Create LEMS_NML2_Ex9_FN docker results table

[stellaprins]

Create overview table like the one below for locally ran LEMS_NML2_Ex9_FN model.

• [x] run with biosimulators docker locally (on all the different engines)
• [ ] run with biosimulators remotely (on all the different engines) pynml API does this currently (check this)

Use helper functions that Rob wrote.

Down the line:

• [ ] incorperate process (for creating the table) in github actions and automate it as a test.

The resulting minimal omex file SBML\LEMS_NML2_Ex9_FN.omex biosimulations tool was used to run simulations on https://run.biosimulations.org/

Simulator: tellurium 2.2.8 (Sensible output was produced) Simulator: copasi 4.42.284 Failed Simulator: amici 0.18.1 (No output was produced) Simulator: vcell 7.5.0.127 (No output was produced) Simulator: pysces 1.2.1 Failed Simulator: gillespy2 1.6.6 (No sensible output was produced, flat line) Simulator: libsbmlsim 1.4.0 (Sensible output was produced) Simulator: masspy 0.1.6 Failed

[stellaprins]

@robertvi do you know where I find the {engine} strings that match the biosimulators URI ghcr.io/biosimulators/{engine}?

[sanjayankur31]

I think the list is here:

https://docs.biosimulations.org/users/biosimulators-packages/

Each link goes to a page that then links to docker container instructions, e.g.: https://docs.biosimulators.org/Biosimulators_LibSBMLSim/installation.html#docker-image-with-a-command-line-entrypoint

Note: For the following engines there was no dedicated biosimulators link to the page that then links to docker container instructions:

• OpenCOR: https://docs.biosimulators.org/Biosimulators_OpenCOR/installation.html#python-package-and-command-line-program
• RBApy: https://docs.biosimulators.org/Biosimulators_RBApy/installation.html#command-line-program
• Smoldyn: https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
• Vcell https://github.com/virtualcell/vcell

[stellaprins]

Add error messages to table indicating whether the models have the right format to be run in the specific engine (for example, OpenCOR is CELL-ML, see here).

[stellaprins]

reports.h5 contains more information about whether a run has created a sensible output or not (some engines may run the model fine but are expected not to create a d1 plot).

• [x] Download HDF viewer and view .h5 files.

[stellaprins]

@robertvi and myself looked at the output .h5 files and found that the models that had a d1.pdf graph also had a d1 and ex9 dataframe packaged inside the .h5 files. We found this h5py package that would allow us to deal with the .h5 files programatically but I will first focus on adding the d1.pdf graphs to the markdown output.

@pgleeson do you know what we would expect to find in cases where there no, or no sensible, d1.pdf graph has been created, but the model ran as it is supposed to run?

This is what a few of the .h5 files look like when I open them with the HDF viewer.

Simulator: tellurium 2.2.8 (Sensible output was produced)

Simulator: gillespy2 1.6.6 (No sensible output was produced, flat line)

Simulator: vcell 7.5.0.127 (No output was produced)

Simulator: masspy 0.1.6 Failed

[stellaprins]

I'm trying to find an easy way to determine whether a given file is an SBML or SED-ML file (to start with, functionality for other filetypes, e.g. CELL-ML, can be added in the future).

From previous discussions I remember that the file extension (e.g. .xml, .sedml, .sbml) are not always coherent with the file type, is this correct @robertvi?

I've tried using some functions from the libsbml library, like validateSBML, which is supposed to return the number of failed checks (errors) encountered.

Interestingly enough, when I use the SBML file returns a non-zero value while the SED-ML file does return a zero value.

libsbml.readSBML(sbml_filepath).validateSBML()

6

libsbml.readSBML(sedml_filepath).validateSBML()

0

When I try to inspect the severity flag in the individual SBMLError objects returned by SBMLDocument.getError() to determine the nature of the failures as suggested in the libsbml documentation.

for i in range(0,libsbml.readSBML(sbml_filepath).validateSBML()):
    print(i)
    print(libsbml.readSBML(sbml_filepath).getError(i))

0 None 1 None 2 None 3 None 4 None 5 None

I'm not sure what may be going on here and am tempted to use the extension to determine the file-type. If anyone has suggestions, let me know!

[sanjayankur31]

I think it's sufficient to use the file extension to determine the file type for the moment. That's what we use in pyNeuroML:

https://github.com/NeuroML/pyNeuroML/blob/abec06302f137aba25d9aa076fa8d8d1e2c2d27e/pyneuroml/archive/__init__.py#L151

(A better way may be to read the file and figure out the type based on the XML root tag, but I don't think we've done this either---it requires reading of the file, and the file can be quite large. Another way could be to read the first few lines to figure out the XML tag, but again, that assumes that the file is well formatted and does have the XML starting in the first few lines..)

[stellaprins]

I've made some progress on the project before my break. My initial goal was to display the PDF files as embedded images rather than links, but this turned out to be rather challenging.

Here are some key updates:

• Collapsible content: I've added collapsible content in the markdown table for better readability.
• D1 Plots: The D1 plots are fetched, renamed to {engine}_d1.pdf, and stored in the d1_plots subfolder for easy reference.
• Error Messages: I've converted most of the markdown-incompatible parts of error messages into markdown-compatible HTML. I also converted the colour coding to HTML, but unfortunately, these colours are not displayed on the GitHub website (they are in the jupyter notebook I've used for trouble shooting).

This is what the biosimulators compatibility results table looks like

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
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
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_Ex9FN.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']