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Merged
stellaprins merged 6 commits into from
Jan 20, 2025
Merged

Feat biomodels #115

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0a174ad
add omex_file_name to remote simulation dictionary instead of generic…
stellaprins Jan 14, 2025
3e849dd
set use_original_files to False to use ammended sedml files and remov…
stellaprins Jan 14, 2025
f82e682
adjust sedml files to replicate curated BioModels figures
stellaprins Jan 14, 2025
b1936d0
add created omex files
stellaprins Jan 14, 2025
24e10f0
update detailed biomodels tables and d1 plots
stellaprins Jan 14, 2025
f986ce4
make results table names more descriptive
stellaprins Jan 14, 2025
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Binary file added BioModels/BIOMD0000000001/BIOMD0000000001_url.omex
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28 changes: 14 additions & 14 deletions BioModels/BIOMD0000000001/BIOMD0000000001_url.sedml
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Expand Up @@ -4,7 +4,7 @@
<model id="BIOMD0000000001_url" language="urn:sedml:language:sbml" source="BIOMD0000000001_url.xml"/>
</listOfModels>
<listOfSimulations>
<uniformTimeCourse id="auto_ten_seconds" initialTime="0" outputStartTime="0" outputEndTime="10" numberOfSteps="1000">
<uniformTimeCourse id="auto_ten_seconds" initialTime="0.1" outputStartTime="0.1" outputEndTime="10000" numberOfSteps="50000">
<algorithm name="ODE solver" kisaoID="KISAO:0000694"/>
</uniformTimeCourse>
</listOfSimulations>
Expand Down Expand Up @@ -613,21 +613,21 @@
</listOfDataSets>
</report>
<plot2D id="autogen_plot_for_task1" name="Auto-generated plot for task1, including all species.">
<xAxis name="Time" type="linear"/>
<xAxis name="Time" type="log10"/>
<yAxis name="Species" type="linear"/>
<listOfCurves>
<curve id="autogen_curve_task1_BLL" name="BLL" logX="false" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_BLL"/>
<curve id="autogen_curve_task1_IL" name="IL" logX="false" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_IL"/>
<curve id="autogen_curve_task1_AL" name="AL" logX="false" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_AL"/>
<curve id="autogen_curve_task1_A" name="A" logX="false" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_A"/>
<curve id="autogen_curve_task1_BL" name="BL" logX="false" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_BL"/>
<curve id="autogen_curve_task1_B" name="B" logX="false" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_B"/>
<curve id="autogen_curve_task1_DLL" name="DLL" logX="false" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_DLL"/>
<curve id="autogen_curve_task1_D" name="D" logX="false" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_D"/>
<curve id="autogen_curve_task1_ILL" name="ILL" logX="false" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_ILL"/>
<curve id="autogen_curve_task1_DL" name="DL" logX="false" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_DL"/>
<curve id="autogen_curve_task1_I" name="I" logX="false" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_I"/>
<curve id="autogen_curve_task1_ALL" name="ALL" logX="false" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_ALL"/>
<curve id="autogen_curve_task1_BLL" name="BLL" logX="true" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_BLL"/>
<curve id="autogen_curve_task1_IL" name="IL" logX="true" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_IL"/>
<curve id="autogen_curve_task1_AL" name="AL" logX="true" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_AL"/>
<curve id="autogen_curve_task1_A" name="A" logX="true" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_A"/>
<curve id="autogen_curve_task1_BL" name="BL" logX="true" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_BL"/>
<curve id="autogen_curve_task1_B" name="B" logX="true" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_B"/>
<curve id="autogen_curve_task1_DLL" name="DLL" logX="true" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_DLL"/>
<curve id="autogen_curve_task1_D" name="D" logX="true" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_D"/>
<curve id="autogen_curve_task1_ILL" name="ILL" logX="true" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_ILL"/>
<curve id="autogen_curve_task1_DL" name="DL" logX="true" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_DL"/>
<curve id="autogen_curve_task1_I" name="I" logX="true" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_I"/>
<curve id="autogen_curve_task1_ALL" name="ALL" logX="true" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_ALL"/>
</listOfCurves>
</plot2D>
</listOfOutputs>
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42 changes: 21 additions & 21 deletions ...ts/results_compatibility_biosimulators.md → ...0001/tests/results_BIOMD0000000001_url.md
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118 changes: 59 additions & 59 deletions BioModels/BIOMD0000000001/tests/results_local.json
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