNotFoundErrorcbmpy
https://docs.biosimulators.org/Biosimulators_CBMPy/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy❌ FAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulationDetails
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrorcobrapy
https://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy❌ FAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulationDetails
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrorcopasi
https://docs.biosimulators.org/Biosimulators_COPASI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasi✅ PASS
view
download
logsgillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2✅ PASS
view
download
logsginsim
https://docs.biosimulators.org/Biosimulators_GINsim/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim⚠ XFAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrorlibsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsim✅ PASS
view
download
logsmasspy
https://docs.biosimulators.org/Biosimulators_MASSpy/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy❌ FAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrornetpyne
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne⚠ XFAIL
view
download
logsDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```MNFE
ModuleNotFoundErrorneuron
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron⚠ XFAIL
view
download
logsDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```MNFE
ModuleNotFoundErroropencor
https://docs.biosimulators.org/Biosimulators_OpenCOR/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor⚠ XFAIL
view
download
logsDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```MNFE
ModuleNotFoundErrorpyneuroml
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml⚠ XFAIL
view
download
logsDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```MNFE
ModuleNotFoundErrorpysces
https://docs.biosimulators.org/Biosimulators_PySCeS/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces❌ FAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrorrbapy
https://docs.biosimulators.org/Biosimulators_RBApy/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy⚠ XFAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrorsmoldyn
https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn⚠ XFAIL
view
download
logsDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```MNFE
ModuleNotFoundErrortellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium✅ PASS
view
download
logsvcell
https://github.com/virtualcell/vcell
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcellNone
view
download
logsDetails
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```xpp
https://docs.biosimulators.org/Biosimulators_XPP/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp⚠ XFAIL
view
download
logsDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```MNFE
ModuleNotFoundErroramici
https://docs.biosimulators.org/Biosimulators_AMICI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici✅ PASS
view
download
logsbionetgen
https://docs.biosimulators.org/Biosimulators_BioNetGen/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen⚠ XFAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrorboolnet
https://docs.biosimulators.org/Biosimulators_BoolNet/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet⚠ XFAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrorbrian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2⚠ XFAIL
view
download
logsDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```MNFE
ModuleNotFoundErrorcbmpy
https://docs.biosimulators.org/Biosimulators_CBMPy/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy❌ FAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulationDetails
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrorcobrapy
https://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy❌ FAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulationDetails
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrorcopasi
https://docs.biosimulators.org/Biosimulators_COPASI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasi✅ PASS
view
download
logsgillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2✅ PASS
view
download
logsginsim
https://docs.biosimulators.org/Biosimulators_GINsim/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim⚠ XFAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrorlibsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsim✅ PASS
view
download
logsmasspy
https://docs.biosimulators.org/Biosimulators_MASSpy/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy❌ FAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrornetpyne
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne⚠ XFAIL
view
download
logsDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```MNFE
ModuleNotFoundErrorneuron
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron⚠ XFAIL
view
download
logsDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```MNFE
ModuleNotFoundErroropencor
https://docs.biosimulators.org/Biosimulators_OpenCOR/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor⚠ XFAIL
view
download
logsDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```MNFE
ModuleNotFoundErrorpyneuroml
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml⚠ XFAIL
view
download
logsDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```MNFE
ModuleNotFoundErrorpysces
https://docs.biosimulators.org/Biosimulators_PySCeS/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces❌ FAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrorrbapy
https://docs.biosimulators.org/Biosimulators_RBApy/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy⚠ XFAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrorsmoldyn
https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn⚠ XFAIL
view
download
logsDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```MNFE
ModuleNotFoundErrortellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium✅ PASS
view
download
logsvcell
https://github.com/virtualcell/vcell
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcellNone
view
download
logsDetails
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```xpp
https://docs.biosimulators.org/Biosimulators_XPP/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp⚠ XFAIL
view
download
logsDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```MNFE
ModuleNotFoundErroramici
https://docs.biosimulators.org/Biosimulators_AMICI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amicibrian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2bionetgen
https://docs.biosimulators.org/Biosimulators_BioNetGen/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgenboolnet
https://docs.biosimulators.org/Biosimulators_BoolNet/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnetcbmpy
https://docs.biosimulators.org/Biosimulators_CBMPy/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpycobrapy
https://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulationsDetails
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapycopasi
https://docs.biosimulators.org/Biosimulators_COPASI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasigillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2ginsim
https://docs.biosimulators.org/Biosimulators_GINsim/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsimlibsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsimmasspy
https://docs.biosimulators.org/Biosimulators_MASSpy/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspynetpyne
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyneneuron
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuronopencor
https://docs.biosimulators.org/Biosimulators_OpenCOR/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencorpyneuroml
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuromlpysces
https://docs.biosimulators.org/Biosimulators_PySCeS/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pyscesrbapy
https://docs.biosimulators.org/Biosimulators_RBApy/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapysmoldyn
https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyntellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with telluriumvcell
https://github.com/virtualcell/vcell
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcellxpp
https://docs.biosimulators.org/Biosimulators_XPP/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xppamici
https://docs.biosimulators.org/Biosimulators_AMICI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amicibrian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2bionetgen
https://docs.biosimulators.org/Biosimulators_BioNetGen/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgenboolnet
https://docs.biosimulators.org/Biosimulators_BoolNet/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnetcbmpy
https://docs.biosimulators.org/Biosimulators_CBMPy/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpycobrapy
https://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulationsDetails
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapycopasi
https://docs.biosimulators.org/Biosimulators_COPASI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasigillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2ginsim
https://docs.biosimulators.org/Biosimulators_GINsim/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsimlibsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsimmasspy
https://docs.biosimulators.org/Biosimulators_MASSpy/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspynetpyne
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyneneuron
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuronopencor
https://docs.biosimulators.org/Biosimulators_OpenCOR/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencorpyneuroml
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuromlpysces
https://docs.biosimulators.org/Biosimulators_PySCeS/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pyscesrbapy
https://docs.biosimulators.org/Biosimulators_RBApy/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapysmoldyn
https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyntellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with telluriumvcell
https://github.com/virtualcell/vcell
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcellxpp
https://docs.biosimulators.org/Biosimulators_XPP/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xppamici
https://docs.biosimulators.org/Biosimulators_AMICI/
✅ PASS
view
download
logs
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amicibrian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logsDetails
No module named 'libsbml'MNFE
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2
'.join([f'{create_hyperlink(results[e][k], title=k)}' for k in results[e].keys() if k in ['view', 'download', 'logs']])
+ if any([l in results[e].keys() for l in links]):
+ results[e]['links'] = '
'.join([f'{create_hyperlink(results[e][k], title=k)}' for k in results[e].keys() if k in links])
results_table = pd.DataFrame.from_dict(results).T
results_table.rename(columns={"status": PASS_FAIL, "error_message": ERROR, "exception_type": TYPE}, inplace=True)
@@ -1131,8 +1132,9 @@ def create_results_table(results, sbml_filepath, sedml_filepath, output_dir):
results_table.loc[results_table[ENGINE] == e, COMPAT] = collapsible_content(compatibility_content[1], title=f'{xfail_html}')
results_table.loc[results_table[ENGINE] == e, PASS_FAIL] = f'{xfail_html}'
- # for PASS_FAIL column in results_table, add collapsible content (add content from combi col if it exists) but keep titles the same as the content at the momtn
- results_table[PASS_FAIL] = results_table.apply(lambda x: collapsible_content(x['combi'], x[PASS_FAIL]), axis=1)
+ # if links column exists add collapsible content to PASS_FAIL column
+ if 'links' in results_table.columns:
+ results_table[PASS_FAIL] = results_table.apply(lambda x: collapsible_content(x['links'], x[PASS_FAIL]), axis=1)
# add status message defined in ENGINES
results_table[ENGINE] = results_table[ENGINE].apply(lambda x: collapsible_content(f'{ENGINES[x]["url"]}
{ENGINES[x]["status"]}', x))
From 41389a64f744bdef86861c43a384cca5dcc226dd Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Tue, 29 Oct 2024 17:34:02 +0000
Subject: [PATCH 04/24] draft for adding the warning messages in the foldout
menu for the pass and fail column
---
.../results_compatibility_biosimulators.md | 46 +++++++++----------
SBML/tests/results_local.md | 46 +++++++++----------
SBML/tests/results_remote.md | 46 +++++++++----------
utils/__init__.py | 46 +++++++++++++++----
4 files changed, 105 insertions(+), 79 deletions(-)
diff --git a/SBML/tests/results_compatibility_biosimulators.md b/SBML/tests/results_compatibility_biosimulators.md
index 4b4e77d7..1e24c0ba 100644
--- a/SBML/tests/results_compatibility_biosimulators.md
+++ b/SBML/tests/results_compatibility_biosimulators.md
@@ -1,23 +1,23 @@
-| | Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | Error (R) | Error (L) | Type (R) | d1 (R) | d1 (L) |
-|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------|
-| 0 | amici
https://docs.biosimulators.org/Biosimulators_AMICI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici✅ PASS
view
download
logsbionetgen
https://docs.biosimulators.org/Biosimulators_BioNetGen/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen⚠ XFAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrorboolnet
https://docs.biosimulators.org/Biosimulators_BoolNet/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet⚠ XFAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrorbrian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2⚠ XFAIL
view
download
logsDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```MNFE
ModuleNotFoundErrorcbmpy
https://docs.biosimulators.org/Biosimulators_CBMPy/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy❌ FAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulationDetails
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrorcobrapy
https://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy❌ FAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulationDetails
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrorcopasi
https://docs.biosimulators.org/Biosimulators_COPASI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasi✅ PASS
view
download
logsgillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2✅ PASS
view
download
logsginsim
https://docs.biosimulators.org/Biosimulators_GINsim/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim⚠ XFAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrorlibsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsim✅ PASS
view
download
logsmasspy
https://docs.biosimulators.org/Biosimulators_MASSpy/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy❌ FAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrornetpyne
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne⚠ XFAIL
view
download
logsDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```MNFE
ModuleNotFoundErrorneuron
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron⚠ XFAIL
view
download
logsDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```MNFE
ModuleNotFoundErroropencor
https://docs.biosimulators.org/Biosimulators_OpenCOR/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor⚠ XFAIL
view
download
logsDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```MNFE
ModuleNotFoundErrorpyneuroml
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml⚠ XFAIL
view
download
logsDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```MNFE
ModuleNotFoundErrorpysces
https://docs.biosimulators.org/Biosimulators_PySCeS/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces❌ FAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrorrbapy
https://docs.biosimulators.org/Biosimulators_RBApy/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy⚠ XFAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrorsmoldyn
https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn⚠ XFAIL
view
download
logsDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```MNFE
ModuleNotFoundErrortellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium✅ PASS
view
download
logsvcell
https://github.com/virtualcell/vcell
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcellNone
view
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logsDetails
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```xpp
https://docs.biosimulators.org/Biosimulators_XPP/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp⚠ XFAIL
view
download
logsDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```MNFE
ModuleNotFoundErroramici
https://docs.biosimulators.org/Biosimulators_AMICI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amicibionetgen
https://docs.biosimulators.org/Biosimulators_BioNetGen/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).
ERROR TYPE:
CombineArchiveExecutionError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```boolnet
https://docs.biosimulators.org/Biosimulators_BoolNet/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).
ERROR TYPE:
CombineArchiveExecutionError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```brian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```cbmpy
https://docs.biosimulators.org/Biosimulators_CBMPy/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
CombineArchiveExecutionError❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```cobrapy
https://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
CombineArchiveExecutionError❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```copasi
https://docs.biosimulators.org/Biosimulators_COPASI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasigillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2ginsim
https://docs.biosimulators.org/Biosimulators_GINsim/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000
ERROR TYPE:
CombineArchiveExecutionError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```libsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsimmasspy
https://docs.biosimulators.org/Biosimulators_MASSpy/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .
ERROR TYPE:
CombineArchiveExecutionError❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```netpyne
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```neuron
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```opencor
https://docs.biosimulators.org/Biosimulators_OpenCOR/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```pyneuroml
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```pysces
https://docs.biosimulators.org/Biosimulators_PySCeS/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
ERROR TYPE:
CombineArchiveExecutionError❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```rbapy
https://docs.biosimulators.org/Biosimulators_RBApy/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).
ERROR TYPE:
CombineArchiveExecutionError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```smoldyn
https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```tellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with telluriumvcell
https://github.com/virtualcell/vcell
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcellNone
view
download
logs
ERROR TYPE:
❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```xpp
https://docs.biosimulators.org/Biosimulators_XPP/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```amici
https://docs.biosimulators.org/Biosimulators_AMICI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amicibrian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2bionetgen
https://docs.biosimulators.org/Biosimulators_BioNetGen/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgenboolnet
https://docs.biosimulators.org/Biosimulators_BoolNet/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnetcbmpy
https://docs.biosimulators.org/Biosimulators_CBMPy/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpycobrapy
https://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulationsDetails
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapycopasi
https://docs.biosimulators.org/Biosimulators_COPASI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasigillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2ginsim
https://docs.biosimulators.org/Biosimulators_GINsim/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsimlibsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsimmasspy
https://docs.biosimulators.org/Biosimulators_MASSpy/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspynetpyne
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyneneuron
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuronopencor
https://docs.biosimulators.org/Biosimulators_OpenCOR/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencorpyneuroml
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuromlpysces
https://docs.biosimulators.org/Biosimulators_PySCeS/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pyscesrbapy
https://docs.biosimulators.org/Biosimulators_RBApy/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapysmoldyn
https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyntellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with telluriumvcell
https://github.com/virtualcell/vcell
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcellxpp
https://docs.biosimulators.org/Biosimulators_XPP/
Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xppamici
https://docs.biosimulators.org/Biosimulators_AMICI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amicibrian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1``` |
+| 2 | bionetgen
https://docs.biosimulators.org/Biosimulators_BioNetGen/
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1``` |
+| 3 | boolnet
https://docs.biosimulators.org/Biosimulators_BoolNet/
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1``` |
+| 4 | cbmpy
https://docs.biosimulators.org/Biosimulators_CBMPy/
❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1``` |
+| 5 | cobrapy
https://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1``` |
+| 6 | copasi
https://docs.biosimulators.org/Biosimulators_COPASI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasigillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2ginsim
https://docs.biosimulators.org/Biosimulators_GINsim/
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1``` |
+| 9 | libsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsimmasspy
https://docs.biosimulators.org/Biosimulators_MASSpy/
❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1``` |
+| 11 | netpyne
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1``` |
+| 12 | neuron
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1``` |
+| 13 | opencor
https://docs.biosimulators.org/Biosimulators_OpenCOR/
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1``` |
+| 14 | pyneuroml
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1``` |
+| 15 | pysces
https://docs.biosimulators.org/Biosimulators_PySCeS/
❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1``` |
+| 16 | rbapy
https://docs.biosimulators.org/Biosimulators_RBApy/
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1``` |
+| 17 | smoldyn
https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1``` |
+| 18 | tellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with telluriumvcell
https://github.com/virtualcell/vcell
❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1``` |
+| 20 | xpp
https://docs.biosimulators.org/Biosimulators_XPP/
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1``` |
\ No newline at end of file
diff --git a/SBML/tests/results_remote.md b/SBML/tests/results_remote.md
index bfa4e799..2a00fe53 100644
--- a/SBML/tests/results_remote.md
+++ b/SBML/tests/results_remote.md
@@ -1,23 +1,23 @@
-| | Engine | response | view | download | logs | pass / FAIL | Error | Type | links | d1 | Compatibility |
-|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|-----------:|:-------------------------------------------------------------|:-------------------------------------------------------------------------|:--------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| 0 | amici
https://docs.biosimulators.org/Biosimulators_AMICI/
✅ PASS
view
download
logs
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amicibrian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logsDetails
No module named 'libsbml'MNFE
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2bionetgen
https://docs.biosimulators.org/Biosimulators_BioNetGen/
⚠ XFAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).CAEE
CombineArchiveExecutionError
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgenboolnet
https://docs.biosimulators.org/Biosimulators_BoolNet/
⚠ XFAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).CAEE
CombineArchiveExecutionError
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnetcbmpy
https://docs.biosimulators.org/Biosimulators_CBMPy/
❌ FAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulationCAEE
CombineArchiveExecutionError
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpycobrapy
https://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations❌ FAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulationCAEE
CombineArchiveExecutionError
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapycopasi
https://docs.biosimulators.org/Biosimulators_COPASI/
✅ PASS
view
download
logs
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasigillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
✅ PASS
view
download
logs
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2ginsim
https://docs.biosimulators.org/Biosimulators_GINsim/
⚠ XFAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000CAEE
CombineArchiveExecutionError
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsimlibsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
✅ PASS
view
download
logs
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsimmasspy
https://docs.biosimulators.org/Biosimulators_MASSpy/
❌ FAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .CAEE
CombineArchiveExecutionError
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspynetpyne
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logsDetails
No module named 'libsbml'MNFE
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyneneuron
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logsDetails
No module named 'libsbml'MNFE
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuronopencor
https://docs.biosimulators.org/Biosimulators_OpenCOR/
⚠ XFAIL
view
download
logsDetails
No module named 'libsbml'MNFE
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencorpyneuroml
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logsDetails
No module named 'libsbml'MNFE
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuromlpysces
https://docs.biosimulators.org/Biosimulators_PySCeS/
❌ FAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
CAEE
CombineArchiveExecutionError
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pyscesrbapy
https://docs.biosimulators.org/Biosimulators_RBApy/
⚠ XFAIL
view
download
logsDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).CAEE
CombineArchiveExecutionError
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapysmoldyn
https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
⚠ XFAIL
view
download
logsDetails
No module named 'libsbml'MNFE
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyntellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
✅ PASS
view
download
logs
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with telluriumvcell
https://github.com/virtualcell/vcell
None
view
download
logs
download
logs | | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcellxpp
https://docs.biosimulators.org/Biosimulators_XPP/
⚠ XFAIL
view
download
logsDetails
No module named 'libsbml'MNFE
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xppamici
https://docs.biosimulators.org/Biosimulators_AMICI/
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amicibrian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError |
+| 2 | bionetgen
https://docs.biosimulators.org/Biosimulators_BioNetGen/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`). | CombineArchiveExecutionError | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).
ERROR TYPE:
CombineArchiveExecutionError |
+| 3 | boolnet
https://docs.biosimulators.org/Biosimulators_BoolNet/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0). | CombineArchiveExecutionError | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).
ERROR TYPE:
CombineArchiveExecutionError |
+| 4 | cbmpy
https://docs.biosimulators.org/Biosimulators_CBMPy/
❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation | CombineArchiveExecutionError | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
CombineArchiveExecutionError |
+| 5 | cobrapy
https://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation | CombineArchiveExecutionError | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
CombineArchiveExecutionError |
+| 6 | copasi
https://docs.biosimulators.org/Biosimulators_COPASI/
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasigillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2ginsim
https://docs.biosimulators.org/Biosimulators_GINsim/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000 | CombineArchiveExecutionError | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000
ERROR TYPE:
CombineArchiveExecutionError |
+| 9 | libsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsimmasspy
https://docs.biosimulators.org/Biosimulators_MASSpy/
❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues . | CombineArchiveExecutionError | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .
ERROR TYPE:
CombineArchiveExecutionError |
+| 11 | netpyne
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError |
+| 12 | neuron
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError |
+| 13 | opencor
https://docs.biosimulators.org/Biosimulators_OpenCOR/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError |
+| 14 | pyneuroml
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError |
+| 15 | pysces
https://docs.biosimulators.org/Biosimulators_PySCeS/
❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
| CombineArchiveExecutionError | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
ERROR TYPE:
CombineArchiveExecutionError |
+| 16 | rbapy
https://docs.biosimulators.org/Biosimulators_RBApy/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`). | CombineArchiveExecutionError | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).
ERROR TYPE:
CombineArchiveExecutionError |
+| 17 | smoldyn
https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError |
+| 18 | tellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with telluriumvcell
https://github.com/virtualcell/vcell
None
view
download
logs
ERROR TYPE:
download
logs | | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
download
logs
ERROR TYPE:
|
+| 20 | xpp
https://docs.biosimulators.org/Biosimulators_XPP/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError |
\ No newline at end of file
diff --git a/utils/__init__.py b/utils/__init__.py
index d9f1f2f6..5eacb5df 100644
--- a/utils/__init__.py
+++ b/utils/__init__.py
@@ -1094,6 +1094,14 @@ def create_results_table(results, sbml_filepath, sedml_filepath, output_dir):
if any([l in results[e].keys() for l in links]):
results[e]['links'] = '
'.join([f'{create_hyperlink(results[e][k], title=k)}' for k in results[e].keys() if k in links])
+ # # add error_message amd exception_type (if it exists) to underneath the links html on new lines
+ # error_info = ['error_message', 'exception_type']
+ # for e in results.keys():
+ # if any([l in results[e].keys() for l in links]):
+ # results[e]['links'] += '
' + '
'.join([f'{results[e][k]}' for k in results[e].keys() if k in error_info])
+ # else:
+ # results[e]['links'] = '
'.join([f'{results[e][k]}' for k in results[e].keys() if k in error_info])
+ #
results_table = pd.DataFrame.from_dict(results).T
results_table.rename(columns={"status": PASS_FAIL, "error_message": ERROR, "exception_type": TYPE}, inplace=True)
@@ -1102,9 +1110,9 @@ def create_results_table(results, sbml_filepath, sedml_filepath, output_dir):
# Error
results_table[ERROR] = results_table.apply(lambda x: None if x[PASS_FAIL] == x[ERROR] else x[ERROR], axis=1)
-
results_table[ERROR] = results_table[ERROR].apply(lambda x: ansi_to_html(x))
- results_table[ERROR] = results_table[ERROR].apply(lambda x: collapsible_content(x))
+
+ # results_table[ERROR] = results_table[ERROR].apply(lambda x: collapsible_content(x))
results_table[PASS_FAIL] = results_table[PASS_FAIL].apply(lambda x: f'{fail_html}' if x == 'FAIL' \
else f'{pass_html}' if x == 'pass' else x)
@@ -1113,9 +1121,6 @@ def create_results_table(results, sbml_filepath, sedml_filepath, output_dir):
results_table[D1] = results_table[ENGINE].apply(lambda x: d1_plots_dict(output_dir).get(x, None))
results_table[D1] = results_table[D1].apply(lambda x: create_hyperlink(x,title='plot'))
- if TYPE in results_table.columns:
- results_table[TYPE] = results_table[TYPE].apply(lambda x: collapsible_content(x,"".join(re.findall(r'[A-Z]', x))))
-
for e in ENGINES.keys():
compatibility_content = check_file_compatibility_test(e, sbml_filepath, sedml_filepath)
if compatibility_content[0] == 'pass':
@@ -1132,9 +1137,32 @@ def create_results_table(results, sbml_filepath, sedml_filepath, output_dir):
results_table.loc[results_table[ENGINE] == e, COMPAT] = collapsible_content(compatibility_content[1], title=f'{xfail_html}')
results_table.loc[results_table[ENGINE] == e, PASS_FAIL] = f'{xfail_html}'
- # if links column exists add collapsible content to PASS_FAIL column
- if 'links' in results_table.columns:
- results_table[PASS_FAIL] = results_table.apply(lambda x: collapsible_content(x['links'], x[PASS_FAIL]), axis=1)
+ for e in results_table[ENGINE]:
+ # only if no 'pass' in pass / fail column
+ if results_table.loc[results_table[ENGINE] == e, PASS_FAIL].values[0] != pass_html:
+ if len(results_table.loc[results_table[ENGINE] == e, ERROR].values[0]) > 1:
+ error_message = f'
ERROR MESSAGE:
{results_table.loc[results_table[ENGINE] == e, ERROR].values[0]}'
+ else:
+ error_message = ""
+ if "links" in results_table.columns:
+ links = results_table.loc[results_table[ENGINE] == e, "links"].values[0]
+ else:
+ links = ""
+ if TYPE in results_table.columns:
+ error_type = f'
ERROR TYPE:
{results_table.loc[results_table[ENGINE] == e, TYPE].values[0]}'
+ else:
+ error_type =""
+
+ links_error = f'{links}{error_message}{error_type}'
+ results_table.loc[results_table[ENGINE] == e, "links_error"] = links_error
+
+ # add links as collapsible content to pass fail col only if pass fail is not pass
+ for e in results_table[ENGINE]:
+ if results_table.loc[results_table[ENGINE] == e, PASS_FAIL].values[0] != pass_html:
+ # add collapsible content links_error to PASS_FAIL column
+ results_table.loc[results_table[ENGINE] == e, PASS_FAIL] = collapsible_content(results_table.loc[results_table[ENGINE] == e, "links_error"].values[0], results_table.loc[results_table[ENGINE] == e, PASS_FAIL].values[0])
+
+ # results_table[PASS_FAIL] = results_table.apply(lambda x: collapsible_content(x['links_error'], x[PASS_FAIL]), axis=1)
# add status message defined in ENGINES
results_table[ENGINE] = results_table[ENGINE].apply(lambda x: collapsible_content(f'{ENGINES[x]["url"]}
{ENGINES[x]["status"]}', x))
@@ -1266,8 +1294,6 @@ def create_combined_results_table(results_remote,
ENGINE,
COMPAT,
f"{PASS_FAIL}{suffix_remote}", f"{PASS_FAIL}{suffix_local}",
- f"{ERROR}{suffix_remote}", f"{ERROR}{suffix_local}",
- f"{TYPE}{suffix_remote}",
f"{D1}{suffix_remote}", f"{D1}{suffix_local}"
]
From 08da4003470a4184041079bd1d02bc0cfe881b10 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Wed, 30 Oct 2024 08:20:01 +0000
Subject: [PATCH 05/24] remove outcommented code and a few of the comments
---
utils/__init__.py | 17 ++---------------
1 file changed, 2 insertions(+), 15 deletions(-)
diff --git a/utils/__init__.py b/utils/__init__.py
index 5eacb5df..6f9598b6 100644
--- a/utils/__init__.py
+++ b/utils/__init__.py
@@ -1094,14 +1094,6 @@ def create_results_table(results, sbml_filepath, sedml_filepath, output_dir):
if any([l in results[e].keys() for l in links]):
results[e]['links'] = '
'.join([f'{create_hyperlink(results[e][k], title=k)}' for k in results[e].keys() if k in links])
- # # add error_message amd exception_type (if it exists) to underneath the links html on new lines
- # error_info = ['error_message', 'exception_type']
- # for e in results.keys():
- # if any([l in results[e].keys() for l in links]):
- # results[e]['links'] += '
' + '
'.join([f'{results[e][k]}' for k in results[e].keys() if k in error_info])
- # else:
- # results[e]['links'] = '
'.join([f'{results[e][k]}' for k in results[e].keys() if k in error_info])
- #
results_table = pd.DataFrame.from_dict(results).T
results_table.rename(columns={"status": PASS_FAIL, "error_message": ERROR, "exception_type": TYPE}, inplace=True)
@@ -1112,8 +1104,6 @@ def create_results_table(results, sbml_filepath, sedml_filepath, output_dir):
results_table[ERROR] = results_table.apply(lambda x: None if x[PASS_FAIL] == x[ERROR] else x[ERROR], axis=1)
results_table[ERROR] = results_table[ERROR].apply(lambda x: ansi_to_html(x))
- # results_table[ERROR] = results_table[ERROR].apply(lambda x: collapsible_content(x))
-
results_table[PASS_FAIL] = results_table[PASS_FAIL].apply(lambda x: f'{fail_html}' if x == 'FAIL' \
else f'{pass_html}' if x == 'pass' else x)
@@ -1138,7 +1128,7 @@ def create_results_table(results, sbml_filepath, sedml_filepath, output_dir):
results_table.loc[results_table[ENGINE] == e, PASS_FAIL] = f'{xfail_html}'
for e in results_table[ENGINE]:
- # only if no 'pass' in pass / fail column
+ # only if no 'pass' in pass / fail column add error messages to links_error
if results_table.loc[results_table[ENGINE] == e, PASS_FAIL].values[0] != pass_html:
if len(results_table.loc[results_table[ENGINE] == e, ERROR].values[0]) > 1:
error_message = f'
ERROR MESSAGE:
{results_table.loc[results_table[ENGINE] == e, ERROR].values[0]}'
@@ -1156,14 +1146,11 @@ def create_results_table(results, sbml_filepath, sedml_filepath, output_dir):
links_error = f'{links}{error_message}{error_type}'
results_table.loc[results_table[ENGINE] == e, "links_error"] = links_error
- # add links as collapsible content to pass fail col only if pass fail is not pass
+ # add links as collapsible content to pass / fail column
for e in results_table[ENGINE]:
if results_table.loc[results_table[ENGINE] == e, PASS_FAIL].values[0] != pass_html:
- # add collapsible content links_error to PASS_FAIL column
results_table.loc[results_table[ENGINE] == e, PASS_FAIL] = collapsible_content(results_table.loc[results_table[ENGINE] == e, "links_error"].values[0], results_table.loc[results_table[ENGINE] == e, PASS_FAIL].values[0])
- # results_table[PASS_FAIL] = results_table.apply(lambda x: collapsible_content(x['links_error'], x[PASS_FAIL]), axis=1)
-
# add status message defined in ENGINES
results_table[ENGINE] = results_table[ENGINE].apply(lambda x: collapsible_content(f'{ENGINES[x]["url"]}
{ENGINES[x]["status"]}', x))
From 30f36a2b4a8e4fad2ceb756ad00a86978f66fb7d Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Wed, 30 Oct 2024 09:40:26 +0000
Subject: [PATCH 06/24] update biosimulator functions to accept engine keys and
add handling of max steps reached cases (eg amici)
---
.../results_compatibility_biosimulators.md | 46 ++---
SBML/tests/results_remote.json | 195 ++++++++++--------
SBML/tests/results_remote.md | 46 ++---
SBML/tests/test_biosimulators_remote.py | 5 +-
.../tests/test_compatibility_biosimulators.py | 5 +-
utils/__init__.py | 37 +++-
6 files changed, 190 insertions(+), 144 deletions(-)
diff --git a/SBML/tests/results_compatibility_biosimulators.md b/SBML/tests/results_compatibility_biosimulators.md
index 1e24c0ba..11b85548 100644
--- a/SBML/tests/results_compatibility_biosimulators.md
+++ b/SBML/tests/results_compatibility_biosimulators.md
@@ -1,23 +1,23 @@
-| | Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) |
-|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------|
-| 0 | amici
https://docs.biosimulators.org/Biosimulators_AMICI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amicibionetgen
https://docs.biosimulators.org/Biosimulators_BioNetGen/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).
ERROR TYPE:
CombineArchiveExecutionError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```boolnet
https://docs.biosimulators.org/Biosimulators_BoolNet/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).
ERROR TYPE:
CombineArchiveExecutionError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```brian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```cbmpy
https://docs.biosimulators.org/Biosimulators_CBMPy/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
CombineArchiveExecutionError❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```cobrapy
https://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
CombineArchiveExecutionError❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```copasi
https://docs.biosimulators.org/Biosimulators_COPASI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasigillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2ginsim
https://docs.biosimulators.org/Biosimulators_GINsim/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000
ERROR TYPE:
CombineArchiveExecutionError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```libsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsimmasspy
https://docs.biosimulators.org/Biosimulators_MASSpy/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .
ERROR TYPE:
CombineArchiveExecutionError❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```netpyne
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```neuron
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```opencor
https://docs.biosimulators.org/Biosimulators_OpenCOR/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```pyneuroml
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```pysces
https://docs.biosimulators.org/Biosimulators_PySCeS/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
ERROR TYPE:
CombineArchiveExecutionError❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```rbapy
https://docs.biosimulators.org/Biosimulators_RBApy/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).
ERROR TYPE:
CombineArchiveExecutionError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```smoldyn
https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```tellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with telluriumvcell
https://github.com/virtualcell/vcell
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcellNone
view
download
logs
ERROR TYPE:
❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```xpp
https://docs.biosimulators.org/Biosimulators_XPP/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```amici
https://docs.biosimulators.org/Biosimulators_AMICI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici⚠ WARNING
view
download
logs
ERROR MESSAGE:
Reached maximum number of steps
ERROR TYPE:
bionetgen
https://docs.biosimulators.org/Biosimulators_BioNetGen/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).
ERROR TYPE:
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```boolnet
https://docs.biosimulators.org/Biosimulators_BoolNet/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).
ERROR TYPE:
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```brian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```cbmpy
https://docs.biosimulators.org/Biosimulators_CBMPy/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```cobrapy
https://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```copasi
https://docs.biosimulators.org/Biosimulators_COPASI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasigillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2ginsim
https://docs.biosimulators.org/Biosimulators_GINsim/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000
ERROR TYPE:
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```libsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsimmasspy
https://docs.biosimulators.org/Biosimulators_MASSpy/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
Only following targets are supported:
- I
- SEC
- V
- W
ERROR TYPE:
❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```netpyne
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```neuron
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```opencor
https://docs.biosimulators.org/Biosimulators_OpenCOR/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```pyneuroml
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```pysces
https://docs.biosimulators.org/Biosimulators_PySCeS/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
ERROR TYPE:
❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```rbapy
https://docs.biosimulators.org/Biosimulators_RBApy/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).
ERROR TYPE:
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```smoldyn
https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```tellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with telluriumvcell
https://github.com/virtualcell/vcell
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcellNone
view
download
logs
ERROR TYPE:
❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```xpp
https://docs.biosimulators.org/Biosimulators_XPP/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```amici
https://docs.biosimulators.org/Biosimulators_AMICI/
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amicibrian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError |
-| 2 | bionetgen
https://docs.biosimulators.org/Biosimulators_BioNetGen/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`). | CombineArchiveExecutionError | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).
ERROR TYPE:
CombineArchiveExecutionError |
-| 3 | boolnet
https://docs.biosimulators.org/Biosimulators_BoolNet/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0). | CombineArchiveExecutionError | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).
ERROR TYPE:
CombineArchiveExecutionError |
-| 4 | cbmpy
https://docs.biosimulators.org/Biosimulators_CBMPy/
❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation | CombineArchiveExecutionError | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
CombineArchiveExecutionError |
-| 5 | cobrapy
https://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation | CombineArchiveExecutionError | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
CombineArchiveExecutionError |
-| 6 | copasi
https://docs.biosimulators.org/Biosimulators_COPASI/
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasigillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2ginsim
https://docs.biosimulators.org/Biosimulators_GINsim/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000 | CombineArchiveExecutionError | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000
ERROR TYPE:
CombineArchiveExecutionError |
-| 9 | libsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsimmasspy
https://docs.biosimulators.org/Biosimulators_MASSpy/
❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues . | CombineArchiveExecutionError | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .
ERROR TYPE:
CombineArchiveExecutionError |
-| 11 | netpyne
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError |
-| 12 | neuron
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError |
-| 13 | opencor
https://docs.biosimulators.org/Biosimulators_OpenCOR/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError |
-| 14 | pyneuroml
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError |
-| 15 | pysces
https://docs.biosimulators.org/Biosimulators_PySCeS/
❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
| CombineArchiveExecutionError | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
ERROR TYPE:
CombineArchiveExecutionError |
-| 16 | rbapy
https://docs.biosimulators.org/Biosimulators_RBApy/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`). | CombineArchiveExecutionError | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).
ERROR TYPE:
CombineArchiveExecutionError |
-| 17 | smoldyn
https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError |
-| 18 | tellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with telluriumvcell
https://github.com/virtualcell/vcell
None
view
download
logs
ERROR TYPE:
download
logs | | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
download
logs
ERROR TYPE:
|
-| 20 | xpp
https://docs.biosimulators.org/Biosimulators_XPP/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError |
\ No newline at end of file
+| | Engine | response | view | download | logs | pass / FAIL | Error | Type | tasks_output | links | d1 | Compatibility | links_error |
+|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|-----------:|:-------------------------------------------------------------|:-------------------------------------------------------------------------|:--------------------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-------|:---------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| 0 | amici
https://docs.biosimulators.org/Biosimulators_AMICI/
⚠ WARNING
view
download
logs
ERROR MESSAGE:
Reached maximum number of steps
ERROR TYPE:
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici
download
logs
ERROR MESSAGE:
Reached maximum number of steps
ERROR TYPE:
|
+| 1 | brian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
|
+| 2 | bionetgen
https://docs.biosimulators.org/Biosimulators_BioNetGen/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).
ERROR TYPE:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`). | | | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).
ERROR TYPE:
|
+| 3 | boolnet
https://docs.biosimulators.org/Biosimulators_BoolNet/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).
ERROR TYPE:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0). | | | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).
ERROR TYPE:
|
+| 4 | cbmpy
https://docs.biosimulators.org/Biosimulators_CBMPy/
❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation | | | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
|
+| 5 | cobrapy
https://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation | | | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
|
+| 6 | copasi
https://docs.biosimulators.org/Biosimulators_COPASI/
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasigillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2ginsim
https://docs.biosimulators.org/Biosimulators_GINsim/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000
ERROR TYPE:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000 | | | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000
ERROR TYPE:
|
+| 9 | libsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsimmasspy
https://docs.biosimulators.org/Biosimulators_MASSpy/
❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
Only following targets are supported:
- I
- SEC
- V
- W
ERROR TYPE:
The SED document did not execute successfully:
The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
Only following targets are supported:
- I
- SEC
- V
- W | | | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
Only following targets are supported:
- I
- SEC
- V
- W
ERROR TYPE:
|
+| 11 | netpyne
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
|
+| 12 | neuron
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
|
+| 13 | opencor
https://docs.biosimulators.org/Biosimulators_OpenCOR/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
|
+| 14 | pyneuroml
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
|
+| 15 | pysces
https://docs.biosimulators.org/Biosimulators_PySCeS/
❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
ERROR TYPE:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
| | | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
ERROR TYPE:
|
+| 16 | rbapy
https://docs.biosimulators.org/Biosimulators_RBApy/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).
ERROR TYPE:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`). | | | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).
ERROR TYPE:
|
+| 17 | smoldyn
https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
|
+| 18 | tellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with telluriumvcell
https://github.com/virtualcell/vcell
None
view
download
logs
ERROR TYPE:
download
logs | | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
download
logs
ERROR TYPE:
|
+| 20 | xpp
https://docs.biosimulators.org/Biosimulators_XPP/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
|
\ No newline at end of file
diff --git a/SBML/tests/test_biosimulators_remote.py b/SBML/tests/test_biosimulators_remote.py
index a4971edb..b494bf0b 100644
--- a/SBML/tests/test_biosimulators_remote.py
+++ b/SBML/tests/test_biosimulators_remote.py
@@ -13,6 +13,7 @@
import argparse
import json
+
# Save the current working directory
cwd = os.getcwd()
print('Current working directory:', cwd)
@@ -39,7 +40,9 @@
print('d1 plots will be saved in:', d1_plots_remote_dir)
-results_remote = utils.run_biosimulators_remotely(sedml_file_name=sedml_file_name,
+engine_keys = list(utils.ENGINES.keys())
+
+results_remote = utils.run_biosimulators_remotely(engine_keys, sedml_file_name=sedml_file_name,
sbml_file_name=sbml_file_name,
d1_plots_remote_dir=d1_plots_remote_dir,
test_folder=test_folder)
diff --git a/SBML/tests/test_compatibility_biosimulators.py b/SBML/tests/test_compatibility_biosimulators.py
index 07bafd33..e712c0b8 100644
--- a/SBML/tests/test_compatibility_biosimulators.py
+++ b/SBML/tests/test_compatibility_biosimulators.py
@@ -42,7 +42,10 @@
print('d1 plots will be saved in:', d1_plots_remote_dir, 'and', d1_plots_local_dir)
-utils.run_biosimulators_remotely_and_locally(sedml_file_name,
+engine_keys = list(utils.ENGINES.keys())
+
+utils.run_biosimulators_remotely_and_locally(engine_keys,
+ sedml_file_name,
sbml_file_name,
d1_plots_remote_dir,
d1_plots_local_dir,
diff --git a/utils/__init__.py b/utils/__init__.py
index 6f9598b6..86c8956f 100644
--- a/utils/__init__.py
+++ b/utils/__init__.py
@@ -1105,7 +1105,9 @@ def create_results_table(results, sbml_filepath, sedml_filepath, output_dir):
results_table[ERROR] = results_table[ERROR].apply(lambda x: ansi_to_html(x))
results_table[PASS_FAIL] = results_table[PASS_FAIL].apply(lambda x: f'{fail_html}' if x == 'FAIL' \
- else f'{pass_html}' if x == 'pass' else x)
+ else f'{pass_html}' if x == 'pass'
+ else f'{warning_html}' if x == 'WARNING'
+ else x)
# d1 plot clickable link
results_table[D1] = results_table[ENGINE].apply(lambda x: d1_plots_dict(output_dir).get(x, None))
@@ -1157,18 +1159,21 @@ def create_results_table(results, sbml_filepath, sedml_filepath, output_dir):
return results_table
-def run_biosimulators_remotely(sedml_file_name,
+def run_biosimulators_remotely(engine_keys,
+ sedml_file_name,
sbml_file_name,
d1_plots_remote_dir,
test_folder='tests'):
""" run with directory pointing towards the location of the sedml and sbml files"""
+ engines = {k: v for k, v in ENGINES.items() if k in engine_keys}
+
remote_output_dir = 'remote_results'
remote_output_dir = os.path.join(test_folder, remote_output_dir)
results_remote = dict()
- for e in ENGINES.keys():
+ for e in engines.keys():
results_remote[e] = run_biosimulators_remote(e, sedml_file_name, sbml_file_name)
results_remote[e]['response'] = results_remote[e]['response'].status_code
@@ -1185,6 +1190,7 @@ def run_biosimulators_remotely(sedml_file_name,
status = ""
error_message = ""
exception_type = ""
+ task_output = ""
log_yml_path = find_file_in_dir('log.yml', extract_dir)[0]
if not log_yml_path:
@@ -1193,18 +1199,25 @@ def run_biosimulators_remotely(sedml_file_name,
continue
with open(log_yml_path) as f:
log_yml_dict = yaml.safe_load(f)
+ log_yml_str = str(log_yml_dict)
if log_yml_dict['status'] == 'SUCCEEDED':
status = 'pass'
+ # to deal with cases like amici where the d1 plot max x is half the expected value
+ pattern_max_number_of_steps = "simulation failed: Reached maximum number of steps"
+ pattern_match = re.search(pattern_max_number_of_steps, log_yml_str)
+ if pattern_match:
+ status = 'WARNING'
+ error_message = 'Reached maximum number of steps'
elif log_yml_dict['status'] == 'FAILED':
status = 'FAIL'
exception = log_yml_dict['exception']
error_message = exception['message']
- exception_type = exception['type']
else:
status = None
results_remote[e]["status"] = status
results_remote[e]["error_message"] = error_message
results_remote[e]["exception_type"] = exception_type
+ results_remote[e]["tasks_output"] = task_output
file_paths = find_files(remote_output_dir, '.pdf')
move_d1_files(file_paths, d1_plots_remote_dir)
@@ -1216,16 +1229,19 @@ def run_biosimulators_remotely(sedml_file_name,
return results_remote
-def run_biosimulators_locally(sedml_file_name,
+def run_biosimulators_locally(engine_keys,
+ sedml_file_name,
sbml_file_name,
d1_plots_local_dir,
test_folder='tests'):
+
+ engines = {k: v for k, v in ENGINES.items() if k in engine_keys}
results_local = {}
output_folder = 'local_results'
local_output_dir = os.path.join(test_folder, output_folder)
- for e in ENGINES.keys():
+ for e in engines.keys():
print('Running ' + e)
local_output_dir_e = os.path.abspath(os.path.join(local_output_dir, e))
print(local_output_dir_e)
@@ -1299,18 +1315,21 @@ def create_combined_results_table(results_remote,
return combined_results
-def run_biosimulators_remotely_and_locally(sedml_file_name,
+def run_biosimulators_remotely_and_locally(engine_keys,
+ sedml_file_name,
sbml_file_name,
d1_plots_remote_dir,
d1_plots_local_dir,
test_folder='tests'):
- results_remote = run_biosimulators_remotely(sedml_file_name=sedml_file_name,
+ results_remote = run_biosimulators_remotely(engine_keys,
+ sedml_file_name=sedml_file_name,
sbml_file_name=sbml_file_name,
d1_plots_remote_dir=d1_plots_remote_dir,
test_folder=test_folder)
- results_local = run_biosimulators_locally(sedml_file_name=sedml_file_name,
+ results_local = run_biosimulators_locally(engine_keys,
+ sedml_file_name=sedml_file_name,
sbml_file_name=sbml_file_name,
d1_plots_local_dir=d1_plots_local_dir,
test_folder=test_folder)
From d70cd8a93df4d4f225dcffe2f03daff7a118e3bb Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Wed, 30 Oct 2024 10:25:15 +0000
Subject: [PATCH 07/24] add links for pass cases in pass fail column
---
.../results_compatibility_biosimulators.md | 46 +++++++++----------
SBML/tests/results_local.md | 10 ++--
SBML/tests/results_remote.md | 46 +++++++++----------
utils/__init__.py | 32 ++++++-------
4 files changed, 66 insertions(+), 68 deletions(-)
diff --git a/SBML/tests/results_compatibility_biosimulators.md b/SBML/tests/results_compatibility_biosimulators.md
index 11b85548..d146d4a2 100644
--- a/SBML/tests/results_compatibility_biosimulators.md
+++ b/SBML/tests/results_compatibility_biosimulators.md
@@ -1,23 +1,23 @@
-| | Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) |
-|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------|
-| 0 | amici
https://docs.biosimulators.org/Biosimulators_AMICI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici⚠ WARNING
view
download
logs
ERROR MESSAGE:
Reached maximum number of steps
ERROR TYPE:
bionetgen
https://docs.biosimulators.org/Biosimulators_BioNetGen/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).
ERROR TYPE:
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```boolnet
https://docs.biosimulators.org/Biosimulators_BoolNet/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).
ERROR TYPE:
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```brian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```cbmpy
https://docs.biosimulators.org/Biosimulators_CBMPy/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```cobrapy
https://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```copasi
https://docs.biosimulators.org/Biosimulators_COPASI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasigillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2ginsim
https://docs.biosimulators.org/Biosimulators_GINsim/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000
ERROR TYPE:
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```libsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsimmasspy
https://docs.biosimulators.org/Biosimulators_MASSpy/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
Only following targets are supported:
- I
- SEC
- V
- W
ERROR TYPE:
❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```netpyne
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```neuron
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```opencor
https://docs.biosimulators.org/Biosimulators_OpenCOR/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```pyneuroml
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```pysces
https://docs.biosimulators.org/Biosimulators_PySCeS/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
ERROR TYPE:
❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```rbapy
https://docs.biosimulators.org/Biosimulators_RBApy/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).
ERROR TYPE:
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```smoldyn
https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```tellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with telluriumvcell
https://github.com/virtualcell/vcell
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcellNone
view
download
logs
ERROR TYPE:
❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```xpp
https://docs.biosimulators.org/Biosimulators_XPP/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```amici
https://docs.biosimulators.org/Biosimulators_AMICI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici⚠ WARNING
view
download
logs
ERROR MESSAGE:
Reached maximum number of stepsbionetgen
https://docs.biosimulators.org/Biosimulators_BioNetGen/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```boolnet
https://docs.biosimulators.org/Biosimulators_BoolNet/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```brian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```cbmpy
https://docs.biosimulators.org/Biosimulators_CBMPy/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```cobrapy
https://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```copasi
https://docs.biosimulators.org/Biosimulators_COPASI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasi✅ PASS
view
download
logsgillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2✅ PASS
view
download
logsginsim
https://docs.biosimulators.org/Biosimulators_GINsim/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```libsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsim✅ PASS
view
download
logsmasspy
https://docs.biosimulators.org/Biosimulators_MASSpy/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
Only following targets are supported:
- I
- SEC
- V
- W❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```netpyne
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```neuron
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```opencor
https://docs.biosimulators.org/Biosimulators_OpenCOR/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```pyneuroml
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```pysces
https://docs.biosimulators.org/Biosimulators_PySCeS/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```rbapy
https://docs.biosimulators.org/Biosimulators_RBApy/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```smoldyn
https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```tellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium✅ PASS
view
download
logsvcell
https://github.com/virtualcell/vcell
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcellNone
view
download
logs❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```xpp
https://docs.biosimulators.org/Biosimulators_XPP/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```amici
https://docs.biosimulators.org/Biosimulators_AMICI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amiciamici
https://docs.biosimulators.org/Biosimulators_AMICI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amicibrian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1``` |
| 2 | bionetgen
https://docs.biosimulators.org/Biosimulators_BioNetGen/
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1``` |
| 3 | boolnet
https://docs.biosimulators.org/Biosimulators_BoolNet/
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1``` |
| 4 | cbmpy
https://docs.biosimulators.org/Biosimulators_CBMPy/
❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1``` |
| 5 | cobrapy
https://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1``` |
-| 6 | copasi
https://docs.biosimulators.org/Biosimulators_COPASI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasigillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2copasi
https://docs.biosimulators.org/Biosimulators_COPASI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasigillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2ginsim
https://docs.biosimulators.org/Biosimulators_GINsim/
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1``` |
-| 9 | libsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsimlibsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsimmasspy
https://docs.biosimulators.org/Biosimulators_MASSpy/
❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1``` |
| 11 | netpyne
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1``` |
| 12 | neuron
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1``` |
@@ -18,6 +18,6 @@
| 15 | pysces
https://docs.biosimulators.org/Biosimulators_PySCeS/
❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1``` |
| 16 | rbapy
https://docs.biosimulators.org/Biosimulators_RBApy/
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1``` |
| 17 | smoldyn
https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1``` |
-| 18 | tellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with telluriumtellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with telluriumvcell
https://github.com/virtualcell/vcell
❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1``` |
| 20 | xpp
https://docs.biosimulators.org/Biosimulators_XPP/
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1``` |
\ No newline at end of file
diff --git a/SBML/tests/results_remote.md b/SBML/tests/results_remote.md
index 2ff68d00..d349ca4b 100644
--- a/SBML/tests/results_remote.md
+++ b/SBML/tests/results_remote.md
@@ -1,23 +1,23 @@
-| | Engine | response | view | download | logs | pass / FAIL | Error | Type | tasks_output | links | d1 | Compatibility | links_error |
-|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|-----------:|:-------------------------------------------------------------|:-------------------------------------------------------------------------|:--------------------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-------|:---------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| 0 | amici
https://docs.biosimulators.org/Biosimulators_AMICI/
⚠ WARNING
view
download
logs
ERROR MESSAGE:
Reached maximum number of steps
ERROR TYPE:
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici
download
logs
ERROR MESSAGE:
Reached maximum number of steps
ERROR TYPE:
|
-| 1 | brian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
|
-| 2 | bionetgen
https://docs.biosimulators.org/Biosimulators_BioNetGen/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).
ERROR TYPE:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`). | | | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).
ERROR TYPE:
|
-| 3 | boolnet
https://docs.biosimulators.org/Biosimulators_BoolNet/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).
ERROR TYPE:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0). | | | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).
ERROR TYPE:
|
-| 4 | cbmpy
https://docs.biosimulators.org/Biosimulators_CBMPy/
❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation | | | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
|
-| 5 | cobrapy
https://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation | | | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
|
-| 6 | copasi
https://docs.biosimulators.org/Biosimulators_COPASI/
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasigillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2ginsim
https://docs.biosimulators.org/Biosimulators_GINsim/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000
ERROR TYPE:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000 | | | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000
ERROR TYPE:
|
-| 9 | libsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsimmasspy
https://docs.biosimulators.org/Biosimulators_MASSpy/
❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
Only following targets are supported:
- I
- SEC
- V
- W
ERROR TYPE:
The SED document did not execute successfully:
The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
Only following targets are supported:
- I
- SEC
- V
- W | | | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
Only following targets are supported:
- I
- SEC
- V
- W
ERROR TYPE:
|
-| 11 | netpyne
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
|
-| 12 | neuron
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
|
-| 13 | opencor
https://docs.biosimulators.org/Biosimulators_OpenCOR/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
|
-| 14 | pyneuroml
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
|
-| 15 | pysces
https://docs.biosimulators.org/Biosimulators_PySCeS/
❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
ERROR TYPE:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
| | | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
ERROR TYPE:
|
-| 16 | rbapy
https://docs.biosimulators.org/Biosimulators_RBApy/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).
ERROR TYPE:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`). | | | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).
ERROR TYPE:
|
-| 17 | smoldyn
https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
|
-| 18 | tellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with telluriumvcell
https://github.com/virtualcell/vcell
None
view
download
logs
ERROR TYPE:
download
logs | | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
download
logs
ERROR TYPE:
|
-| 20 | xpp
https://docs.biosimulators.org/Biosimulators_XPP/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
|
\ No newline at end of file
+| | Engine | response | view | download | logs | pass / FAIL | Error | Type | tasks_output | links | d1 | Compatibility | links_error |
+|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|-----------:|:-------------------------------------------------------------|:-------------------------------------------------------------------------|:--------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-------|:---------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| 0 | amici
https://docs.biosimulators.org/Biosimulators_AMICI/
⚠ WARNING
view
download
logs
ERROR MESSAGE:
Reached maximum number of steps
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici
download
logs
ERROR MESSAGE:
Reached maximum number of steps |
+| 1 | brian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2
download
logs
ERROR MESSAGE:
No module named 'libsbml' |
+| 2 | bionetgen
https://docs.biosimulators.org/Biosimulators_BioNetGen/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`). | | | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`). |
+| 3 | boolnet
https://docs.biosimulators.org/Biosimulators_BoolNet/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0). | | | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0). |
+| 4 | cbmpy
https://docs.biosimulators.org/Biosimulators_CBMPy/
❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation | | | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation |
+| 5 | cobrapy
https://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation | | | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation |
+| 6 | copasi
https://docs.biosimulators.org/Biosimulators_COPASI/
✅ PASS
view
download
logs
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasi
download
logs |
+| 7 | gillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
✅ PASS
view
download
logs
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2
download
logs |
+| 8 | ginsim
https://docs.biosimulators.org/Biosimulators_GINsim/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000 | | | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000 |
+| 9 | libsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
✅ PASS
view
download
logs
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsim
download
logs |
+| 10 | masspy
https://docs.biosimulators.org/Biosimulators_MASSpy/
❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
Only following targets are supported:
- I
- SEC
- V
- W
The SED document did not execute successfully:
The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
Only following targets are supported:
- I
- SEC
- V
- W | | | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
Only following targets are supported:
- I
- SEC
- V
- W |
+| 11 | netpyne
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne
download
logs
ERROR MESSAGE:
No module named 'libsbml' |
+| 12 | neuron
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
download
logs
ERROR MESSAGE:
No module named 'libsbml' |
+| 13 | opencor
https://docs.biosimulators.org/Biosimulators_OpenCOR/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor
download
logs
ERROR MESSAGE:
No module named 'libsbml' |
+| 14 | pyneuroml
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
download
logs
ERROR MESSAGE:
No module named 'libsbml' |
+| 15 | pysces
https://docs.biosimulators.org/Biosimulators_PySCeS/
❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
| | | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
|
+| 16 | rbapy
https://docs.biosimulators.org/Biosimulators_RBApy/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`). | | | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`). |
+| 17 | smoldyn
https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn
download
logs
ERROR MESSAGE:
No module named 'libsbml' |
+| 18 | tellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
✅ PASS
view
download
logs
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium
download
logs |
+| 19 | vcell
https://github.com/virtualcell/vcell
None
view
download
logs
download
logs | | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
download
logs |
+| 20 | xpp
https://docs.biosimulators.org/Biosimulators_XPP/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp
download
logs
ERROR MESSAGE:
No module named 'libsbml' |
\ No newline at end of file
diff --git a/utils/__init__.py b/utils/__init__.py
index 86c8956f..46470e27 100644
--- a/utils/__init__.py
+++ b/utils/__init__.py
@@ -1130,28 +1130,26 @@ def create_results_table(results, sbml_filepath, sedml_filepath, output_dir):
results_table.loc[results_table[ENGINE] == e, PASS_FAIL] = f'{xfail_html}'
for e in results_table[ENGINE]:
- # only if no 'pass' in pass / fail column add error messages to links_error
- if results_table.loc[results_table[ENGINE] == e, PASS_FAIL].values[0] != pass_html:
- if len(results_table.loc[results_table[ENGINE] == e, ERROR].values[0]) > 1:
- error_message = f'
ERROR MESSAGE:
{results_table.loc[results_table[ENGINE] == e, ERROR].values[0]}'
- else:
- error_message = ""
- if "links" in results_table.columns:
- links = results_table.loc[results_table[ENGINE] == e, "links"].values[0]
- else:
- links = ""
- if TYPE in results_table.columns:
+ links = ""
+ error_message = ""
+ error_type = ""
+
+ if len(results_table.loc[results_table[ENGINE] == e, ERROR].values[0]) > 1:
+ error_message = f'
ERROR MESSAGE:
{results_table.loc[results_table[ENGINE] == e, ERROR].values[0]}'
+ if "links" in results_table.columns:
+ links = results_table.loc[results_table[ENGINE] == e, "links"].values[0]
+ if TYPE in results_table.columns:
+ if len(results_table.loc[results_table[ENGINE] == e, TYPE].values[0])>1:
error_type = f'
ERROR TYPE:
{results_table.loc[results_table[ENGINE] == e, TYPE].values[0]}'
- else:
- error_type =""
- links_error = f'{links}{error_message}{error_type}'
- results_table.loc[results_table[ENGINE] == e, "links_error"] = links_error
+ links_error = f'{links}{error_message}{error_type}'
+ results_table.loc[results_table[ENGINE] == e, "links_error"] = links_error
# add links as collapsible content to pass / fail column
for e in results_table[ENGINE]:
- if results_table.loc[results_table[ENGINE] == e, PASS_FAIL].values[0] != pass_html:
- results_table.loc[results_table[ENGINE] == e, PASS_FAIL] = collapsible_content(results_table.loc[results_table[ENGINE] == e, "links_error"].values[0], results_table.loc[results_table[ENGINE] == e, PASS_FAIL].values[0])
+ title = results_table.loc[results_table[ENGINE] == e, PASS_FAIL].values[0]
+ content = results_table.loc[results_table[ENGINE] == e, "links_error"].values[0]
+ results_table.loc[results_table[ENGINE] == e, PASS_FAIL] = collapsible_content(content, title)
# add status message defined in ENGINES
results_table[ENGINE] = results_table[ENGINE].apply(lambda x: collapsible_content(f'{ENGINES[x]["url"]}
{ENGINES[x]["status"]}', x))
From 52f139c9baff112d755fa9286cec4f999f2ca3a6 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Wed, 30 Oct 2024 10:39:59 +0000
Subject: [PATCH 08/24] modify collapsible content function to handle no
content cases
---
SBML/tests/results_compatibility_biosimulators.md | 10 +++++-----
SBML/tests/results_local.md | 10 +++++-----
utils/__init__.py | 2 +-
3 files changed, 11 insertions(+), 11 deletions(-)
diff --git a/SBML/tests/results_compatibility_biosimulators.md b/SBML/tests/results_compatibility_biosimulators.md
index d146d4a2..0e53e32b 100644
--- a/SBML/tests/results_compatibility_biosimulators.md
+++ b/SBML/tests/results_compatibility_biosimulators.md
@@ -1,15 +1,15 @@
| | Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) |
|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------|
-| 0 | amici
https://docs.biosimulators.org/Biosimulators_AMICI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici⚠ WARNING
view
download
logs
ERROR MESSAGE:
Reached maximum number of stepsamici
https://docs.biosimulators.org/Biosimulators_AMICI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici⚠ WARNING
view
download
logs
ERROR MESSAGE:
Reached maximum number of stepsbionetgen
https://docs.biosimulators.org/Biosimulators_BioNetGen/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```boolnet
https://docs.biosimulators.org/Biosimulators_BoolNet/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```brian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```cbmpy
https://docs.biosimulators.org/Biosimulators_CBMPy/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```cobrapy
https://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```copasi
https://docs.biosimulators.org/Biosimulators_COPASI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasi✅ PASS
view
download
logsgillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2✅ PASS
view
download
logscopasi
https://docs.biosimulators.org/Biosimulators_COPASI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasi✅ PASS
view
download
logsgillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2✅ PASS
view
download
logsginsim
https://docs.biosimulators.org/Biosimulators_GINsim/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```libsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsim✅ PASS
view
download
logslibsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsim✅ PASS
view
download
logsmasspy
https://docs.biosimulators.org/Biosimulators_MASSpy/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
Only following targets are supported:
- I
- SEC
- V
- W❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```netpyne
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```neuron
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```pysces
https://docs.biosimulators.org/Biosimulators_PySCeS/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```rbapy
https://docs.biosimulators.org/Biosimulators_RBApy/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```smoldyn
https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```tellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium✅ PASS
view
download
logstellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium✅ PASS
view
download
logsvcell
https://github.com/virtualcell/vcell
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcellNone
view
download
logs❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```xpp
https://docs.biosimulators.org/Biosimulators_XPP/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```amici
https://docs.biosimulators.org/Biosimulators_AMICI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amiciamici
https://docs.biosimulators.org/Biosimulators_AMICI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amicibrian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1``` |
| 2 | bionetgen
https://docs.biosimulators.org/Biosimulators_BioNetGen/
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1``` |
| 3 | boolnet
https://docs.biosimulators.org/Biosimulators_BoolNet/
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1``` |
| 4 | cbmpy
https://docs.biosimulators.org/Biosimulators_CBMPy/
❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1``` |
| 5 | cobrapy
https://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1``` |
-| 6 | copasi
https://docs.biosimulators.org/Biosimulators_COPASI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasigillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2copasi
https://docs.biosimulators.org/Biosimulators_COPASI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasigillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2ginsim
https://docs.biosimulators.org/Biosimulators_GINsim/
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1``` |
-| 9 | libsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsimlibsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsimmasspy
https://docs.biosimulators.org/Biosimulators_MASSpy/
❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1``` |
| 11 | netpyne
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1``` |
| 12 | neuron
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1``` |
@@ -18,6 +18,6 @@
| 15 | pysces
https://docs.biosimulators.org/Biosimulators_PySCeS/
❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1``` |
| 16 | rbapy
https://docs.biosimulators.org/Biosimulators_RBApy/
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1``` |
| 17 | smoldyn
https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1``` |
-| 18 | tellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with telluriumtellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with telluriumvcell
https://github.com/virtualcell/vcell
❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1``` |
| 20 | xpp
https://docs.biosimulators.org/Biosimulators_XPP/
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1``` |
\ No newline at end of file
diff --git a/utils/__init__.py b/utils/__init__.py
index 46470e27..9a1f487a 100644
--- a/utils/__init__.py
+++ b/utils/__init__.py
@@ -469,7 +469,7 @@ def collapsible_content(content, title='Details'):
if content:
return f'{title}
{content}amici
https://docs.biosimulators.org/Biosimulators_AMICI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici⚠ WARNING
view
download
logs
ERROR MESSAGE:
Reached maximum number of stepsbionetgen
https://docs.biosimulators.org/Biosimulators_BioNetGen/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```boolnet
https://docs.biosimulators.org/Biosimulators_BoolNet/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```brian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```cbmpy
https://docs.biosimulators.org/Biosimulators_CBMPy/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```cobrapy
https://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```copasi
https://docs.biosimulators.org/Biosimulators_COPASI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasi✅ PASS
view
download
logsgillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2✅ PASS
view
download
logsginsim
https://docs.biosimulators.org/Biosimulators_GINsim/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```libsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsim✅ PASS
view
download
logsmasspy
https://docs.biosimulators.org/Biosimulators_MASSpy/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
Only following targets are supported:
- I
- SEC
- V
- W❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```netpyne
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```neuron
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```opencor
https://docs.biosimulators.org/Biosimulators_OpenCOR/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```pyneuroml
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```pysces
https://docs.biosimulators.org/Biosimulators_PySCeS/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```rbapy
https://docs.biosimulators.org/Biosimulators_RBApy/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```smoldyn
https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```tellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium✅ PASS
view
download
logsvcell
https://github.com/virtualcell/vcell
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcellNone
view
download
logs❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```xpp
https://docs.biosimulators.org/Biosimulators_XPP/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```amici
https://docs.biosimulators.org/Biosimulators_AMICI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici❌ FAIL
view
download
logs
ERROR MESSAGE:
Reached maximum number of stepsbionetgen
https://docs.biosimulators.org/Biosimulators_BioNetGen/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```boolnet
https://docs.biosimulators.org/Biosimulators_BoolNet/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```brian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```cbmpy
https://docs.biosimulators.org/Biosimulators_CBMPy/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```cobrapy
https://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```copasi
https://docs.biosimulators.org/Biosimulators_COPASI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasi✅ PASS
view
download
logsgillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2✅ PASS
view
download
logsginsim
https://docs.biosimulators.org/Biosimulators_GINsim/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```libsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsim✅ PASS
view
download
logsmasspy
https://docs.biosimulators.org/Biosimulators_MASSpy/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
Only following targets are supported:
- I
- SEC
- V
- W❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```netpyne
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```neuron
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```opencor
https://docs.biosimulators.org/Biosimulators_OpenCOR/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```pyneuroml
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```pysces
https://docs.biosimulators.org/Biosimulators_PySCeS/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```rbapy
https://docs.biosimulators.org/Biosimulators_RBApy/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```smoldyn
https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```tellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium✅ PASS
view
download
logsvcell
https://github.com/virtualcell/vcell
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcellNone
view
download
logs❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```xpp
https://docs.biosimulators.org/Biosimulators_XPP/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```amici
https://docs.biosimulators.org/Biosimulators_AMICI/
⚠ WARNING
view
download
logs
ERROR MESSAGE:
Reached maximum number of steps
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici
download
logs
ERROR MESSAGE:
Reached maximum number of steps |
-| 1 | brian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2
download
logs
ERROR MESSAGE:
No module named 'libsbml' |
-| 2 | bionetgen
https://docs.biosimulators.org/Biosimulators_BioNetGen/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`). | | | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`). |
-| 3 | boolnet
https://docs.biosimulators.org/Biosimulators_BoolNet/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0). | | | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0). |
-| 4 | cbmpy
https://docs.biosimulators.org/Biosimulators_CBMPy/
❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation | | | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation |
-| 5 | cobrapy
https://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation | | | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation |
-| 6 | copasi
https://docs.biosimulators.org/Biosimulators_COPASI/
✅ PASS
view
download
logs
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasi
download
logs |
-| 7 | gillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
✅ PASS
view
download
logs
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2
download
logs |
-| 8 | ginsim
https://docs.biosimulators.org/Biosimulators_GINsim/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000 | | | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000 |
-| 9 | libsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
✅ PASS
view
download
logs
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsim
download
logs |
-| 10 | masspy
https://docs.biosimulators.org/Biosimulators_MASSpy/
❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
Only following targets are supported:
- I
- SEC
- V
- W
The SED document did not execute successfully:
The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
Only following targets are supported:
- I
- SEC
- V
- W | | | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
Only following targets are supported:
- I
- SEC
- V
- W |
-| 11 | netpyne
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne
download
logs
ERROR MESSAGE:
No module named 'libsbml' |
-| 12 | neuron
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
download
logs
ERROR MESSAGE:
No module named 'libsbml' |
-| 13 | opencor
https://docs.biosimulators.org/Biosimulators_OpenCOR/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor
download
logs
ERROR MESSAGE:
No module named 'libsbml' |
-| 14 | pyneuroml
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
download
logs
ERROR MESSAGE:
No module named 'libsbml' |
-| 15 | pysces
https://docs.biosimulators.org/Biosimulators_PySCeS/
❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
| | | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
|
-| 16 | rbapy
https://docs.biosimulators.org/Biosimulators_RBApy/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`). | | | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`). |
-| 17 | smoldyn
https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn
download
logs
ERROR MESSAGE:
No module named 'libsbml' |
-| 18 | tellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
✅ PASS
view
download
logs
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium
download
logs |
-| 19 | vcell
https://github.com/virtualcell/vcell
None
view
download
logs
download
logs | | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
download
logs |
-| 20 | xpp
https://docs.biosimulators.org/Biosimulators_XPP/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp
download
logs
ERROR MESSAGE:
No module named 'libsbml' |
\ No newline at end of file
+| 0 | amici
https://docs.biosimulators.org/Biosimulators_AMICI/
❌ FAIL
view
download
logs
ERROR MESSAGE:
Reached maximum number of steps
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici
download
logs
ERROR MESSAGE:
Reached maximum number of steps |
+| 1 | brian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2
download
logs
ERROR MESSAGE:
No module named 'libsbml' |
+| 2 | bionetgen
https://docs.biosimulators.org/Biosimulators_BioNetGen/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`). | | | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`). |
+| 3 | boolnet
https://docs.biosimulators.org/Biosimulators_BoolNet/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0). | | | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0). |
+| 4 | cbmpy
https://docs.biosimulators.org/Biosimulators_CBMPy/
❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation | | | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation |
+| 5 | cobrapy
https://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation | | | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation |
+| 6 | copasi
https://docs.biosimulators.org/Biosimulators_COPASI/
✅ PASS
view
download
logs
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasi
download
logs |
+| 7 | gillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
✅ PASS
view
download
logs
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2
download
logs |
+| 8 | ginsim
https://docs.biosimulators.org/Biosimulators_GINsim/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000 | | | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000 |
+| 9 | libsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
✅ PASS
view
download
logs
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsim
download
logs |
+| 10 | masspy
https://docs.biosimulators.org/Biosimulators_MASSpy/
❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
Only following targets are supported:
- I
- SEC
- V
- W
The SED document did not execute successfully:
The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
Only following targets are supported:
- I
- SEC
- V
- W | | | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
Only following targets are supported:
- I
- SEC
- V
- W |
+| 11 | netpyne
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne
download
logs
ERROR MESSAGE:
No module named 'libsbml' |
+| 12 | neuron
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
download
logs
ERROR MESSAGE:
No module named 'libsbml' |
+| 13 | opencor
https://docs.biosimulators.org/Biosimulators_OpenCOR/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor
download
logs
ERROR MESSAGE:
No module named 'libsbml' |
+| 14 | pyneuroml
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
download
logs
ERROR MESSAGE:
No module named 'libsbml' |
+| 15 | pysces
https://docs.biosimulators.org/Biosimulators_PySCeS/
❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
| | | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
|
+| 16 | rbapy
https://docs.biosimulators.org/Biosimulators_RBApy/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`). | | | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`). |
+| 17 | smoldyn
https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn
download
logs
ERROR MESSAGE:
No module named 'libsbml' |
+| 18 | tellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
✅ PASS
view
download
logs
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium
download
logs |
+| 19 | vcell
https://github.com/virtualcell/vcell
None
view
download
logs
download
logs | | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
download
logs |
+| 20 | xpp
https://docs.biosimulators.org/Biosimulators_XPP/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp
download
logs
ERROR MESSAGE:
No module named 'libsbml' |
\ No newline at end of file
diff --git a/utils/__init__.py b/utils/__init__.py
index 9a1f487a..ab1041b7 100644
--- a/utils/__init__.py
+++ b/utils/__init__.py
@@ -1204,7 +1204,7 @@ def run_biosimulators_remotely(engine_keys,
pattern_max_number_of_steps = "simulation failed: Reached maximum number of steps"
pattern_match = re.search(pattern_max_number_of_steps, log_yml_str)
if pattern_match:
- status = 'WARNING'
+ status = 'FAIL'
error_message = 'Reached maximum number of steps'
elif log_yml_dict['status'] == 'FAILED':
status = 'FAIL'
From 4842812b67903ce1ad52f7fad3fcf3efa2691b95 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Wed, 30 Oct 2024 14:23:48 +0000
Subject: [PATCH 10/24] add engine_keys input to run_biosimulators_locally
function
---
SBML/tests/test_biosimulators_local.py | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/SBML/tests/test_biosimulators_local.py b/SBML/tests/test_biosimulators_local.py
index 8fb2eb22..e206d92a 100644
--- a/SBML/tests/test_biosimulators_local.py
+++ b/SBML/tests/test_biosimulators_local.py
@@ -39,7 +39,10 @@
print('d1 plots will be saved in:', d1_plots_local_dir)
-results_local = utils.run_biosimulators_locally(sedml_file_name=sedml_file_name,
+engine_keys = list(utils.ENGINES.keys())
+
+results_local = utils.run_biosimulators_locally(engine_keys,
+ sedml_file_name=sedml_file_name,
sbml_file_name=sbml_file_name,
d1_plots_local_dir=d1_plots_local_dir,
test_folder=test_folder)
From a9681bcfed8b8b7189d6c7ffa5651f6122e3aa0d Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Wed, 30 Oct 2024 14:56:56 +0000
Subject: [PATCH 11/24] add draft process_log_yml and fetch exeption_type from
log yml
---
.../results_compatibility_biosimulators.md | 46 +++---
SBML/tests/results_remote.json | 156 +++++++++---------
SBML/tests/results_remote.md | 46 +++---
utils/__init__.py | 27 +++
4 files changed, 151 insertions(+), 124 deletions(-)
diff --git a/SBML/tests/results_compatibility_biosimulators.md b/SBML/tests/results_compatibility_biosimulators.md
index fda86f64..fb969c89 100644
--- a/SBML/tests/results_compatibility_biosimulators.md
+++ b/SBML/tests/results_compatibility_biosimulators.md
@@ -1,23 +1,23 @@
-| | Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) |
-|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------|
-| 0 | amici
https://docs.biosimulators.org/Biosimulators_AMICI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici❌ FAIL
view
download
logs
ERROR MESSAGE:
Reached maximum number of stepsbionetgen
https://docs.biosimulators.org/Biosimulators_BioNetGen/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```boolnet
https://docs.biosimulators.org/Biosimulators_BoolNet/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```brian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```cbmpy
https://docs.biosimulators.org/Biosimulators_CBMPy/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```cobrapy
https://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```copasi
https://docs.biosimulators.org/Biosimulators_COPASI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasi✅ PASS
view
download
logsgillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2✅ PASS
view
download
logsginsim
https://docs.biosimulators.org/Biosimulators_GINsim/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```libsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsim✅ PASS
view
download
logsmasspy
https://docs.biosimulators.org/Biosimulators_MASSpy/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
Only following targets are supported:
- I
- SEC
- V
- W❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```netpyne
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```neuron
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```opencor
https://docs.biosimulators.org/Biosimulators_OpenCOR/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```pyneuroml
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```pysces
https://docs.biosimulators.org/Biosimulators_PySCeS/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```rbapy
https://docs.biosimulators.org/Biosimulators_RBApy/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```smoldyn
https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```tellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium✅ PASS
view
download
logsvcell
https://github.com/virtualcell/vcell
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcellNone
view
download
logs❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```xpp
https://docs.biosimulators.org/Biosimulators_XPP/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```amici
https://docs.biosimulators.org/Biosimulators_AMICI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici❌ FAIL
view
download
logs
ERROR MESSAGE:
Reached maximum number of stepsbionetgen
https://docs.biosimulators.org/Biosimulators_BioNetGen/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).
ERROR TYPE:
CombineArchiveExecutionError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```boolnet
https://docs.biosimulators.org/Biosimulators_BoolNet/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).
ERROR TYPE:
CombineArchiveExecutionError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```brian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```cbmpy
https://docs.biosimulators.org/Biosimulators_CBMPy/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
CombineArchiveExecutionError❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```cobrapy
https://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
CombineArchiveExecutionError❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```copasi
https://docs.biosimulators.org/Biosimulators_COPASI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasi✅ PASS
view
download
logsgillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2✅ PASS
view
download
logsginsim
https://docs.biosimulators.org/Biosimulators_GINsim/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000
ERROR TYPE:
CombineArchiveExecutionError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```libsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsim✅ PASS
view
download
logsmasspy
https://docs.biosimulators.org/Biosimulators_MASSpy/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
Only following targets are supported:
- I
- SEC
- V
- W
ERROR TYPE:
CombineArchiveExecutionError❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```netpyne
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```neuron
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```opencor
https://docs.biosimulators.org/Biosimulators_OpenCOR/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```pyneuroml
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```pysces
https://docs.biosimulators.org/Biosimulators_PySCeS/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
ERROR TYPE:
CombineArchiveExecutionError❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```rbapy
https://docs.biosimulators.org/Biosimulators_RBApy/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).
ERROR TYPE:
CombineArchiveExecutionError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```smoldyn
https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```tellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium✅ PASS
view
download
logsvcell
https://github.com/virtualcell/vcell
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcellNone
view
download
logs❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```xpp
https://docs.biosimulators.org/Biosimulators_XPP/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```amici
https://docs.biosimulators.org/Biosimulators_AMICI/
❌ FAIL
view
download
logs
ERROR MESSAGE:
Reached maximum number of steps
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici
download
logs
ERROR MESSAGE:
Reached maximum number of steps |
-| 1 | brian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2
download
logs
ERROR MESSAGE:
No module named 'libsbml' |
-| 2 | bionetgen
https://docs.biosimulators.org/Biosimulators_BioNetGen/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`). | | | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`). |
-| 3 | boolnet
https://docs.biosimulators.org/Biosimulators_BoolNet/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0). | | | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0). |
-| 4 | cbmpy
https://docs.biosimulators.org/Biosimulators_CBMPy/
❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation | | | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation |
-| 5 | cobrapy
https://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation | | | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation |
-| 6 | copasi
https://docs.biosimulators.org/Biosimulators_COPASI/
✅ PASS
view
download
logs
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasi
download
logs |
-| 7 | gillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
✅ PASS
view
download
logs
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2
download
logs |
-| 8 | ginsim
https://docs.biosimulators.org/Biosimulators_GINsim/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000 | | | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000 |
-| 9 | libsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
✅ PASS
view
download
logs
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsim
download
logs |
-| 10 | masspy
https://docs.biosimulators.org/Biosimulators_MASSpy/
❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
Only following targets are supported:
- I
- SEC
- V
- W
The SED document did not execute successfully:
The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
Only following targets are supported:
- I
- SEC
- V
- W | | | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
Only following targets are supported:
- I
- SEC
- V
- W |
-| 11 | netpyne
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne
download
logs
ERROR MESSAGE:
No module named 'libsbml' |
-| 12 | neuron
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
download
logs
ERROR MESSAGE:
No module named 'libsbml' |
-| 13 | opencor
https://docs.biosimulators.org/Biosimulators_OpenCOR/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor
download
logs
ERROR MESSAGE:
No module named 'libsbml' |
-| 14 | pyneuroml
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
download
logs
ERROR MESSAGE:
No module named 'libsbml' |
-| 15 | pysces
https://docs.biosimulators.org/Biosimulators_PySCeS/
❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
| | | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
|
-| 16 | rbapy
https://docs.biosimulators.org/Biosimulators_RBApy/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`). | | | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`). |
-| 17 | smoldyn
https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn
download
logs
ERROR MESSAGE:
No module named 'libsbml' |
-| 18 | tellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
✅ PASS
view
download
logs
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium
download
logs |
-| 19 | vcell
https://github.com/virtualcell/vcell
None
view
download
logs
download
logs | | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
download
logs |
-| 20 | xpp
https://docs.biosimulators.org/Biosimulators_XPP/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp
download
logs
ERROR MESSAGE:
No module named 'libsbml' |
\ No newline at end of file
+| | Engine | response | view | download | logs | pass / FAIL | Error | Type | tasks_output | links | d1 | Compatibility | links_error |
+|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|-----------:|:-------------------------------------------------------------|:-------------------------------------------------------------------------|:--------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------|:---------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| 0 | amici
https://docs.biosimulators.org/Biosimulators_AMICI/
❌ FAIL
view
download
logs
ERROR MESSAGE:
Reached maximum number of steps
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici
download
logs
ERROR MESSAGE:
Reached maximum number of steps |
+| 1 | brian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError |
+| 2 | bionetgen
https://docs.biosimulators.org/Biosimulators_BioNetGen/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`). | CombineArchiveExecutionError | | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).
ERROR TYPE:
CombineArchiveExecutionError |
+| 3 | boolnet
https://docs.biosimulators.org/Biosimulators_BoolNet/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0). | CombineArchiveExecutionError | | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).
ERROR TYPE:
CombineArchiveExecutionError |
+| 4 | cbmpy
https://docs.biosimulators.org/Biosimulators_CBMPy/
❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation | CombineArchiveExecutionError | | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
CombineArchiveExecutionError |
+| 5 | cobrapy
https://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation | CombineArchiveExecutionError | | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
CombineArchiveExecutionError |
+| 6 | copasi
https://docs.biosimulators.org/Biosimulators_COPASI/
✅ PASS
view
download
logs
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasi
download
logs |
+| 7 | gillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
✅ PASS
view
download
logs
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2
download
logs |
+| 8 | ginsim
https://docs.biosimulators.org/Biosimulators_GINsim/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000 | CombineArchiveExecutionError | | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000
ERROR TYPE:
CombineArchiveExecutionError |
+| 9 | libsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
✅ PASS
view
download
logs
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsim
download
logs |
+| 10 | masspy
https://docs.biosimulators.org/Biosimulators_MASSpy/
❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
Only following targets are supported:
- I
- SEC
- V
- W
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
Only following targets are supported:
- I
- SEC
- V
- W | CombineArchiveExecutionError | | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
Only following targets are supported:
- I
- SEC
- V
- W
ERROR TYPE:
CombineArchiveExecutionError |
+| 11 | netpyne
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError |
+| 12 | neuron
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError |
+| 13 | opencor
https://docs.biosimulators.org/Biosimulators_OpenCOR/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError |
+| 14 | pyneuroml
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError |
+| 15 | pysces
https://docs.biosimulators.org/Biosimulators_PySCeS/
❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
| CombineArchiveExecutionError | | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
ERROR TYPE:
CombineArchiveExecutionError |
+| 16 | rbapy
https://docs.biosimulators.org/Biosimulators_RBApy/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`). | CombineArchiveExecutionError | | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).
ERROR TYPE:
CombineArchiveExecutionError |
+| 17 | smoldyn
https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError |
+| 18 | tellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
✅ PASS
view
download
logs
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium
download
logs |
+| 19 | vcell
https://github.com/virtualcell/vcell
None
view
download
logs
download
logs | | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
download
logs |
+| 20 | xpp
https://docs.biosimulators.org/Biosimulators_XPP/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError |
\ No newline at end of file
diff --git a/utils/__init__.py b/utils/__init__.py
index ab1041b7..df235bfa 100644
--- a/utils/__init__.py
+++ b/utils/__init__.py
@@ -1156,6 +1156,32 @@ def create_results_table(results, sbml_filepath, sedml_filepath, output_dir):
return results_table
+def process_log_yml(log_yml_path):
+ status = ""
+ error_message = ""
+ exception_type = ""
+
+ with open(log_yml_path) as f:
+ log_yml_dict = yaml.safe_load(f)
+ log_yml_str = str(log_yml_dict)
+ if log_yml_dict['status'] == 'SUCCEEDED':
+ status = 'pass'
+ # to deal with cases like amici where the d1 plot max x is half the expected value
+ pattern_max_number_of_steps = "simulation failed: Reached maximum number of steps"
+ pattern_match = re.search(pattern_max_number_of_steps, log_yml_str)
+ if pattern_match:
+ status = 'FAIL'
+ error_message = 'Reached maximum number of steps'
+ elif log_yml_dict['status'] == 'FAILED':
+ status = 'FAIL'
+ exception = log_yml_dict['exception']
+ error_message = exception['message']
+ exception_type = exception['type']
+ else:
+ status = None
+
+ return status, error_message, exception_type
+
def run_biosimulators_remotely(engine_keys,
sedml_file_name,
@@ -1210,6 +1236,7 @@ def run_biosimulators_remotely(engine_keys,
status = 'FAIL'
exception = log_yml_dict['exception']
error_message = exception['message']
+ exception_type = exception['type']
else:
status = None
results_remote[e]["status"] = status
From f99697f4ca4e128760e9831be48fe2a211d9583f Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Wed, 30 Oct 2024 16:59:28 +0000
Subject: [PATCH 12/24] Add same error handling to local results and update
table. Also remove tasks_output from results output.
---
.../results_compatibility_biosimulators.md | 46 ++---
SBML/tests/results_local.json | 67 ++++---
SBML/tests/results_local.md | 46 ++---
SBML/tests/results_remote.json | 189 ++++++++----------
SBML/tests/results_remote.md | 46 ++---
utils/__init__.py | 118 +++++------
6 files changed, 245 insertions(+), 267 deletions(-)
diff --git a/SBML/tests/results_compatibility_biosimulators.md b/SBML/tests/results_compatibility_biosimulators.md
index fb969c89..1b4c96dd 100644
--- a/SBML/tests/results_compatibility_biosimulators.md
+++ b/SBML/tests/results_compatibility_biosimulators.md
@@ -1,23 +1,23 @@
-| | Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) |
-|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------|
-| 0 | amici
https://docs.biosimulators.org/Biosimulators_AMICI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici❌ FAIL
view
download
logs
ERROR MESSAGE:
Reached maximum number of stepsbionetgen
https://docs.biosimulators.org/Biosimulators_BioNetGen/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).
ERROR TYPE:
CombineArchiveExecutionError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```boolnet
https://docs.biosimulators.org/Biosimulators_BoolNet/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).
ERROR TYPE:
CombineArchiveExecutionError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```brian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```cbmpy
https://docs.biosimulators.org/Biosimulators_CBMPy/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
CombineArchiveExecutionError❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```cobrapy
https://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
CombineArchiveExecutionError❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```copasi
https://docs.biosimulators.org/Biosimulators_COPASI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasi✅ PASS
view
download
logsgillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2✅ PASS
view
download
logsginsim
https://docs.biosimulators.org/Biosimulators_GINsim/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000
ERROR TYPE:
CombineArchiveExecutionError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```libsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsim✅ PASS
view
download
logsmasspy
https://docs.biosimulators.org/Biosimulators_MASSpy/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
Only following targets are supported:
- I
- SEC
- V
- W
ERROR TYPE:
CombineArchiveExecutionError❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```netpyne
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```neuron
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```opencor
https://docs.biosimulators.org/Biosimulators_OpenCOR/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```pyneuroml
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```pysces
https://docs.biosimulators.org/Biosimulators_PySCeS/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
ERROR TYPE:
CombineArchiveExecutionError❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```rbapy
https://docs.biosimulators.org/Biosimulators_RBApy/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).
ERROR TYPE:
CombineArchiveExecutionError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```smoldyn
https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```tellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium✅ PASS
view
download
logsvcell
https://github.com/virtualcell/vcell
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcellNone
view
download
logs❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```xpp
https://docs.biosimulators.org/Biosimulators_XPP/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```amici
https://docs.biosimulators.org/Biosimulators_AMICI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici❌ FAIL
view
download
logs
ERROR MESSAGE:
Reached maximum number of steps❌ FAIL
ERROR MESSAGE:
Reached maximum number of stepsbionetgen
https://docs.biosimulators.org/Biosimulators_BioNetGen/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).
ERROR TYPE:
CombineArchiveExecutionError⚠ XFAIL
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).
ERROR TYPE:
CombineArchiveExecutionErrorboolnet
https://docs.biosimulators.org/Biosimulators_BoolNet/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).
ERROR TYPE:
CombineArchiveExecutionError⚠ XFAIL
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).
ERROR TYPE:
CombineArchiveExecutionErrorbrian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError⚠ XFAIL
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundErrorcbmpy
https://docs.biosimulators.org/Biosimulators_CBMPy/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
CombineArchiveExecutionError❌ FAIL
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
CombineArchiveExecutionErrorcobrapy
https://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
CombineArchiveExecutionError❌ FAIL
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
CombineArchiveExecutionErrorcopasi
https://docs.biosimulators.org/Biosimulators_COPASI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasi✅ PASS
view
download
logsgillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2✅ PASS
view
download
logsginsim
https://docs.biosimulators.org/Biosimulators_GINsim/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000
ERROR TYPE:
CombineArchiveExecutionError⚠ XFAIL
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000
ERROR TYPE:
CombineArchiveExecutionErrorlibsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsim✅ PASS
view
download
logsmasspy
https://docs.biosimulators.org/Biosimulators_MASSpy/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
Only following targets are supported:
- I
- SEC
- V
- W
ERROR TYPE:
CombineArchiveExecutionError❌ FAIL
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .
ERROR TYPE:
CombineArchiveExecutionErrornetpyne
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError⚠ XFAIL
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundErrorneuron
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError⚠ XFAIL
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundErroropencor
https://docs.biosimulators.org/Biosimulators_OpenCOR/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError⚠ XFAIL
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundErrorpyneuroml
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError⚠ XFAIL
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundErrorpysces
https://docs.biosimulators.org/Biosimulators_PySCeS/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
ERROR TYPE:
CombineArchiveExecutionError❌ FAIL
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
ERROR TYPE:
CombineArchiveExecutionErrorrbapy
https://docs.biosimulators.org/Biosimulators_RBApy/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).
ERROR TYPE:
CombineArchiveExecutionError⚠ XFAIL
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).
ERROR TYPE:
CombineArchiveExecutionErrorsmoldyn
https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError⚠ XFAIL
ERROR MESSAGE:
did not runtellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium✅ PASS
view
download
logsvcell
https://github.com/virtualcell/vcell
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcellNone
view
download
logsxpp
https://docs.biosimulators.org/Biosimulators_XPP/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError⚠ XFAIL
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundErroramici
https://docs.biosimulators.org/Biosimulators_AMICI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amicibrian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1``` |
-| 2 | bionetgen
https://docs.biosimulators.org/Biosimulators_BioNetGen/
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1``` |
-| 3 | boolnet
https://docs.biosimulators.org/Biosimulators_BoolNet/
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1``` |
-| 4 | cbmpy
https://docs.biosimulators.org/Biosimulators_CBMPy/
❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1``` |
-| 5 | cobrapy
https://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1``` |
-| 6 | copasi
https://docs.biosimulators.org/Biosimulators_COPASI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasigillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2ginsim
https://docs.biosimulators.org/Biosimulators_GINsim/
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1``` |
-| 9 | libsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsimmasspy
https://docs.biosimulators.org/Biosimulators_MASSpy/
❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1``` |
-| 11 | netpyne
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1``` |
-| 12 | neuron
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1``` |
-| 13 | opencor
https://docs.biosimulators.org/Biosimulators_OpenCOR/
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1``` |
-| 14 | pyneuroml
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1``` |
-| 15 | pysces
https://docs.biosimulators.org/Biosimulators_PySCeS/
❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1``` |
-| 16 | rbapy
https://docs.biosimulators.org/Biosimulators_RBApy/
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1``` |
-| 17 | smoldyn
https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1``` |
-| 18 | tellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with telluriumvcell
https://github.com/virtualcell/vcell
❌ FAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1``` |
-| 20 | xpp
https://docs.biosimulators.org/Biosimulators_XPP/
⚠ XFAIL
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp
ERROR MESSAGE:
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1``` |
\ No newline at end of file
+| | Engine | pass / FAIL | Error | Type | d1 | Compatibility | links_error |
+|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------|:----------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| 0 | amici
https://docs.biosimulators.org/Biosimulators_AMICI/
❌ FAIL
ERROR MESSAGE:
Reached maximum number of steps✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici
ERROR MESSAGE:
Reached maximum number of steps |
+| 1 | brian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError |
+| 2 | bionetgen
https://docs.biosimulators.org/Biosimulators_BioNetGen/
⚠ XFAIL
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`). | CombineArchiveExecutionError | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).
ERROR TYPE:
CombineArchiveExecutionError |
+| 3 | boolnet
https://docs.biosimulators.org/Biosimulators_BoolNet/
⚠ XFAIL
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0). | CombineArchiveExecutionError | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).
ERROR TYPE:
CombineArchiveExecutionError |
+| 4 | cbmpy
https://docs.biosimulators.org/Biosimulators_CBMPy/
❌ FAIL
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation | CombineArchiveExecutionError | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
CombineArchiveExecutionError |
+| 5 | cobrapy
https://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations❌ FAIL
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation | CombineArchiveExecutionError | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
CombineArchiveExecutionError |
+| 6 | copasi
https://docs.biosimulators.org/Biosimulators_COPASI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasigillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2ginsim
https://docs.biosimulators.org/Biosimulators_GINsim/
⚠ XFAIL
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000 | CombineArchiveExecutionError | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000
ERROR TYPE:
CombineArchiveExecutionError |
+| 9 | libsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsimmasspy
https://docs.biosimulators.org/Biosimulators_MASSpy/
❌ FAIL
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues . | CombineArchiveExecutionError | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .
ERROR TYPE:
CombineArchiveExecutionError |
+| 11 | netpyne
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError |
+| 12 | neuron
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError |
+| 13 | opencor
https://docs.biosimulators.org/Biosimulators_OpenCOR/
⚠ XFAIL
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError |
+| 14 | pyneuroml
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError |
+| 15 | pysces
https://docs.biosimulators.org/Biosimulators_PySCeS/
❌ FAIL
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
| CombineArchiveExecutionError | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
ERROR TYPE:
CombineArchiveExecutionError |
+| 16 | rbapy
https://docs.biosimulators.org/Biosimulators_RBApy/
⚠ XFAIL
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`). | CombineArchiveExecutionError | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).
ERROR TYPE:
CombineArchiveExecutionError |
+| 17 | smoldyn
https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
⚠ XFAIL
ERROR MESSAGE:
did not run⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn
ERROR MESSAGE:
did not run |
+| 18 | tellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with telluriumvcell
https://github.com/virtualcell/vcell
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcellxpp
https://docs.biosimulators.org/Biosimulators_XPP/
⚠ XFAIL
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError |
\ No newline at end of file
diff --git a/SBML/tests/results_remote.json b/SBML/tests/results_remote.json
index b737227a..e236559f 100644
--- a/SBML/tests/results_remote.json
+++ b/SBML/tests/results_remote.json
@@ -1,212 +1,191 @@
{
"amici": {
"response": 201,
- "view": "https://api.biosimulations.org/runs/67224854953bc3bf105ef4f7",
- "download": "https://api.biosimulations.org/results/67224854953bc3bf105ef4f7/download",
- "logs": "https://api.biosimulations.org/logs/67224854953bc3bf105ef4f7?includeOutput=true",
+ "view": "https://api.biosimulations.org/runs/67224a98953bc3bf105ef9c7",
+ "download": "https://api.biosimulations.org/results/67224a98953bc3bf105ef9c7/download",
+ "logs": "https://api.biosimulations.org/logs/67224a98953bc3bf105ef9c7?includeOutput=true",
"status": "FAIL",
"error_message": "Reached maximum number of steps",
- "exception_type": "",
- "tasks_output": ""
+ "exception_type": ""
},
"brian2": {
"response": 201,
- "view": "https://api.biosimulations.org/runs/672248562e0c0591a7c893ea",
- "download": "https://api.biosimulations.org/results/672248562e0c0591a7c893ea/download",
- "logs": "https://api.biosimulations.org/logs/672248562e0c0591a7c893ea?includeOutput=true",
+ "view": "https://api.biosimulations.org/runs/67224a9a953bc3bf105ef9ca",
+ "download": "https://api.biosimulations.org/results/67224a9a953bc3bf105ef9ca/download",
+ "logs": "https://api.biosimulations.org/logs/67224a9a953bc3bf105ef9ca?includeOutput=true",
"status": "FAIL",
"error_message": "No module named 'libsbml'",
- "exception_type": "ModuleNotFoundError",
- "tasks_output": ""
+ "exception_type": "ModuleNotFoundError"
},
"bionetgen": {
"response": 201,
- "view": "https://api.biosimulations.org/runs/67224858f9c43d155d41cf8f",
- "download": "https://api.biosimulations.org/results/67224858f9c43d155d41cf8f/download",
- "logs": "https://api.biosimulations.org/logs/67224858f9c43d155d41cf8f?includeOutput=true",
+ "view": "https://api.biosimulations.org/runs/67224a9cf9c43d155d41d432",
+ "download": "https://api.biosimulations.org/results/67224a9cf9c43d155d41d432/download",
+ "logs": "https://api.biosimulations.org/logs/67224a9cf9c43d155d41d432?includeOutput=true",
"status": "FAIL",
"error_message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n Language for model `net1` is not supported.\n - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\\.|$)` such as `urn:sedml:language:bngl`).",
- "exception_type": "CombineArchiveExecutionError",
- "tasks_output": ""
+ "exception_type": "CombineArchiveExecutionError"
},
"boolnet": {
"response": 201,
- "view": "https://api.biosimulations.org/runs/6722485a953bc3bf105ef500",
- "download": "https://api.biosimulations.org/results/6722485a953bc3bf105ef500/download",
- "logs": "https://api.biosimulations.org/logs/6722485a953bc3bf105ef500?includeOutput=true",
+ "view": "https://api.biosimulations.org/runs/67224a9ff9c43d155d41d435",
+ "download": "https://api.biosimulations.org/results/67224a9ff9c43d155d41d435/download",
+ "logs": "https://api.biosimulations.org/logs/67224a9ff9c43d155d41d435?includeOutput=true",
"status": "FAIL",
"error_message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n Simulation `sim1` is invalid.\n - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).",
- "exception_type": "CombineArchiveExecutionError",
- "tasks_output": ""
+ "exception_type": "CombineArchiveExecutionError"
},
"cbmpy": {
"response": 201,
- "view": "https://api.biosimulations.org/runs/6722485cf9c43d155d41cf93",
- "download": "https://api.biosimulations.org/results/6722485cf9c43d155d41cf93/download",
- "logs": "https://api.biosimulations.org/logs/6722485cf9c43d155d41cf93?includeOutput=true",
+ "view": "https://api.biosimulations.org/runs/67224aa12e0c0591a7c89863",
+ "download": "https://api.biosimulations.org/results/67224aa12e0c0591a7c89863/download",
+ "logs": "https://api.biosimulations.org/logs/67224aa12e0c0591a7c89863?includeOutput=true",
"status": "FAIL",
"error_message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n UniformTimeCourseSimulation `sim1` is not supported.\n - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:\n - SteadyStateSimulation",
- "exception_type": "CombineArchiveExecutionError",
- "tasks_output": ""
+ "exception_type": "CombineArchiveExecutionError"
},
"cobrapy": {
"response": 201,
- "view": "https://api.biosimulations.org/runs/6722485ef9c43d155d41cf96",
- "download": "https://api.biosimulations.org/results/6722485ef9c43d155d41cf96/download",
- "logs": "https://api.biosimulations.org/logs/6722485ef9c43d155d41cf96?includeOutput=true",
+ "view": "https://api.biosimulations.org/runs/67224aa32e0c0591a7c89869",
+ "download": "https://api.biosimulations.org/results/67224aa32e0c0591a7c89869/download",
+ "logs": "https://api.biosimulations.org/logs/67224aa32e0c0591a7c89869?includeOutput=true",
"status": "FAIL",
"error_message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n UniformTimeCourseSimulation `sim1` is not supported.\n - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:\n - SteadyStateSimulation",
- "exception_type": "CombineArchiveExecutionError",
- "tasks_output": ""
+ "exception_type": "CombineArchiveExecutionError"
},
"copasi": {
"response": 201,
- "view": "https://api.biosimulations.org/runs/67224861f9c43d155d41cf9c",
- "download": "https://api.biosimulations.org/results/67224861f9c43d155d41cf9c/download",
- "logs": "https://api.biosimulations.org/logs/67224861f9c43d155d41cf9c?includeOutput=true",
+ "view": "https://api.biosimulations.org/runs/67224aa6f9c43d155d41d43e",
+ "download": "https://api.biosimulations.org/results/67224aa6f9c43d155d41d43e/download",
+ "logs": "https://api.biosimulations.org/logs/67224aa6f9c43d155d41d43e?includeOutput=true",
"status": "pass",
"error_message": "",
- "exception_type": "",
- "tasks_output": ""
+ "exception_type": ""
},
"gillespy2": {
"response": 201,
- "view": "https://api.biosimulations.org/runs/672248632e0c0591a7c893fb",
- "download": "https://api.biosimulations.org/results/672248632e0c0591a7c893fb/download",
- "logs": "https://api.biosimulations.org/logs/672248632e0c0591a7c893fb?includeOutput=true",
+ "view": "https://api.biosimulations.org/runs/67224aa82e0c0591a7c8986f",
+ "download": "https://api.biosimulations.org/results/67224aa82e0c0591a7c8986f/download",
+ "logs": "https://api.biosimulations.org/logs/67224aa82e0c0591a7c8986f?includeOutput=true",
"status": "pass",
"error_message": "",
- "exception_type": "",
- "tasks_output": ""
+ "exception_type": ""
},
"ginsim": {
"response": 201,
- "view": "https://api.biosimulations.org/runs/672248652e0c0591a7c89402",
- "download": "https://api.biosimulations.org/results/672248652e0c0591a7c89402/download",
- "logs": "https://api.biosimulations.org/logs/672248652e0c0591a7c89402?includeOutput=true",
+ "view": "https://api.biosimulations.org/runs/67224aaaf9c43d155d41d448",
+ "download": "https://api.biosimulations.org/results/67224aaaf9c43d155d41d448/download",
+ "logs": "https://api.biosimulations.org/logs/67224aaaf9c43d155d41d448?includeOutput=true",
"status": "FAIL",
"error_message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n Simulation `sim1` is invalid.\n - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:\n Output start time: 0.0\n Output end time: 200.0\n Number of steps: 20000",
- "exception_type": "CombineArchiveExecutionError",
- "tasks_output": ""
+ "exception_type": "CombineArchiveExecutionError"
},
"libsbmlsim": {
"response": 201,
- "view": "https://api.biosimulations.org/runs/67224867f9c43d155d41cfa3",
- "download": "https://api.biosimulations.org/results/67224867f9c43d155d41cfa3/download",
- "logs": "https://api.biosimulations.org/logs/67224867f9c43d155d41cfa3?includeOutput=true",
+ "view": "https://api.biosimulations.org/runs/67224aac953bc3bf105ef9ed",
+ "download": "https://api.biosimulations.org/results/67224aac953bc3bf105ef9ed/download",
+ "logs": "https://api.biosimulations.org/logs/67224aac953bc3bf105ef9ed?includeOutput=true",
"status": "pass",
"error_message": "",
- "exception_type": "",
- "tasks_output": ""
+ "exception_type": ""
},
"masspy": {
"response": 201,
- "view": "https://api.biosimulations.org/runs/67224869f9c43d155d41cfb3",
- "download": "https://api.biosimulations.org/results/67224869f9c43d155d41cfb3/download",
- "logs": "https://api.biosimulations.org/logs/67224869f9c43d155d41cfb3?includeOutput=true",
+ "view": "https://api.biosimulations.org/runs/67224aae2e0c0591a7c8988a",
+ "download": "https://api.biosimulations.org/results/67224aae2e0c0591a7c8988a/download",
+ "logs": "https://api.biosimulations.org/logs/67224aae2e0c0591a7c8988a?includeOutput=true",
"status": "FAIL",
"error_message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n The following targets are not supported:\n - /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']\n - /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']\n - /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']\n - /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']\n \n Only following targets are supported:\n - I\n - SEC\n - V\n - W",
- "exception_type": "CombineArchiveExecutionError",
- "tasks_output": ""
+ "exception_type": "CombineArchiveExecutionError"
},
"netpyne": {
"response": 201,
- "view": "https://api.biosimulations.org/runs/6722486bf9c43d155d41cfb8",
- "download": "https://api.biosimulations.org/results/6722486bf9c43d155d41cfb8/download",
- "logs": "https://api.biosimulations.org/logs/6722486bf9c43d155d41cfb8?includeOutput=true",
+ "view": "https://api.biosimulations.org/runs/67224ab0953bc3bf105efa03",
+ "download": "https://api.biosimulations.org/results/67224ab0953bc3bf105efa03/download",
+ "logs": "https://api.biosimulations.org/logs/67224ab0953bc3bf105efa03?includeOutput=true",
"status": "FAIL",
"error_message": "No module named 'libsbml'",
- "exception_type": "ModuleNotFoundError",
- "tasks_output": ""
+ "exception_type": "ModuleNotFoundError"
},
"neuron": {
"response": 201,
- "view": "https://api.biosimulations.org/runs/6722486c2e0c0591a7c8941c",
- "download": "https://api.biosimulations.org/results/6722486c2e0c0591a7c8941c/download",
- "logs": "https://api.biosimulations.org/logs/6722486c2e0c0591a7c8941c?includeOutput=true",
+ "view": "https://api.biosimulations.org/runs/67224ab22e0c0591a7c89898",
+ "download": "https://api.biosimulations.org/results/67224ab22e0c0591a7c89898/download",
+ "logs": "https://api.biosimulations.org/logs/67224ab22e0c0591a7c89898?includeOutput=true",
"status": "FAIL",
"error_message": "No module named 'libsbml'",
- "exception_type": "ModuleNotFoundError",
- "tasks_output": ""
+ "exception_type": "ModuleNotFoundError"
},
"opencor": {
"response": 201,
- "view": "https://api.biosimulations.org/runs/6722486e2e0c0591a7c89429",
- "download": "https://api.biosimulations.org/results/6722486e2e0c0591a7c89429/download",
- "logs": "https://api.biosimulations.org/logs/6722486e2e0c0591a7c89429?includeOutput=true",
+ "view": "https://api.biosimulations.org/runs/67224ab5f9c43d155d41d476",
+ "download": "https://api.biosimulations.org/results/67224ab5f9c43d155d41d476/download",
+ "logs": "https://api.biosimulations.org/logs/67224ab5f9c43d155d41d476?includeOutput=true",
"status": "FAIL",
"error_message": "No module named 'libsbml'",
- "exception_type": "ModuleNotFoundError",
- "tasks_output": ""
+ "exception_type": "ModuleNotFoundError"
},
"pyneuroml": {
"response": 201,
- "view": "https://api.biosimulations.org/runs/67224870f9c43d155d41cfcf",
- "download": "https://api.biosimulations.org/results/67224870f9c43d155d41cfcf/download",
- "logs": "https://api.biosimulations.org/logs/67224870f9c43d155d41cfcf?includeOutput=true",
+ "view": "https://api.biosimulations.org/runs/67224ab7f9c43d155d41d47c",
+ "download": "https://api.biosimulations.org/results/67224ab7f9c43d155d41d47c/download",
+ "logs": "https://api.biosimulations.org/logs/67224ab7f9c43d155d41d47c?includeOutput=true",
"status": "FAIL",
"error_message": "No module named 'libsbml'",
- "exception_type": "ModuleNotFoundError",
- "tasks_output": ""
+ "exception_type": "ModuleNotFoundError"
},
"pysces": {
"response": 201,
- "view": "https://api.biosimulations.org/runs/672248722e0c0591a7c89434",
- "download": "https://api.biosimulations.org/results/672248722e0c0591a7c89434/download",
- "logs": "https://api.biosimulations.org/logs/672248722e0c0591a7c89434?includeOutput=true",
+ "view": "https://api.biosimulations.org/runs/67224ab9f9c43d155d41d48a",
+ "download": "https://api.biosimulations.org/results/67224ab9f9c43d155d41d48a/download",
+ "logs": "https://api.biosimulations.org/logs/67224ab9f9c43d155d41d48a?includeOutput=true",
"status": "FAIL",
"error_message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n :\n Unable to generate Stoichiometric Matrix! model has:\n 0 reactions\n 0 species\n what did you have in mind?\n ",
- "exception_type": "CombineArchiveExecutionError",
- "tasks_output": ""
+ "exception_type": "CombineArchiveExecutionError"
},
"rbapy": {
"response": 201,
- "view": "https://api.biosimulations.org/runs/672248742e0c0591a7c89440",
- "download": "https://api.biosimulations.org/results/672248742e0c0591a7c89440/download",
- "logs": "https://api.biosimulations.org/logs/672248742e0c0591a7c89440?includeOutput=true",
+ "view": "https://api.biosimulations.org/runs/67224abb2e0c0591a7c898cb",
+ "download": "https://api.biosimulations.org/results/67224abb2e0c0591a7c898cb/download",
+ "logs": "https://api.biosimulations.org/logs/67224abb2e0c0591a7c898cb?includeOutput=true",
"status": "FAIL",
"error_message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n Language for model `net1` is not supported.\n - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\\.|$)` such as `urn:sedml:language:rba`).",
- "exception_type": "CombineArchiveExecutionError",
- "tasks_output": ""
+ "exception_type": "CombineArchiveExecutionError"
},
"smoldyn": {
"response": 201,
- "view": "https://api.biosimulations.org/runs/67224876953bc3bf105ef568",
- "download": "https://api.biosimulations.org/results/67224876953bc3bf105ef568/download",
- "logs": "https://api.biosimulations.org/logs/67224876953bc3bf105ef568?includeOutput=true",
+ "view": "https://api.biosimulations.org/runs/67224abef9c43d155d41d4a1",
+ "download": "https://api.biosimulations.org/results/67224abef9c43d155d41d4a1/download",
+ "logs": "https://api.biosimulations.org/logs/67224abef9c43d155d41d4a1?includeOutput=true",
"status": "FAIL",
"error_message": "No module named 'libsbml'",
- "exception_type": "ModuleNotFoundError",
- "tasks_output": ""
+ "exception_type": "ModuleNotFoundError"
},
"tellurium": {
"response": 201,
- "view": "https://api.biosimulations.org/runs/672248782e0c0591a7c89457",
- "download": "https://api.biosimulations.org/results/672248782e0c0591a7c89457/download",
- "logs": "https://api.biosimulations.org/logs/672248782e0c0591a7c89457?includeOutput=true",
+ "view": "https://api.biosimulations.org/runs/67224ac02e0c0591a7c898d7",
+ "download": "https://api.biosimulations.org/results/67224ac02e0c0591a7c898d7/download",
+ "logs": "https://api.biosimulations.org/logs/67224ac02e0c0591a7c898d7?includeOutput=true",
"status": "pass",
"error_message": "",
- "exception_type": "",
- "tasks_output": ""
+ "exception_type": ""
},
"vcell": {
"response": 201,
- "view": "https://api.biosimulations.org/runs/6722487c953bc3bf105ef57e",
- "download": "https://api.biosimulations.org/results/6722487c953bc3bf105ef57e/download",
- "logs": "https://api.biosimulations.org/logs/6722487c953bc3bf105ef57e?includeOutput=true",
+ "view": "https://api.biosimulations.org/runs/67224ac3f9c43d155d41d4be",
+ "download": "https://api.biosimulations.org/results/67224ac3f9c43d155d41d4be/download",
+ "logs": "https://api.biosimulations.org/logs/67224ac3f9c43d155d41d4be?includeOutput=true",
"status": null,
"error_message": "",
- "exception_type": "",
- "tasks_output": ""
+ "exception_type": ""
},
"xpp": {
"response": 201,
- "view": "https://api.biosimulations.org/runs/6722487e953bc3bf105ef59c",
- "download": "https://api.biosimulations.org/results/6722487e953bc3bf105ef59c/download",
- "logs": "https://api.biosimulations.org/logs/6722487e953bc3bf105ef59c?includeOutput=true",
+ "view": "https://api.biosimulations.org/runs/67224ac6953bc3bf105efa68",
+ "download": "https://api.biosimulations.org/results/67224ac6953bc3bf105efa68/download",
+ "logs": "https://api.biosimulations.org/logs/67224ac6953bc3bf105efa68?includeOutput=true",
"status": "FAIL",
"error_message": "No module named 'libsbml'",
- "exception_type": "ModuleNotFoundError",
- "tasks_output": ""
+ "exception_type": "ModuleNotFoundError"
}
}
\ No newline at end of file
diff --git a/SBML/tests/results_remote.md b/SBML/tests/results_remote.md
index 64791b4d..0388c0a8 100644
--- a/SBML/tests/results_remote.md
+++ b/SBML/tests/results_remote.md
@@ -1,23 +1,23 @@
-| | Engine | response | view | download | logs | pass / FAIL | Error | Type | tasks_output | links | d1 | Compatibility | links_error |
-|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|-----------:|:-------------------------------------------------------------|:-------------------------------------------------------------------------|:--------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------|:---------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| 0 | amici
https://docs.biosimulators.org/Biosimulators_AMICI/
❌ FAIL
view
download
logs
ERROR MESSAGE:
Reached maximum number of steps
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici
download
logs
ERROR MESSAGE:
Reached maximum number of steps |
-| 1 | brian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError |
-| 2 | bionetgen
https://docs.biosimulators.org/Biosimulators_BioNetGen/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`). | CombineArchiveExecutionError | | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).
ERROR TYPE:
CombineArchiveExecutionError |
-| 3 | boolnet
https://docs.biosimulators.org/Biosimulators_BoolNet/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0). | CombineArchiveExecutionError | | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).
ERROR TYPE:
CombineArchiveExecutionError |
-| 4 | cbmpy
https://docs.biosimulators.org/Biosimulators_CBMPy/
❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation | CombineArchiveExecutionError | | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
CombineArchiveExecutionError |
-| 5 | cobrapy
https://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation | CombineArchiveExecutionError | | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
CombineArchiveExecutionError |
-| 6 | copasi
https://docs.biosimulators.org/Biosimulators_COPASI/
✅ PASS
view
download
logs
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasi
download
logs |
-| 7 | gillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
✅ PASS
view
download
logs
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2
download
logs |
-| 8 | ginsim
https://docs.biosimulators.org/Biosimulators_GINsim/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000 | CombineArchiveExecutionError | | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000
ERROR TYPE:
CombineArchiveExecutionError |
-| 9 | libsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
✅ PASS
view
download
logs
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsim
download
logs |
-| 10 | masspy
https://docs.biosimulators.org/Biosimulators_MASSpy/
❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
Only following targets are supported:
- I
- SEC
- V
- W
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
Only following targets are supported:
- I
- SEC
- V
- W | CombineArchiveExecutionError | | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
Only following targets are supported:
- I
- SEC
- V
- W
ERROR TYPE:
CombineArchiveExecutionError |
-| 11 | netpyne
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError |
-| 12 | neuron
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError |
-| 13 | opencor
https://docs.biosimulators.org/Biosimulators_OpenCOR/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError |
-| 14 | pyneuroml
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError |
-| 15 | pysces
https://docs.biosimulators.org/Biosimulators_PySCeS/
❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
| CombineArchiveExecutionError | | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
ERROR TYPE:
CombineArchiveExecutionError |
-| 16 | rbapy
https://docs.biosimulators.org/Biosimulators_RBApy/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`). | CombineArchiveExecutionError | | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).
ERROR TYPE:
CombineArchiveExecutionError |
-| 17 | smoldyn
https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError |
-| 18 | tellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
✅ PASS
view
download
logs
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium
download
logs |
-| 19 | vcell
https://github.com/virtualcell/vcell
None
view
download
logs
download
logs | | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
download
logs |
-| 20 | xpp
https://docs.biosimulators.org/Biosimulators_XPP/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError |
\ No newline at end of file
+| | Engine | response | view | download | logs | pass / FAIL | Error | Type | links | d1 | Compatibility | links_error |
+|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|-----------:|:-------------------------------------------------------------|:-------------------------------------------------------------------------|:--------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| 0 | amici
https://docs.biosimulators.org/Biosimulators_AMICI/
❌ FAIL
view
download
logs
ERROR MESSAGE:
Reached maximum number of steps
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici
download
logs
ERROR MESSAGE:
Reached maximum number of steps |
+| 1 | brian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError |
+| 2 | bionetgen
https://docs.biosimulators.org/Biosimulators_BioNetGen/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`). | CombineArchiveExecutionError | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).
ERROR TYPE:
CombineArchiveExecutionError |
+| 3 | boolnet
https://docs.biosimulators.org/Biosimulators_BoolNet/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0). | CombineArchiveExecutionError | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).
ERROR TYPE:
CombineArchiveExecutionError |
+| 4 | cbmpy
https://docs.biosimulators.org/Biosimulators_CBMPy/
❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation | CombineArchiveExecutionError | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
CombineArchiveExecutionError |
+| 5 | cobrapy
https://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation | CombineArchiveExecutionError | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
ERROR TYPE:
CombineArchiveExecutionError |
+| 6 | copasi
https://docs.biosimulators.org/Biosimulators_COPASI/
✅ PASS
view
download
logs
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasi
download
logs |
+| 7 | gillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
✅ PASS
view
download
logs
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2
download
logs |
+| 8 | ginsim
https://docs.biosimulators.org/Biosimulators_GINsim/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000 | CombineArchiveExecutionError | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000
ERROR TYPE:
CombineArchiveExecutionError |
+| 9 | libsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
✅ PASS
view
download
logs
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsim
download
logs |
+| 10 | masspy
https://docs.biosimulators.org/Biosimulators_MASSpy/
❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
Only following targets are supported:
- I
- SEC
- V
- W
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
Only following targets are supported:
- I
- SEC
- V
- W | CombineArchiveExecutionError | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
- /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='W']
Only following targets are supported:
- I
- SEC
- V
- W
ERROR TYPE:
CombineArchiveExecutionError |
+| 11 | netpyne
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError |
+| 12 | neuron
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError |
+| 13 | opencor
https://docs.biosimulators.org/Biosimulators_OpenCOR/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError |
+| 14 | pyneuroml
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError |
+| 15 | pysces
https://docs.biosimulators.org/Biosimulators_PySCeS/
❌ FAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
| CombineArchiveExecutionError | view
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
ERROR TYPE:
CombineArchiveExecutionError |
+| 16 | rbapy
https://docs.biosimulators.org/Biosimulators_RBApy/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).
ERROR TYPE:
CombineArchiveExecutionError
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`). | CombineArchiveExecutionError | view
download
logs | plot | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
download
logs
ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).
ERROR TYPE:
CombineArchiveExecutionError |
+| 17 | smoldyn
https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError |
+| 18 | tellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
✅ PASS
view
download
logs
download
logs | plot | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium
download
logs |
+| 19 | vcell
https://github.com/virtualcell/vcell
None
view
download
logs
download
logs | | ✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
download
logs |
+| 20 | xpp
https://docs.biosimulators.org/Biosimulators_XPP/
⚠ XFAIL
view
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
download
logs | | ⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError |
\ No newline at end of file
diff --git a/utils/__init__.py b/utils/__init__.py
index df235bfa..8180fe7d 100644
--- a/utils/__init__.py
+++ b/utils/__init__.py
@@ -157,6 +157,7 @@
# (currently only tellurium)
# key is the tag/category used to report the category, value is a regex matching the error message
# see MarkdownTable.process_engine_outcomes
+# TODO: use error categories in process_log_yml
error_categories=\
{
"tellurium":
@@ -559,7 +560,7 @@ def rename_files_in_extract_dir(extract_dir, engine):
return extract_dir
-def run_biosimulators_docker(engine,sedml_filepath,sbml_filepath,output_dir='output',error_categories=error_categories,chown_outputs=True):
+def run_biosimulators_docker(engine,sedml_filepath,sbml_filepath,output_dir='output',chown_outputs=True):
'''
put the sedml and sbml file into an omex archive
run it locally using a biosimulators docker
@@ -568,14 +569,27 @@ def run_biosimulators_docker(engine,sedml_filepath,sbml_filepath,output_dir='out
#put the sedml and sbml into a combine archive
omex_filepath = create_omex(sedml_filepath,sbml_filepath)
- error_str = None
+ log_yml_path = os.path.join(output_dir,"log.yml")
+
+ status = ""
+ error_message = ""
+ exception_type = ""
+
try:
biosimulators_core(engine,omex_filepath,output_dir=output_dir)
except Exception as e:
#capture the error as a string which won't break markdown tables
# error_str = safe_md_string(e)
- error_str = str(e)
+ error_message = str(e)
+ status = "FAIL"
+ error_message = "did not run"
+
+ if os.path.exists(log_yml_path):
+ status, error_message, exception_type = process_log_yml(log_yml_path)
+
+ results_dict = {"status": status, "error_message": error_message, "exception_type": exception_type}
+ return results_dict
#ensure outputs are owned by the user
if 'getuid' in dir(os) and chown_outputs:
@@ -583,23 +597,11 @@ def run_biosimulators_docker(engine,sedml_filepath,sbml_filepath,output_dir='out
gid = os.getgid()
os.system(f'sudo chown -R {uid}:{gid} {output_dir}')
- if not error_str: return {"status": 'pass', "error_message": ''}
-
- # #try to load the cleaner error message from the log.yml file
- log_str = read_log_yml(os.path.join(os.path.dirname(omex_filepath),"log.yml"))
-
- if log_str:
- error_str = str(log_str)
- # if log_str:
- # error_str = safe_md_string(log_str)
-
- #categorise the error string
- if engine in error_categories:
- for tag in error_categories[engine]:
- if re.search(error_categories[engine][tag],error_str):
- return [tag,f"```{error_str}```"]
-
- return {"status":"FAIL", "error_message": f"```{error_str}```"}
+ if os.path.exists(log_yml_path):
+ status, error_message, exception_type = process_log_yml(log_yml_path)
+
+ results_dict = {"status": status, "error_message": error_message, "exception_type": exception_type}
+ return results_dict
def biosimulators_core(engine,omex_filepath,output_dir=None):
'''
@@ -1160,26 +1162,29 @@ def process_log_yml(log_yml_path):
status = ""
error_message = ""
exception_type = ""
-
- with open(log_yml_path) as f:
- log_yml_dict = yaml.safe_load(f)
- log_yml_str = str(log_yml_dict)
- if log_yml_dict['status'] == 'SUCCEEDED':
- status = 'pass'
- # to deal with cases like amici where the d1 plot max x is half the expected value
- pattern_max_number_of_steps = "simulation failed: Reached maximum number of steps"
- pattern_match = re.search(pattern_max_number_of_steps, log_yml_str)
- if pattern_match:
- status = 'FAIL'
- error_message = 'Reached maximum number of steps'
- elif log_yml_dict['status'] == 'FAILED':
- status = 'FAIL'
- exception = log_yml_dict['exception']
- error_message = exception['message']
- exception_type = exception['type']
- else:
- status = None
+ if not log_yml_path:
+ status = None
+ error_message = 'log.yml not found'
+ else:
+ with open(log_yml_path) as f:
+ log_yml_dict = yaml.safe_load(f)
+ log_yml_str = str(log_yml_dict)
+ if log_yml_dict['status'] == 'SUCCEEDED':
+ status = 'pass'
+ # to deal with cases like amici where the d1 plot max x is half the expected value
+ pattern_max_number_of_steps = "simulation failed: Reached maximum number of steps"
+ pattern_match = re.search(pattern_max_number_of_steps, log_yml_str)
+ if pattern_match:
+ status = 'FAIL'
+ error_message = 'Reached maximum number of steps'
+ elif log_yml_dict['status'] == 'FAILED':
+ status = 'FAIL'
+ exception = log_yml_dict['exception']
+ error_message = exception['message']
+ exception_type = exception['type']
+ else:
+ status = None
return status, error_message, exception_type
@@ -1211,38 +1216,11 @@ def run_biosimulators_remotely(engine_keys,
extract_dir_dict[e] = extract_dir
for e, extract_dir in extract_dir_dict.items():
- status = ""
- error_message = ""
- exception_type = ""
- task_output = ""
-
log_yml_path = find_file_in_dir('log.yml', extract_dir)[0]
- if not log_yml_path:
- status = None
- error_message = 'log.yml not found'
- continue
- with open(log_yml_path) as f:
- log_yml_dict = yaml.safe_load(f)
- log_yml_str = str(log_yml_dict)
- if log_yml_dict['status'] == 'SUCCEEDED':
- status = 'pass'
- # to deal with cases like amici where the d1 plot max x is half the expected value
- pattern_max_number_of_steps = "simulation failed: Reached maximum number of steps"
- pattern_match = re.search(pattern_max_number_of_steps, log_yml_str)
- if pattern_match:
- status = 'FAIL'
- error_message = 'Reached maximum number of steps'
- elif log_yml_dict['status'] == 'FAILED':
- status = 'FAIL'
- exception = log_yml_dict['exception']
- error_message = exception['message']
- exception_type = exception['type']
- else:
- status = None
- results_remote[e]["status"] = status
- results_remote[e]["error_message"] = error_message
- results_remote[e]["exception_type"] = exception_type
- results_remote[e]["tasks_output"] = task_output
+ status, error_message, exception_type = process_log_yml(log_yml_path)
+ results_remote[e]["status"] = status
+ results_remote[e]["error_message"] = error_message
+ results_remote[e]["exception_type"] = exception_type
file_paths = find_files(remote_output_dir, '.pdf')
move_d1_files(file_paths, d1_plots_remote_dir)
From 87b640e1c5ceabef5df90569a6bfbfc28eb9baf3 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Thu, 31 Oct 2024 09:48:48 +0000
Subject: [PATCH 13/24] save log_yml dicts in results dictionary for easier
testing
---
SBML/tests/results_local.json | 1218 ++++++++++++++++++++++++++-
SBML/tests/results_remote.json | 1402 ++++++++++++++++++++++++++++++--
utils/__init__.py | 12 +-
3 files changed, 2523 insertions(+), 109 deletions(-)
diff --git a/SBML/tests/results_local.json b/SBML/tests/results_local.json
index 50dc2696..e2b84796 100644
--- a/SBML/tests/results_local.json
+++ b/SBML/tests/results_local.json
@@ -2,106 +2,1282 @@
"amici": {
"status": "FAIL",
"error_message": "Reached maximum number of steps",
- "exception_type": ""
+ "exception_type": "",
+ "log": {
+ "duration": 13.754801,
+ "exception": null,
+ "output": "",
+ "sedDocuments": [
+ {
+ "duration": 13.412763,
+ "exception": null,
+ "location": "tmp408321",
+ "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp408321:\r\n Tasks (1):\r\n sim1_net1\r\n Reports (1):\r\n ex9: 3 data sets\r\n Plots (1):\r\n d1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp408321 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `sim1_net1`\r\n Outputs:\r\n `d1`\r\n `ex9`\r\n Executing task 1: `sim1_net1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `d1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `ex9` ...",
+ "outputs": [
+ {
+ "curves": [
+ {
+ "id": "curve_V",
+ "status": "SUCCEEDED"
+ },
+ {
+ "id": "curve_W",
+ "status": "SUCCEEDED"
+ }
+ ],
+ "duration": 0.699112,
+ "exception": null,
+ "id": "d1",
+ "output": "",
+ "skipReason": null,
+ "status": "SUCCEEDED"
+ },
+ {
+ "dataSets": [
+ {
+ "id": "ex9_time",
+ "status": "SUCCEEDED"
+ },
+ {
+ "id": "ex9_V",
+ "status": "SUCCEEDED"
+ },
+ {
+ "id": "ex9_W",
+ "status": "SUCCEEDED"
+ }
+ ],
+ "duration": 0.282498,
+ "exception": null,
+ "id": "ex9",
+ "output": "",
+ "skipReason": null,
+ "status": "SUCCEEDED"
+ }
+ ],
+ "skipReason": null,
+ "status": "SUCCEEDED",
+ "tasks": [
+ {
+ "algorithm": "KISAO_0000496",
+ "duration": 12.334193,
+ "exception": null,
+ "id": "sim1_net1",
+ "output": "2024-10-31 09:43:34.470 - amici.swig_wrappers - ERROR - [OTHER] AMICI simulation failed: Reached maximum number of steps 10000 before reaching tout at t=99.66.\r\n2024-10-31 09:43:34.470 - amici.swig_wrappers - DEBUG - [BACKTRACE] The previous error occurred at:\r\n2 0x7f249c0d7a8b /usr/local/lib/python3.11/site-packages/amici/_amici.cpython-311-x86_64-linux-gnu.so(+0xb5a8b) [0x7f249c0d7a8b]\r\n3 0x7f249c1cb262 amici::Solver::run(double) const + 34\r\n4 0x7f249c2035d0 amici::ForwardProblem::workForwardProblem() + 1728\r\n5 0x7f249c1b7763 amici::runAmiciSimulation(amici::Solver&, amici::ExpData const*, amici::Model&, bool) + 435\r\n6 0x7f249c161280 /usr/local/lib/python3.11/site-packages/amici/_amici.cpython-311-x86_64-linux-gnu.so(+0x13f\r\n",
+ "simulatorDetails": [
+ {
+ "key": "solver",
+ "value": "amici.amici.CVodeSolver"
+ },
+ {
+ "key": "method",
+ "value": "amici.swig_wrappers.runAmiciSimulation"
+ },
+ {
+ "key": "arguments",
+ "value": {}
+ }
+ ],
+ "skipReason": null,
+ "status": "SUCCEEDED"
+ }
+ ]
+ }
+ ],
+ "skipReason": null,
+ "status": "SUCCEEDED"
+ }
},
"brian2": {
"status": "FAIL",
"error_message": "No module named 'libsbml'",
- "exception_type": "ModuleNotFoundError"
+ "exception_type": "ModuleNotFoundError",
+ "log": {
+ "duration": 0.055724,
+ "exception": {
+ "message": "No module named 'libsbml'",
+ "type": "ModuleNotFoundError"
+ },
+ "output": "",
+ "sedDocuments": [],
+ "skipReason": null,
+ "status": "FAILED"
+ }
},
"bionetgen": {
"status": "FAIL",
"error_message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n Language for model `net1` is not supported.\n - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\\.|$)` such as `urn:sedml:language:bngl`).",
- "exception_type": "CombineArchiveExecutionError"
+ "exception_type": "CombineArchiveExecutionError",
+ "log": {
+ "duration": 3.920847,
+ "exception": {
+ "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n Language for model `net1` is not supported.\n - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\\.|$)` such as `urn:sedml:language:bngl`).",
+ "type": "CombineArchiveExecutionError"
+ },
+ "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `net1` has warnings.\r\n - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.\r\n - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the