results_compatibility_biosimulators.md

Engine	Compatibility	pass / FAIL (R)	pass / FAIL (L)	d1 (R)	d1 (L)
AMICI https://docs.biosimulators.org/Biosimulators_AMICI/	✅ PASS The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with amici. ['SBML', 'SED-ML'] are compatible with amici.	✅ PASS view download logs	✅ PASS	plot	plot
BioNetGen https://docs.biosimulators.org/Biosimulators_BioNetGen/	⚠ XFAIL EXPECTED FAIL The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen.	⚠ XFAIL EXPECTED FAIL view download logs ERROR MESSAGE: The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: Language for model model_1 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(\.$) such as urn:sedml:language:bngl). ERROR TYPE: CombineArchiveExecutionError	⚠ XFAIL EXPECTED FAIL ERROR MESSAGE: The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: Language for model model_1 is not supported. - Model language urn:sedml:language:sbml is not supported. Models must be in BNGL format (e.g., sed:model/@language must match ^urn:sedml:language:bngl(\.$) such as urn:sedml:language:bngl). ERROR TYPE: CombineArchiveExecutionError	plot	plot
BoolNet https://docs.biosimulators.org/Biosimulators_BoolNet/	⚠ XFAIL EXPECTED FAIL The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet.	⚠ XFAIL EXPECTED FAIL view download logs ERROR MESSAGE: The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: Simulation simulation_1 is invalid. - Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0). ERROR TYPE: CombineArchiveExecutionError	⚠ XFAIL EXPECTED FAIL ERROR MESSAGE: The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: Simulation simulation_1 is invalid. - Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0). ERROR TYPE: CombineArchiveExecutionError	plot	plot
Brian 2 https://docs.biosimulators.org/Biosimulators_pyNeuroML/	⚠ XFAIL EXPECTED FAIL The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2.	⚠ XFAIL EXPECTED FAIL view download logs ERROR MESSAGE: No module named 'libsbml' ERROR TYPE: ModuleNotFoundError	⚠ XFAIL EXPECTED FAIL ERROR MESSAGE: No module named 'libsbml' ERROR TYPE: ModuleNotFoundError
CBMPy https://docs.biosimulators.org/Biosimulators_CBMPy/	✅ PASS The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with cbmpy. ['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 simulation_1 is not supported. - Simulation simulation_1 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 simulation_1 is not supported. - Simulation simulation_1 of type UniformTimeCourseSimulation is not supported. Simulation must be an instance of one of the following: - SteadyStateSimulation ERROR TYPE: CombineArchiveExecutionError	plot	plot
COBRApy https://docs.biosimulators.org/Biosimulators_COBRApy/ Only allows steady state simulations	✅ PASS The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with cobrapy. ['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 simulation_1 is not supported. - Simulation simulation_1 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 simulation_1 is not supported. - Simulation simulation_1 of type UniformTimeCourseSimulation is not supported. Simulation must be an instance of one of the following: - SteadyStateSimulation ERROR TYPE: CombineArchiveExecutionError	plot	plot
COPASI https://docs.biosimulators.org/Biosimulators_COPASI/	✅ PASS The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with copasi. ['SBML', 'SED-ML'] are compatible with copasi.	✅ PASS view download logs	✅ PASS	plot	plot
GillesPy2 https://docs.biosimulators.org/Biosimulators_GillesPy2/	✅ PASS The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2.	✅ PASS view download logs	✅ PASS	plot	plot
GINsim https://docs.biosimulators.org/Biosimulators_GINsim/	⚠ XFAIL EXPECTED FAIL The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim.	⚠ XFAIL EXPECTED FAIL view download logs ERROR MESSAGE: The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: Simulation simulation_1 is invalid. - The interval between the output start and time time must be an integer multiple of the number of steps, not 0.1: Output start time: 0.0 Output end time: 5.0 Number of steps: 50 ERROR TYPE: CombineArchiveExecutionError	⚠ XFAIL EXPECTED FAIL ERROR MESSAGE: The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: Simulation simulation_1 is invalid. - The interval between the output start and time time must be an integer multiple of the number of steps, not 0.1: Output start time: 0.0 Output end time: 5.0 Number of steps: 50 ERROR TYPE: CombineArchiveExecutionError	plot	plot
LibSBMLSim https://docs.biosimulators.org/Biosimulators_LibSBMLSim/	✅ PASS The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsim.	✅ PASS view download logs	✅ PASS	plot	plot
MASSpy https://docs.biosimulators.org/Biosimulators_MASSpy/	✅ PASS The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with masspy. ['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:listOfCompartments/sbml:compartment[@id='compartment'] - /sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment'] Only following targets are supported: - M_S1 - M_S2 - R_reaction1 - S1 - S2 - k1 - reaction1 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: CombineArchiveExecutionError	plot	plot
NetPyNE https://docs.biosimulators.org/Biosimulators_pyNeuroML/	⚠ XFAIL EXPECTED FAIL The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne.	⚠ XFAIL EXPECTED FAIL view download logs ERROR MESSAGE: No module named 'libsbml' ERROR TYPE: ModuleNotFoundError	⚠ XFAIL EXPECTED FAIL ERROR MESSAGE: No module named 'libsbml' ERROR TYPE: ModuleNotFoundError
NEURON https://docs.biosimulators.org/Biosimulators_pyNeuroML/	⚠ XFAIL EXPECTED FAIL The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron.	⚠ XFAIL EXPECTED FAIL view download logs ERROR MESSAGE: No module named 'libsbml' ERROR TYPE: ModuleNotFoundError	⚠ XFAIL EXPECTED FAIL ERROR MESSAGE: No module named 'libsbml' ERROR TYPE: ModuleNotFoundError
OpenCOR https://docs.biosimulators.org/Biosimulators_OpenCOR/	⚠ XFAIL EXPECTED FAIL The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with opencor. ['CellML', 'SED-ML'] are compatible with opencor.	⚠ XFAIL EXPECTED FAIL view download logs ERROR MESSAGE: No module named 'libsbml' ERROR TYPE: ModuleNotFoundError	⚠ XFAIL EXPECTED FAIL ERROR MESSAGE: No module named 'libsbml' ERROR TYPE: ModuleNotFoundError
pyNeuroML https://docs.biosimulators.org/Biosimulators_pyNeuroML/	⚠ XFAIL EXPECTED FAIL The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml.	⚠ XFAIL EXPECTED FAIL view download logs ERROR MESSAGE: No module named 'libsbml' ERROR TYPE: ModuleNotFoundError	⚠ XFAIL EXPECTED FAIL ERROR MESSAGE: No module named 'libsbml' ERROR TYPE: ModuleNotFoundError
PySCeS https://docs.biosimulators.org/Biosimulators_PySCeS/	✅ PASS The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with pysces. ['SBML', 'SED-ML'] are compatible with pysces.	✅ PASS view download logs	✅ PASS	plot	plot
RBApy https://docs.biosimulators.org/Biosimulators_RBApy/	⚠ XFAIL EXPECTED FAIL The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy.	⚠ XFAIL EXPECTED FAIL view download logs ERROR MESSAGE: The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: Language for model model_1 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(\.$) such as urn:sedml:language:rba). ERROR TYPE: CombineArchiveExecutionError	⚠ XFAIL EXPECTED FAIL ERROR MESSAGE: The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: Language for model model_1 is not supported. - Model language urn:sedml:language:sbml is not supported. Models must be in RBA format (e.g., sed:model/@language must match ^urn:sedml:language:rba(\.$) such as urn:sedml:language:rba). ERROR TYPE: CombineArchiveExecutionError	plot	plot
Smoldyn https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api	⚠ XFAIL EXPECTED FAIL The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn.	⚠ XFAIL EXPECTED FAIL view download logs ERROR MESSAGE: No module named 'libsbml' ERROR TYPE: ModuleNotFoundError	⚠ XFAIL EXPECTED FAIL ERROR MESSAGE: Error unknown. The log.yml containing error information was not found.
Tellurium https://docs.biosimulators.org/Biosimulators_tellurium/	✅ PASS The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with tellurium. ['SBML', 'SED-ML'] are compatible with tellurium.	✅ PASS view download logs	✅ PASS	plot	plot
VCell https://github.com/virtualcell/vcell	✅ PASS The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell.	❌ FAIL view download logs ERROR MESSAGE: status: QUEUED	❌ FAIL ERROR MESSAGE: Runtime Exception
XPP https://docs.biosimulators.org/Biosimulators_XPP/	⚠ XFAIL EXPECTED FAIL The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with xpp. ['XPP', 'SED-ML'] are compatible with xpp.	⚠ XFAIL EXPECTED FAIL view download logs ERROR MESSAGE: No module named 'libsbml' ERROR TYPE: ModuleNotFoundError	⚠ XFAIL EXPECTED FAIL ERROR MESSAGE: No module named 'libsbml' ERROR TYPE: ModuleNotFoundError