results_compatibility_biosimulators.md

Engine	pass/FAIL	Error	Compatibility	d1
amici	pass		pass The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with amici	amici_d1.pdf
brian2	FAIL	Details No module named 'libsbml'	pass The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with brian2
bionetgen	FAIL	Details /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. Model net1 has warnings. - The model file LEMS_NML2_Ex9_FN.sbml has warnings. - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12: - 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. The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12: - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The parameter with the id 'I' does not have a 'units' attribute. /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive has warnings. OMEX manifests should not contain content entries for themselves. The SED-ML file at location ./tmp179064 has warnings. - Model net1 has warnings. - The model file LEMS_NML2_Ex9_FN.sbml has warnings. - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12: - 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. The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12: - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The parameter with the id 'I' does not have a 'units' attribute. 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).	FAIL The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']	bionetgen_d1.pdf
boolnet	FAIL	Details /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. Model net1 may be invalid. - The model file LEMS_NML2_Ex9_FN.sbml may be invalid. - 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. The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - 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. The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The parameter with the id 'I' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The parameter with the id 'SEC' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The parameter with the id 'V' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The parameter with the id 'W' does not have a 'units' attribute. /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. OMEX manifests should not contain content entries for themselves. The SED-ML file at location ./tmp515819 may be invalid. - Model net1 may be invalid. - The model file LEMS_NML2_Ex9_FN.sbml may be invalid. - 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. The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - 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. The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The parameter with the id 'I' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The parameter with the id 'SEC' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The parameter with the id 'V' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The parameter with the id 'W' does not have a 'units' attribute. 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). R[write to console]: Warning message: R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE, : R[write to console]: R[write to console]: library �/usr/lib/R/site-library� contains no packages	FAIL The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']	boolnet_d1.pdf
cbmpy	FAIL	Details INFO: No xlwt module available, Excel spreadsheet creation disabled No module named 'cplex' CPLEX not available Using GLPK INFO: No xlrd module available, Excel spreadsheet reading disabled CBMPy environment Revision: r689 * Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling http://cbmpy.sourceforge.net Copyright(C) Brett G. Olivier 2014 - 2019 Dept. of Systems Bioinformatics Vrije Universiteit Amsterdam, Amsterdam, The Netherlands CBMPy is developed as part of the BeBasic MetaToolKit Project Distributed under the GNU GPL v 3.0 licence, see LICENCE (supplied with this release) for details * ****************** /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. Model net1 has warnings. - The model file LEMS_NML2_Ex9_FN.sbml has warnings. - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12: - 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. The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12: - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The parameter with the id 'I' does not have a 'units' attribute. /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive has warnings. OMEX manifests should not contain content entries for themselves. The SED-ML file at location ./tmp133820 has warnings. - Model net1 has warnings. - The model file LEMS_NML2_Ex9_FN.sbml has warnings. - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12: - 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. The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12: - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The parameter with the id 'I' does not have a 'units' attribute. 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	pass The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cbmpy	cbmpy_d1.pdf
cobrapy	FAIL	Details /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. Model net1 has warnings. - The model file LEMS_NML2_Ex9_FN.sbml has warnings. - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12: - 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. The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12: - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The parameter with the id 'I' does not have a 'units' attribute. /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive has warnings. OMEX manifests should not contain content entries for themselves. The SED-ML file at location ./tmp818452 has warnings. - Model net1 has warnings. - The model file LEMS_NML2_Ex9_FN.sbml has warnings. - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12: - 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. The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12: - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The parameter with the id 'I' does not have a 'units' attribute. 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	pass The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cobrapy	cobrapy_d1.pdf
copasi	FAIL	Details /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. Model net1 has warnings. - The model file LEMS_NML2_Ex9_FN.sbml has warnings. - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12: - 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. The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12: - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The parameter with the id 'I' does not have a 'units' attribute. /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive has warnings. OMEX manifests should not contain content entries for themselves. The SED-ML file at location ./tmp443395 has warnings. - Model net1 has warnings. - The model file LEMS_NML2_Ex9_FN.sbml has warnings. - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12: - 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. The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12: - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The parameter with the id 'I' does not have a 'units' attribute. The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: could not convert string to float: 'Values[W]'	pass The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with copasi	copasi_d1.pdf
gillespy2	pass		pass The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with gillespy2	gillespy2_d1.pdf
ginsim	FAIL	Details /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. Model net1 may be invalid. - The model file LEMS_NML2_Ex9_FN.sbml may be invalid. - 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. The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - 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. The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The parameter with the id 'I' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The parameter with the id 'SEC' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The parameter with the id 'V' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The parameter with the id 'W' does not have a 'units' attribute. /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. OMEX manifests should not contain content entries for themselves. The SED-ML file at location ./tmp737874 may be invalid. - Model net1 may be invalid. - The model file LEMS_NML2_Ex9_FN.sbml may be invalid. - 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. The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - 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. The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The parameter with the id 'I' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The parameter with the id 'SEC' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The parameter with the id 'V' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The parameter with the id 'W' does not have a 'units' attribute. 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	FAIL The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']	ginsim_d1.pdf
libsbmlsim	pass		pass The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with libsbmlsim	libsbmlsim_d1.pdf
masspy	FAIL	Details /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 �[1;31m BioSimulatorsWarning: The SED document is potentially incorrect. Model net1 has warnings. - The model file LEMS_NML2_Ex9_FN.sbml has warnings. - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12: - 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. The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12: - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The parameter with the id 'I' does not have a 'units' attribute. /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 �[1;31m BioSimulatorsWarning: The COMBINE/OMEX archive has warnings. OMEX manifests should not contain content entries for themselves. The SED-ML file at location ./tmp539402 has warnings. - Model net1 has warnings. - The model file LEMS_NML2_Ex9_FN.sbml has warnings. - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12: - 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. The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12: - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The parameter with the id 'I' does not have a 'units' attribute. 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 .	pass The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with masspy	masspy_d1.pdf
netpyne	FAIL	Details No module named 'libsbml'	pass The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with netpyne
neuron	FAIL	Details No module named 'libsbml'	FAIL The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with neuron. The following file types will be compatible ['LEMS', 'NeuroML', 'SED-ML']
opencor	FAIL	Details No module named 'libsbml'	pass The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with opencor
pyneuroml	FAIL	Details No module named 'libsbml'	FAIL The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['LEMS', 'NeuroML', 'SED-ML']
pysces	FAIL	Details Could not find GLIMDA. /usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. Model net1 has warnings. - The model file LEMS_NML2_Ex9_FN.sbml has warnings. - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12: - 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. The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12: - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The parameter with the id 'I' does not have a 'units' attribute. /usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive has warnings. OMEX manifests should not contain content entries for themselves. The SED-ML file at location ./tmp82785 has warnings. - Model net1 has warnings. - The model file LEMS_NML2_Ex9_FN.sbml has warnings. - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12: - 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. The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12: - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The parameter with the id 'I' does not have a 'units' attribute. The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: Model at /tmp/tmpd0feybh_/./LEMS_NML2_Ex9_FN.sbml could not be imported: File /tmp/tmpd0feybh_/./LEMS_NML2_Ex9_FN.sbml.xml does not exist	pass The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with pysces	pysces_d1.pdf
rbapy	FAIL	Details /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. Model net1 may be invalid. - The model file LEMS_NML2_Ex9_FN.sbml may be invalid. - 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. The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - 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. The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The parameter with the id 'I' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The parameter with the id 'SEC' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The parameter with the id 'V' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The parameter with the id 'W' does not have a 'units' attribute. /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. OMEX manifests should not contain content entries for themselves. The SED-ML file at location ./tmp129913 may be invalid. - Model net1 may be invalid. - The model file LEMS_NML2_Ex9_FN.sbml may be invalid. - 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. The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - 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. The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The parameter with the id 'I' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The parameter with the id 'SEC' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The parameter with the id 'V' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The parameter with the id 'W' does not have a 'units' attribute. 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).	FAIL The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']	rbapy_d1.pdf
smoldyn	FAIL	Details [Errno 2] No such file or directory: '/tmp/tmpss9737_4/model.txt'	FAIL smoldyn compatible file types unknown.
tellurium	pass		pass The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with tellurium	tellurium_d1.pdf
vcell	FAIL	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: b' Root(root) OMEX_EXECUTE(LEMS_NML2_Ex9_FN_missing_xmlns.omex) PROCESSING_SEDML(preProcessDoc) **** Error: SED-ML processing for /tmp/vcell_temp_365be07b-5fd9-47bf-9fe9-8a37eb03827f17379398015478899102/tmp584011 failed with error: \n Root(root) OMEX_EXECUTE(LEMS_NML2_Ex9_FN_missing_xmlns.omex) SIMULATIONS_RUN(runSimulations) **** Error: \n Root(root) OMEX_EXECUTE(LEMS_NML2_Ex9_FN_missing_xmlns.omex) PROCESSING_SIMULATION_OUTPUTS(processOutputs) **** Error: Error processing outputs\n'	FAIL vcell compatible file types unknown.
xpp	FAIL	Details No module named 'libsbml'	FAIL The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']