Submit PySceS 0.9.9

[biosimulators-daemon]

---

id: pysces version: 0.9.9 specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_PySCeS/1fa99758dfc575f91a13f35547bfcb71166e9f9a/biosimulators.json specificationsPatch: version: 0.9.9 image: url: ghcr.io/biosimulators/biosimulators_pysces/pysces:0.9.9 validateImage: true commitSimulator: true

---

[biosimulators-daemon]

Thank you @biosimulators-daemon for your submission to the BioSimulators simulator validation/submission system!

The BioSimulators validator bot is validating the specifications of your simulator, validating your Docker image, and committing your simulator to the BioSimulators registry.

We will discuss any concerns with your submission in this issue.

A complete log of your simulator submission job will be available for 90 days here. The results of the validation of your tool will also be saved as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

[biosimulators-daemon]

The specifications of your simulator is valid!

[biosimulators-daemon]

Summary of tests

• Executed 72 test cases

• Passed 10 test cases:

  • cli.CliDescribesSupportedEnvironmentVariablesInline
  • cli.CliDisplaysHelpInline
  • cli.CliDisplaysVersionInformationInline
  • docker_image.DeclaresSupportedEnvironmentVariables
  • docker_image.DefaultUserIsRoot
  • docker_image.HasBioContainersLabels
  • docker_image.HasOciLabels
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator

• Failed 17 test cases:

  • combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
  • combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
  • combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
  • combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
  • docker_image.SingularityImageExecutesSimulationsSuccessfully
  • published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
  • results_report.SimulatorGeneratesReportsOfSimulationResults
  • sedml.SimulatorProducesLinear2DPlots
  • sedml.SimulatorProducesLogarithmic2DPlots
  • sedml.SimulatorProducesMultiplePlots
  • sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
  • sedml.SimulatorSupportsAlgorithmParameters
  • sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
  • sedml.SimulatorSupportsMultipleReportsPerSedDocument
  • sedml.SimulatorSupportsMultipleTasksPerSedDocument
  • sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

• Skipped 45 test cases:

  • log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
  • log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
  • log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
  • log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
  • published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
  • published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
  • published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator
  • published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
  • published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE
  • published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA
  • published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism
  • published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling
  • published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle
  • published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra
  • published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells
  • sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
  • sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
  • sedml.SimulatorProducesLinear3DPlots
  • sedml.SimulatorProducesLogarithmic3DPlots
  • sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
  • sedml.SimulatorSupportsComputeModelChanges
  • sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
  • sedml.SimulatorSupportsDataSetsWithDifferentShapes
  • sedml.SimulatorSupportsModelAttributeChanges
  • sedml.SimulatorSupportsRepeatedTasksWithChanges
  • sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
  • sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
  • sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges
  • sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
  • sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
  • sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
  • sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
  • sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
  • sedml.SimulatorSupportsRepeatedTasksWithVectorRanges
  • sedml.SimulatorSupportsSubstitutingAlgorithms
  • sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes

[biosimulators-daemon]

Failures

combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories (11.0 s)

Test that SED documents in nested directories can be executed

Exception:

  The image 'ghcr.io/biosimulators/biosimulators_pysces/pysces:0.9.9' could not execute the archive:

    Unknown error

Log:

  libtk8.6.so: cannot open shared object file: No such file or directory

  PySCeS defaults to matplotlib's TKagg backend if not specified                      in the user configuration file, set "matplotlib_backend = <backend>" 

  Matplotlib interface loaded (pysces.plt.m)

  Attempting alternate pitcon import ...

  Attempting alternate nleq2 import ...

  Continuation routines available (A)

  NLEQ2 routines available (A)

  SBML support available

  You are using NumPy (1.21.2) with SciPy (1.7.1)

  Could not find libgfortran.so.5: cannot open shared object file: No such file or directory

  Could not find libgfortran.so.5: cannot open shared object file: No such file or directory

  Could not find libgfortran.so.5: cannot open shared object file: No such file or directory

  Could not find libgfortran.so.5: cannot open shared object file: No such file or directory

  Could not find ODEPACK functions.

  /usr/local/lib/python3.9/site-packages/assimulo/solvers/odepack.py:710: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray.

    N.array([[0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.],  # 5th order

  Could not find RADAR5

  Could not find GLIMDA.

  Assimulo CVode available

  RateChar is available

  No module named 'ipyparallel'

  PARSCANNER: Requires ipyparallel version >=4.0 (http://ipython.org).

  INFO: Parallel scanner not available

  PySCeS environment

  ******************

  pysces.model_dir = /root/Pysces/psc

  pysces.output_dir = /root/Pysces

  ***********************************************************************

  * Welcome to PySCeS (0.9.9) - Python Simulator for Cellular Systems   *

  *                http://pysces.sourceforge.net                        *

  * Copyright(C) B.G. Olivier, J.M. Rohwer, J.-H.S. Hofmeyr, 2004-2020  *

  * Triple-J Group for Molecular Cell Physiology                        *

  * Stellenbosch University, ZA and VU University Amsterdam, NL         *

  * PySCeS is distributed under the PySCeS (BSD style) licence, see     *

  * LICENCE.txt (supplied with this release) for details                *

  * Please cite PySCeS with: doi:10.1093/bioinformatics/bti046          *

  ***********************************************************************

  /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect.

    - Model `model` may be invalid.

      - The model file `WholeCellRBC_MA_Rates.xml` may be invalid.

        - In situations where a mathematical expression refers to time, the units of time should be consistent with the global time units of the model. In models where the 'timeUnits' attribute has not been declared, libSBML does not yet have the functionality to verify accurately the consistency of the units in such expressions. 

        - In situations where a mathematical expression refers to extent, the units of extent should be consistent with the global extent units of the model. In models where the 'extentUnits' attribute has not been declared, libSBML does not yet have the functionality to verify accurately the consistency of the units in such expressions. 

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <compartment> 'c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'units' on a Compartment object having a 'spatialDimensions' attribute value of '3' has not been set, then the unit of measurement associated with the compartment's size is determined by the value of the enclosing Model object's 'volumeUnits' attribute. If neither the Compartment object's 'units' nor the enclosing Model object's 'volumeUnits' attributes are set, the unit of compartment size is undefined.

          Reference: L3V1 Section 4.5.4

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <compartment> 'e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'units' on a Compartment object having a 'spatialDimensions' attribute value of '3' has not been set, then the unit of measurement associated with the compartment's size is determined by the value of the enclosing Model object's 'volumeUnits' attribute. If neither the Compartment object's 'units' nor the enclosing Model object's 'volumeUnits' attributes are set, the unit of compartment size is undefined.

          Reference: L3V1 Section 4.5.4

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M__13dpg_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M__13dpg_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M__23dpg_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M__23dpg_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M__2kmb_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M__2kmb_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M__2pg_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M__2pg_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M__35cgmp_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M__35cgmp_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M__35cgmp_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M__35cgmp_e' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M__3pg_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M__3pg_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M__5mdr1p_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M__5mdr1p_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M__5mdru1p_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M__5mdru1p_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M__5mta_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M__5mta_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M__5oxpro_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M__5oxpro_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M__5oxpro_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M__5oxpro_e' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M__6pgc_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M__6pgc_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M__6pgl_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M__6pgl_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_accoa_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_accoa_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_ade_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_ade_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_ade_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_ade_e' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_adn_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_adn_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_adn_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_adn_e' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_adp_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_adp_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_ahcys_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_ahcys_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_akg_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_akg_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_akg_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_akg_e' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_ala__L_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_ala__L_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_ala__L_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_ala__L_e' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_amet_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_amet_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_ametam_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_ametam_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_amp_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_amp_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_arg__L_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_arg__L_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_arg__L_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_arg__L_e' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_ascb__L_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_ascb__L_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_ascb__L_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_ascb__L_e' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_asn__L_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_asn__L_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_asn__L_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_asn__L_e' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_atp_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_atp_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_band_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_band_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_bandmt_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_bandmt_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_ca2_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_ca2_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_ca2_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_ca2_e' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_camp_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_camp_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_camp_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_camp_e' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_cit_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_cit_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_cit_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_cit_e' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_cl_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_cl_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_cl_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_cl_e' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_co2_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_co2_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_co2_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_co2_e' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_coa_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_coa_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_cys__L_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_cys__L_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_cys__L_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not b ...

[biosimulators-daemon]

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (4.0 s)

Test that the inline help for a command-line interface describes the environment variables that the simulator supports.

Warnings:

  The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports.

  The command-line interface does not describe the following standard environment variables recognized by BioSimulators:
    - 'ALGORITHM_SUBSTITUTION_POLICY'
    - 'BUNDLE_OUTPUTS'
    - 'H5_REPORTS_PATH'
    - 'KEEP_INDIVIDUAL_OUTPUTS'
    - 'LOG_PATH'
    - 'PLOTS_PATH'
    - 'REPORTS_PATH'
    - 'REPORT_FORMATS'
    - 'SAVE_PLOT_DATA'
    - 'VALIDATE_IMAGES'
    - 'VALIDATE_OMEX_MANIFESTS'
    - 'VALIDATE_OMEX_METADATA'
    - 'VALIDATE_SEDML'
    - 'VALIDATE_SEDML_MODELS'
    - 'VERBOSE'
    - 'VIZ_FORMATS'

  If the simulation tool implements these variables, they should be described in the inline help for its command-line interface.

  Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log:

docker_image.DeclaresSupportedEnvironmentVariables (0.8 s)

Test if a Docker image declares the environment variables that is supports

Warnings:

  Docker images for simulation tools should declare the environment variables that they support.

  The Docker image does not declare the following standard environment variables recognized by BioSimulators:
    - 'BUNDLE_OUTPUTS'
    - 'H5_REPORTS_PATH'
    - 'KEEP_INDIVIDUAL_OUTPUTS'
    - 'LOG_PATH'
    - 'PLOTS_PATH'
    - 'REPORTS_PATH'
    - 'REPORT_FORMATS'
    - 'SAVE_PLOT_DATA'
    - 'VALIDATE_IMAGES'
    - 'VALIDATE_OMEX_MANIFESTS'
    - 'VALIDATE_OMEX_METADATA'
    - 'VALIDATE_SEDML'
    - 'VALIDATE_SEDML_MODELS'
    - 'VIZ_FORMATS'

  If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator.

  Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (5.2 s)

Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000019

  Warnings:

  Unexpected reports were produced:
  BIOMD0000000912_sim.sedml/Figure_1_bottom_left

  Plots were not produced:
  BIOMD0000000912_sim.sedml/plot_1

  Extra plots were produced:
  BIOMD0000000912_sim.sedml/Figure_1_bottom_left

  Log:

  
  libtk8.6.so: cannot open shared object file: No such file or directory
  
  PySCeS defaults to matplotlib's TKagg backend if not specified                      in the user configuration file, set "matplotlib_backend = <backend>" 
  
  Matplotlib interface loaded (pysces.plt.m)
  
  Attempting alternate pitcon import ...
  
  Attempting alternate nleq2 import ...
  
  Continuation routines available (A)
  
  NLEQ2 routines available (A)
  
  SBML support available
  
  You are using NumPy (1.21.2) with SciPy (1.7.1)
  
  Could not find libgfortran.so.5: cannot open shared object file: No such file or directory
  
  Could not find libgfortran.so.5: cannot open shared object file: No such file or directory
  
  Could not find libgfortran.so.5: cannot open shared object file: No such file or directory
  
  Could not find libgfortran.so.5: cannot open shared object file: No such file or directory
  
  Could not find ODEPACK functions.
  
  /usr/local/lib/python3.9/site-packages/assimulo/solvers/odepack.py:710: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray.
  
  N.array([[0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.],  # 5th order
  
  Could not find RADAR5
  
  Could not find GLIMDA.
  
  Assimulo CVode available
  
  RateChar is available
  
  No module named 'ipyparallel'
  
  PARSCANNER: Requires ipyparallel version >=4.0 (http://ipython.org).
  
  INFO: Parallel scanner not available
  
  PySCeS environment
  
  ******************
  
  pysces.model_dir = /root/Pysces/psc
  
  pysces.output_dir = /root/Pysces
  
  ***********************************************************************

• Welcome to PySCeS (0.9.9) - Python Simulator for Cellular Systems *

• http://pysces.sourceforge.net *

• Copyright(C) B.G. Olivier, J.M. Rohwer, J.-H.S. Hofmeyr, 2004-2020 *

• Triple-J Group for Molecular Cell Physiology *

• Stellenbosch University, ZA and VU University Amsterdam, NL *

• PySCeS is distributed under the PySCeS (BSD style) licence, see *

• LICENCE.txt (supplied with this release) for details *

• Please cite PySCeS with: doi:10.1093/bioinformatics/bti046 *

  ---

  /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect.

  • Model BIOMD0000000912 may be invalid.

    • The model file Caravagna2010.xml 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 $expression\; \text{'}compartment\; *\; Function\_for\_induction\_of\_tumor(r2,\; T,\; b,\; V)\text{'}\; cannot\; be\; fully\; checked.\; Unit\; consistency\; reported\; as\; either\; no\; errors\; or\; further\; unit\; errors\; related\; to\; this\; object\; may\; not\; be\; accurate.$

    • 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 $expression\; \text{'}compartment\; *\; Function\_for\_removal\_of\_the\_tumor(a,\; T,\; g2,\; V,\; E)\text{'}\; cannot\; be\; fully\; checked.\; Unit\; consistency\; reported\; as\; either\; no\; errors\; or\; further\; unit\; errors\; related\; to\; this\; object\; may\; not\; be\; accurate.$

    • 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 $expression\; \text{'}compartment\; *\; Function\_for\_activation\_and\_transfer\_of\_effector\_cells\_to\_the\_tumor\_site(p1,\; I,\; g1,\; E,\; c,\; T,\; V,\; s1)\text{'}\; cannot\; be\; fully\; checked.\; Unit\; consistency\; reported\; as\; either\; no\; errors\; or\; further\; unit\; errors\; related\; to\; this\; object\; may\; not\; be\; accurate.$

    • 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 $expression\; \text{'}compartment\; *\; Function\_for\_deactivation\_and\_removal\_of\_effector\_cells\_from\_the\_site\_of\_tumor(mu2,\; E)\text{'}\; cannot\; be\; fully\; checked.\; Unit\; consistency\; reported\; as\; either\; no\; errors\; or\; further\; unit\; errors\; related\; to\; this\; object\; may\; not\; be\; accurate.$

    • 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 $expression\; \text{'}compartment\; *\; Function\_for\_activation\_of\_interleukin\_2(p2,\; V,\; T,\; E,\; g3,\; s2)\text{'}\; cannot\; be\; fully\; checked.\; Unit\; consistency\; reported\; as\; either\; no\; errors\; or\; further\; unit\; errors\; related\; to\; this\; object\; may\; not\; be\; accurate.$

    • 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 $expression\; \text{'}compartment\; *\; Function\_for\_deactivation\_of\_interleukin\_2(mu3,\; I)\text{'}\; cannot\; be\; fully\; checked.\; Unit\; consistency\; reported\; as\; either\; no\; errors\; or\; further\; unit\; errors\; related\; to\; this\; object\; may\; not\; be\; accurate.$

    • As a principle of best modeling practice, the units of a 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 with the id 'r2' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'b' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'a' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'g2' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'p1' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'g1' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'mu2' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'c' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'p2' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'g3' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'mu3' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'V' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 's1' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 's2' does not have a 'units' attribute.

      

  warnings.warn(termcolor.colored(message, Colors.warning.value), category)

  /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid.

  • The SED-ML file at location ./BIOMD0000000912_sim.sedml may be invalid.

    • Model BIOMD0000000912 may be invalid.

    • The model file Caravagna2010.xml 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 $expression\; \text{'}compartment\; *\; Function\_for\_induction\_of\_tumor(r2,\; T,\; b,\; V)\text{'}\; cannot\; be\; fully\; checked.\; Unit\; consistency\; reported\; as\; either\; no\; errors\; or\; further\; unit\; errors\; related\; to\; this\; object\; may\; not\; be\; accurate.$

      • 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 $expression\; \text{'}compartment\; *\; Function\_for\_removal\_of\_the\_tumor(a,\; T,\; g2,\; V,\; E)\text{'}\; cannot\; be\; fully\; checked.\; Unit\; consistency\; reported\; as\; either\; no\; errors\; or\; further\; unit\; errors\; related\; to\; this\; object\; may\; not\; be\; accurate.$

      • 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 $expression\; \text{'}compartment\; *\; Function\_for\_activation\_and\_transfer\_of\_effector\_cells\_to\_the\_tumor\_site(p1,\; I,\; g1,\; E,\; c,\; T,\; V,\; s1)\text{'}\; cannot\; be\; fully\; checked.\; Unit\; consistency\; reported\; as\; either\; no\; errors\; or\; further\; unit\; errors\; related\; to\; this\; object\; may\; not\; be\; accurate.$

      • 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 $expression\; \text{'}compartment\; *\; Function\_for\_deactivation\_and\_removal\_of\_effector\_cells\_from\_the\_site\_of\_tumor(mu2,\; E)\text{'}\; cannot\; be\; fully\; checked.\; Unit\; consistency\; reported\; as\; either\; no\; errors\; or\; further\; unit\; errors\; related\; to\; this\; object\; may\; not\; be\; accurate.$

      • 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 $expression\; \text{'}compartment\; *\; Function\_for\_activation\_of\_interleukin\_2(p2,\; V,\; T,\; E,\; g3,\; s2)\text{'}\; cannot\; be\; fully\; checked.\; Unit\; consistency\; reported\; as\; either\; no\; errors\; or\; further\; unit\; errors\; related\; to\; this\; object\; may\; not\; be\; accurate.$

      • 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 $expression\; \text{'}compartment\; *\; Function\_for\_deactivation\_of\_interleukin\_2(mu3,\; I)\text{'}\; cannot\; be\; fully\; checked.\; Unit\; consistency\; reported\; as\; either\; no\; errors\; or\; further\; unit\; errors\; related\; to\; this\; object\; may\; not\; be\; accurate.$

      • As a principle of best modeling practice, the units of a 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 with the id 'r2' does not have a 'units' attribute.

      • As a principle of best modeling practice, the units of a 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 with the id 'b' does not have a 'units' attribute.

      • As a principle of best modeling practice, the units of a 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 with the id 'a' does not have a 'units' attribute.

      • As a principle of best modeling practice, the units of a 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 with the id 'g2' does not have a 'units' attribute.

      • As a principle of best modeling practice, the units of a 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 with the id 'p1' does not have a 'units' attribute.

      • As a principle of best modeling practice, the units of a 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 with the id 'g1' does not have a 'units' attribute.

      • As a principle of best modeling practice, the units of a 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 with the id 'mu2' does not have a 'units' attribute.

      • As a principle of best modeling practice, the units of a 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 with the id 'c' does not have a 'units' attribute.

      • As a principle of best modeling practice, the units of a 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 with the id 'p2' does not have a 'units' attribute.

      • As a principle of best modeling practice, the units of a 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 with the id 'g3' does not have a 'units' attribute.

      • As a principle of best modeling practice, the units of a 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 with the id 'mu3' does not have a 'units' attribute.

      • As a principle of best modeling practice, the units of a 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 with the id 'V' does not have a 'units' attribute.

      • As a principle of best modeling practice, the units of a 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 with the id 's1' does not have a 'units' attribute.

      • As a principle of best modeling practice, the units of a 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 with the id 's2' does not have a 'units' attribute.

      

  warnings.warn(termcolor.colored(message, Colors.warning.value), category)

  Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:

  BIOMD0000000912_sim.sedml:

  Tasks (1):

  BIOMD0000000912_task

  Reports (1):

  report: 4 data sets

  Plots (1):

  Figure_1_bottom_left: 3 curves

  Executing SED-ML file 0: BIOMD0000000912_sim.sedml ...

  Bundling outputs ...

  Cleaning up ...

  ============= SUMMARY =============

  Executed 1 SED documents:

  SED documents (1):

  Succeeded: 1

  Skipped: 0

  Failed: 0

  Tasks (1):

  Succeeded: 1

  Skipped: 0

  Failed: 0

  Outputs (2):

  Succeeded: 2

  Skipped: 0

  Failed: 0

  
  ### `published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation` (4.8 s)
  
  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000088

  Warnings:

  Unexpected reports were produced:
  BIOMD0000000002_sim.sedml/Figure_4b

  Log:

  
  libtk8.6.so: cannot open shared object file: No such file or directory
  
  PySCeS defaults to matplotlib's TKagg backend if not specified                      in the user configuration file, set "matplotlib_backend = <backend>" 
  
  Matplotlib interface loaded (pysces.plt.m)
  
  Attempting alternate pitcon import ...
  
  Attempting alternate nleq2 import ...
  
  Continuation routines available (A)
  
  NLEQ2 routines available (A)
  
  SBML support available
  
  You are using NumPy (1.21.2) with SciPy (1.7.1)
  
  Could not find libgfortran.so.5: cannot open shared object file: No such file or directory
  
  Could not find libgfortran.so.5: cannot open shared object file: No such file or directory
  
  Could not find libgfortran.so.5: cannot open shared object file: No such file or directory
  
  Could not find libgfortran.so.5: cannot open shared object file: No such file or directory
  
  Could not find ODEPACK functions.
  
  /usr/local/lib/python3.9/site-packages/assimulo/solvers/odepack.py:710: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray.
  
  N.array([[0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.],  # 5th order
  
  Could not find RADAR5
  
  Could not find GLIMDA.
  
  Assimulo CVode available
  
  RateChar is available
  
  No module named 'ipyparallel'
  
  PARSCANNER: Requires ipyparallel version >=4.0 (http://ipython.org).
  
  INFO: Parallel scanner not available
  
  PySCeS environment
  
  ******************
  
  pysces.model_dir = /root/Pysces/psc
  
  pysces.output_dir = /root/Pysces
  
  ***********************************************************************

• Welcome to PySCeS (0.9.9) - Python Simulator for Cellular Systems *

• http://pysces.sourceforge.net *

• Copyright(C) B.G. Olivier, J.M. Rohwer, J.-H.S. Hofmeyr, 2004-2020 *

• Triple-J Group for Molecular Cell Physiology *

• Stellenbosch University, ZA and VU University Amsterdam, NL *

• PySCeS is distributed under the PySCeS (BSD style) licence, see *

• LICENCE.txt (supplied with this release) for details *

• Please cite PySCeS with: doi:10.1093/bioinformatics/bti046 *

  ---

  /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect.

  • Model BIOMD0000000002 may be invalid.

    • The model file BIOMD0000000002_url.xml 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 $expression\; \text{'}comp1$ (kf_0 B L - kr_0 BL)' 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 $expression\; \text{'}comp1$ (kf_1 BL L - kr_1 BLL)' 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 $expression\; \text{'}comp1$ (kf_2 BLL - kr_2 * ALL)' 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 $expression\; \text{'}comp1$ (kf_3 A L - kr_3 AL)' 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 $expression\; \text{'}comp1$ (kf_4 AL L - kr_4 ALL)' 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 $expression\; \text{'}comp1$ (kf_5 B - kr_5 * A)' 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 $expression\; \text{'}comp1$ (kf_6 BL - kr_6 * AL)' 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 $expression\; \text{'}comp1$ (kf_7 I L - kr_7 IL)' 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 $expression\; \text{'}comp1$ (kf_8 IL L - kr_8 ILL)' 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 $expression\; \text{'}comp1$ (kf_9 A - kr_9 * I)' 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 $expression\; \text{'}comp1$ (kf_10 AL - kr_10 * IL)' 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 $expression\; \text{'}comp1$ (kf_11 ALL - kr_11 * ILL)' 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 $expression\; \text{'}comp1$ (kf_12 D L - kr_12 DL)' 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 $expression\; \text{'}comp1$ (kf_13 DL L - kr_13 DLL)' 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 $expression\; \text{'}comp1$ (kf_14 I - kr_14 * D)' 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 $expression\; \text{'}comp1$ (kf_15 IL - kr_15 * DL)' 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 $expression\; \text{'}comp1$ (kf_16 ILL - kr_16 * DLL)' 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 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 with the id 'kf_0' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'kr_0' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'kf_1' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'kr_1' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'kf_2' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'kr_2' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'kf_3' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'kr_3' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'kf_4' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'kr_4' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'kf_5' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'kr_5' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'kf_6' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'kr_6' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'kf_7' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'kr_7' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'kf_8' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'kr_8' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'kf_9' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'kr_9' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'kf_10' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'kr_10' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'kf_11' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'kr_11' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'kf_12' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'kr_12' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'kf_13' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'kr_13' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'kf_14' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'kr_14' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'kf_15' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'kr_15' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'kf_16' does not have a 'units' attribute.

    • As a principle of best modeling practice, the units of a 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 with the id 'kr_16' does not have a 'units' attribute.

      

  warnings.warn(termcolor.colored(message, Colors.warning.value), category)

  /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid.

  • The SED-ML file at location ./BIOMD0000000002_sim.sedml may be invalid.

    • Model BIOMD0000000002 may be invalid.

    • The model file BIOMD0000000002_url.xml 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 $expression\; \text{'}comp1$ (kf_0 B L - kr_0 BL)' 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 $expression\; \text{'}comp1$ (kf_1 BL L - kr_1 BLL)' 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 $expression\; \text{'}comp1$ (kf_2 BLL - kr_2 * ALL)' 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 $expression\; \text{'}comp1$ (kf_3 A L - kr_3 AL)' 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 $expression\; \text{'}comp1$ (kf_4 AL L - kr_4 ALL)' 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 $expression\; \text{'}comp1$ (kf_5 B - kr_5 * A)' 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 $expression\; \text{'}comp1$ (kf_6 BL - kr_6 * AL)' 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 $expression\; \text{'}comp1$ (kf_7 I L - kr_7 IL)' 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 $expression\; \text{'}comp1$ (kf_8 IL L - kr_8 ILL)' 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 $expression\; \text{'}comp1$ (kf_9 A - kr_9 * I)' 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 $expression\; \text{'}comp1$ (kf_10 AL - kr_10 * IL)' 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 $expression\; \text{'}comp1$ (kf_11 ALL - kr_11 * ILL)' 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 $expression\; \text{'}comp1$ (kf_12 D L - kr_12 DL)' 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 $expression\; \text{'}comp1$ (kf_13 DL L - kr_13 DLL)' 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 $expression\; \text{'}comp1$ (kf_14 I - kr_14 * D)' 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 $expression\; \text{'}comp1$ (kf_15 IL - kr_15 * DL)' 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 $expression\; \text{'}comp1$ (kf_16 ILL - kr_16 * DLL)' 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 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 with the id 'kf_0' does not have a 'units' attribute.

      • As a principle of best modeling practice, the units of a 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 with the id 'kr_0' does not have a 'units' attribute.

      • As a principle of best modeling practice, the units of a 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 with the id 'kf_1' does not have a 'units' attribute.

      • As a principle of best modeling practice, the units of a 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 with the id 'kr_1' does not have a 'units' attribute.

      • As a principle of best modeling practice, the units of a 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 with the id 'kf_2' does not have a 'units' attribute.

      • As a principle of best modeling practice, the units of a 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 with the id 'kr_2' does not have a 'units' attribute.

      • As a principle of best modeling practice, the units of a 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 with the id 'kf_3' does not have a 'units' attribute.

      • As a principle of best modeling practice, the units of a 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 with the id 'kr_3' does not have a 'units' attribute.

      • As a principle of best modeling practice, the units of a 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 with the id 'kf_4' does not have a 'units' attribute.

      • As a principle of best modeling practice, the units of a 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 with the id 'kr_4' does not have a 'units' attribute.

      • As a principle of best modeling practice, the units of a 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 with the id 'kf_5' does not have a 'units' attribute.

      • As a principle of best modeling practice, the units of a 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 with the id 'kr_5' does not have a 'units' attribute.

      • As a principle of best modeling practice, the units of a 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 with the id 'kf_6' does not have a 'units' attribute.

      • As a principle of best modeling practice, the units of a 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 with the id 'kr_6' does not have a 'units' attribute.

      • As a principle of best modeling practice, the units of a 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 with the id 'kf_7' does not have a 'units' attribute.

      • As a principle of best modeling practice, the units of a 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 with the id 'kr_7' does not have a 'units' attribute.

      • As a principle of best modeling practice, the units of a 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 with the id 'kf_8' does not have a 'units' attribute.

      • As a principle of best modeling practice, the units of a 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 with the id 'kr_8' does not have a 'units' attribute.

      • As a principle of best modeling practice, the units of a 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 with the id 'kf_9' does not have a 'units' attribute.

      • As a principle of best modeling practice, the units of a 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 with the id 'kr_9' does not have a 'units' attribute.

      • As a principle of best modeling practice, the units of a 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 with the id 'kf_10' does not have a 'units' attribute.

      • As a principle of best modeling practice, the units of a 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 with the id 'kr_10' does not have a 'units' attribute.

      • As a principle of best modeling practice, the units of a 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 with the id 'kf_11' does not have a 'units' attribute.

      • As a principle of best modeling practice, the units of a 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 with the id 'kr_11' does not have a 'units' attribute.

      • As a principle of best modeling practice, the units of a 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 with the id ' ...

[biosimulators-daemon]

Skips

log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (9.8 s)

Test that simulator logs the execution of COMBINE/OMEX archives

Reason for skip:

  The image 'ghcr.io/biosimulators/biosimulators_pysces/pysces:0.9.9' could not execute the archive:

    Unknown error

Log:

  libtk8.6.so: cannot open shared object file: No such file or directory

  PySCeS defaults to matplotlib's TKagg backend if not specified                      in the user configuration file, set "matplotlib_backend = <backend>" 

  Matplotlib interface loaded (pysces.plt.m)

  Attempting alternate pitcon import ...

  Attempting alternate nleq2 import ...

  Continuation routines available (A)

  NLEQ2 routines available (A)

  SBML support available

  You are using NumPy (1.21.2) with SciPy (1.7.1)

  Could not find libgfortran.so.5: cannot open shared object file: No such file or directory

  Could not find libgfortran.so.5: cannot open shared object file: No such file or directory

  Could not find libgfortran.so.5: cannot open shared object file: No such file or directory

  Could not find libgfortran.so.5: cannot open shared object file: No such file or directory

  Could not find ODEPACK functions.

  /usr/local/lib/python3.9/site-packages/assimulo/solvers/odepack.py:710: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray.

    N.array([[0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.],  # 5th order

  Could not find RADAR5

  Could not find GLIMDA.

  Assimulo CVode available

  RateChar is available

  No module named 'ipyparallel'

  PARSCANNER: Requires ipyparallel version >=4.0 (http://ipython.org).

  INFO: Parallel scanner not available

  PySCeS environment

  ******************

  pysces.model_dir = /root/Pysces/psc

  pysces.output_dir = /root/Pysces

  ***********************************************************************

  * Welcome to PySCeS (0.9.9) - Python Simulator for Cellular Systems   *

  *                http://pysces.sourceforge.net                        *

  * Copyright(C) B.G. Olivier, J.M. Rohwer, J.-H.S. Hofmeyr, 2004-2020  *

  * Triple-J Group for Molecular Cell Physiology                        *

  * Stellenbosch University, ZA and VU University Amsterdam, NL         *

  * PySCeS is distributed under the PySCeS (BSD style) licence, see     *

  * LICENCE.txt (supplied with this release) for details                *

  * Please cite PySCeS with: doi:10.1093/bioinformatics/bti046          *

  ***********************************************************************

  /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect.

    - Model `model` may be invalid.

      - The model file `WholeCellRBC_MA_Rates.xml` may be invalid.

        - In situations where a mathematical expression refers to time, the units of time should be consistent with the global time units of the model. In models where the 'timeUnits' attribute has not been declared, libSBML does not yet have the functionality to verify accurately the consistency of the units in such expressions. 

        - In situations where a mathematical expression refers to extent, the units of extent should be consistent with the global extent units of the model. In models where the 'extentUnits' attribute has not been declared, libSBML does not yet have the functionality to verify accurately the consistency of the units in such expressions. 

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <compartment> 'c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'units' on a Compartment object having a 'spatialDimensions' attribute value of '3' has not been set, then the unit of measurement associated with the compartment's size is determined by the value of the enclosing Model object's 'volumeUnits' attribute. If neither the Compartment object's 'units' nor the enclosing Model object's 'volumeUnits' attributes are set, the unit of compartment size is undefined.

          Reference: L3V1 Section 4.5.4

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <compartment> 'e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'units' on a Compartment object having a 'spatialDimensions' attribute value of '3' has not been set, then the unit of measurement associated with the compartment's size is determined by the value of the enclosing Model object's 'volumeUnits' attribute. If neither the Compartment object's 'units' nor the enclosing Model object's 'volumeUnits' attributes are set, the unit of compartment size is undefined.

          Reference: L3V1 Section 4.5.4

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M__13dpg_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M__13dpg_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M__23dpg_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M__23dpg_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M__2kmb_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M__2kmb_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M__2pg_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M__2pg_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M__35cgmp_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M__35cgmp_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M__35cgmp_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M__35cgmp_e' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M__3pg_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M__3pg_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M__5mdr1p_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M__5mdr1p_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M__5mdru1p_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M__5mdru1p_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M__5mta_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M__5mta_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M__5oxpro_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M__5oxpro_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M__5oxpro_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M__5oxpro_e' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M__6pgc_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M__6pgc_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M__6pgl_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M__6pgl_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_accoa_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_accoa_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_ade_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_ade_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_ade_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_ade_e' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_adn_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_adn_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_adn_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_adn_e' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_adp_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_adp_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_ahcys_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_ahcys_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_akg_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_akg_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_akg_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_akg_e' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_ala__L_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_ala__L_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_ala__L_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_ala__L_e' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_amet_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_amet_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_ametam_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_ametam_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_amp_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_amp_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_arg__L_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_arg__L_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_arg__L_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_arg__L_e' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_ascb__L_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_ascb__L_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_ascb__L_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_ascb__L_e' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_asn__L_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_asn__L_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_asn__L_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_asn__L_e' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_atp_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_atp_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_band_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_band_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_bandmt_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_bandmt_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_ca2_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_ca2_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_ca2_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_ca2_e' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_camp_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_camp_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_camp_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_camp_e' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_cit_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_cit_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_cit_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_cit_e' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_cl_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_cl_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_cl_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_cl_e' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_co2_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_co2_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_co2_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_co2_e' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_coa_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_coa_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_cys__L_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.

          Reference: L3V1 Section 4.6.5

           The <species> with id 'M_cys__L_c' does not have a substanceUnits attribute, nor does its enclosing <model>.

        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 

           The units of the <species> 'M_cys__L_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - If the attribute 'substanceUnits' in a Species object has not b ...

[biosimulators-daemon]

- After correcting your simulator, please edit the first block of this issue to re-initiate this validation.
- 
- The complete log of your validation/submission job, including further information about the failure, is available for 90 days [here](https://github.com/biosimulators/Biosimulators/actions/runs/1142159687). The results of the validation of your image will also be available shortly as a JSON file. A link to this file will be available from the "Artifacts" section at the bottom of [this page](https://github.com/biosimulators/Biosimulators/actions/runs/1142159687).