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Update morpheus.json #1

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73 changes: 63 additions & 10 deletions simulator_schemas/morpheus.json
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Original file line number Diff line number Diff line change
@@ -1,29 +1,36 @@
{
"simulator_id": "sim_004",
"name": "Morpheus",
"version": "",
"version": "2.3.8",
"category": "Virtual Tissue",
"description": "A modeling and simulation environment for the study of multi-scale and multicellular systems, able to couple ODEs, PDEs and cellular Potts models.",
"platform": "Cross-platform",
"input_formats": [],
"output_formats": [],
"developer": "Morpheus Development Team",
"license": "Open-source",
"input_formats": ["XML", "SBML", "CSV", "TIFF", "Python"],
"output_formats": ["CSV", "PNG", "PDF", "SVG", "MP4"],
"developer": "Morpheus.Lab, TUD Dresden University of Technology, Germany",
"license": "BSD-3-Clause",
"website": "https://morpheus.gitlab.io/",
"documentation": "",
"last_updated": "2024-06-01",
"documentation": "https://morpheus.gitlab.io/courses/",
"last_updated": "2024-08-30",
"objects": [
{
"object_id": "obj_001",
"name": "Cell",
"attributes": ["type", "volume", "surface_area"],
"processes": ["proc_001", "proc_002"]
"attributes": ["position", "surface_area", "type", "volume"],
"processes": ["proc_001", "proc_002", "proc_004", "proc_005", "proc_006", "proc_007"],
"boundary_conditions": ["bc_001", "gc_001"]
},
{
"object_id": "obj_002",
"name": "ChemicalField",
"attributes": ["name", "concentration", "diffusion_coefficient"],
"processes": ["proc_003"]
"processes": ["proc_003"],
"boundary_conditions": ["bc_001", "bc_002", "gc_001"]
},
{
"object_id": "obj_003",
"name": "Microenvironment",
"attributes": ["oxygen", "nutrients", "waste"]
}
],
"processes": [
Expand All @@ -41,12 +48,58 @@
"process_id": "proc_003",
"name": "ChemicalDiffusion",
"description": "Process describing the diffusion of chemicals within the tissue."
},
{
"process_id": "proc_004",
"name": "Apoptosis",
"description": "Programmed cell death process."
},
{
"process_id": "proc_005",
"name": "CellProliferation",
"description": "Process describing the proliferation and growth of cells."
},
{
"process_id": "proc_006",
"name": "CellMigration",
"description": "Process describing the movement and migration of cells."
},
{
"process_id": "proc_007",
"name": "CellDeath",
"description": "Process describing programmed cell death (apoptosis) and necrosis."
}
],
"boundaries": {
"pde_boundary_conditions": [
{
"bc_id": "bc_001",
"description": "Dirichlet boundary condition for chemical concentration",
"type": "Dirichlet"
},
{
"bc_id": "bc_002",
"description": "Neumann boundary condition for chemical flux",
"type": "Neumann"
}
],
"geometric_constraints": [
{
"gc_id": "gc_001",
"description": "Periodic boundary condition for cell movement",
"type": "Periodic",
"dimensions": ["x", "y"]
}
]
},
"containment": [
{
"outer_object_id": "obj_002",
"inner_object_id": "obj_001"
},
{
"outer_object_id": "obj_003",
"inner_object_id": "obj_001"
}
]
}