Submit PySceS 0.9.9 - Githubissues

id: pysces version: 0.9.9 specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_PySCeS/4a4f0c8ccd98865121d208967f88c97fc315c223/biosimulators.json specificationsPatch: version: 0.9.9 image: url: ghcr.io/biosimulators/biosimulators_pysces/pysces:0.9.9 validateImage: true commitSimulator: true

Changelog

Debugged test suite

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 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 from the "Artifacts" section at the bottom of this page.

The specifications of your simulator is valid!

Summary of tests

Executed 61 test cases
Passed 46 test cases:
- cli.CliDescribesSupportedEnvironmentVariablesInline
- cli.CliDisplaysHelpInline
- cli.CliDisplaysVersionInformationInline
- combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
- combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
- combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
- combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
- docker_image.DeclaresSupportedEnvironmentVariables
- docker_image.DefaultUserIsRoot
- docker_image.HasBioContainersLabels
- docker_image.HasOciLabels
- log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
- log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
- log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
- log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
- results_report.SimulatorGeneratesReportsOfSimulationResults
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
- sedml.SimulatorProducesLinear2DPlots
- sedml.SimulatorProducesLogarithmic2DPlots
- sedml.SimulatorProducesMultiplePlots
- sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
- sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
- sedml.SimulatorSupportsAlgorithmParameters
- sedml.SimulatorSupportsComputeModelChanges
- sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
- sedml.SimulatorSupportsDataSetsWithDifferentShapes
- sedml.SimulatorSupportsModelAttributeChanges
- sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
- sedml.SimulatorSupportsMultipleTasksPerSedDocument
- sedml.SimulatorSupportsRepeatedTasksWithChanges
- sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
- sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
- sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges
- sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
- sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
- sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
- sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
- sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
- sedml.SimulatorSupportsRepeatedTasksWithVectorRanges
- sedml.SimulatorSupportsSubstitutingAlgorithms
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes
Failed 1 test cases:
- sedml.SimulatorSupportsMultipleReportsPerSedDocument
Skipped 14 test cases:
- published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
- published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
- 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
- sedml.SimulatorProducesLinear3DPlots
- sedml.SimulatorProducesLogarithmic3DPlots

Failures

`sedml.SimulatorSupportsMultipleReportsPerSedDocument` (3.5 s)

Test that a simulator supports multiple reports per SED document

Exception:

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

    Unknown error

Log:

  Cannot load backend 'TkAgg' which requires the 'tk' interactive framework, as 'headless' is currently running

  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)

  Pitcon routines available

  NLEQ2 routines available

  SBML support available

  You are using NumPy (1.20.2) with SciPy (1.6.3)

  /opt/conda/envs/py/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

  Assimulo CVode available

  RateChar is available

  Parallel scanner is 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          *

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

  /opt/conda/envs/py/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe 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 <kineticLaw> <math> expression 'compartment * Function_for_induction_of_tumor(r2, T, b, V)' 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 <kineticLaw> <math> expression 'compartment * Function_for_removal_of_the_tumor(a, T, g2, V, E)' 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 <kineticLaw> <math> expression 'compartment * Function_for_activation_and_transfer_of_effector_cells_to_the_tumor_site(p1, I, g1, E, c, T, V, s1)' 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 <kineticLaw> <math> expression 'compartment * Function_for_deactivation_and_removal_of_effector_cells_from_the_site_of_tumor(mu2, E)' 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 <kineticLaw> <math> expression 'compartment * Function_for_activation_of_interleukin_2(p2, V, T, E, g3, s2)' 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 <kineticLaw> <math> expression 'compartment * Function_for_deactivation_of_interleukin_2(mu3, I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.

           The <parameter> with the id 'r2' does not have a 'units' attribute.

        - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.

           The <parameter> with the id 'b' does not have a 'units' attribute.

        - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.

           The <parameter> with the id 'a' does not have a 'units' attribute.

        - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.

           The <parameter> with the id 'g2' does not have a 'units' attribute.

        - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.

           The <parameter> with the id 'p1' does not have a 'units' attribute.

        - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.

           The <parameter> with the id 'g1' does not have a 'units' attribute.

        - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.

           The <parameter> with the id 'mu2' does not have a 'units' attribute.

        - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.

           The <parameter> with the id 'c' does not have a 'units' attribute.

        - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.

           The <parameter> with the id 'p2' does not have a 'units' attribute.

        - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.

           The <parameter> with the id 'g3' does not have a 'units' attribute.

        - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.

           The <parameter> with the id 'mu3' does not have a 'units' attribute.

        - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.

           The <parameter> with the id 'V' does not have a 'units' attribute.

        - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.

           The <parameter> with the id 's1' does not have a 'units' attribute.

        - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.

           The <parameter> with the id 's2' does not have a 'units' attribute.

          [0m

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

  /opt/conda/envs/py/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe 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 <kineticLaw> <math> expression 'compartment * Function_for_induction_of_tumor(r2, T, b, V)' 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 <kineticLaw> <math> expression 'compartment * Function_for_removal_of_the_tumor(a, T, g2, V, E)' 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 <kineticLaw> <math> expression 'compartment * Function_for_activation_and_transfer_of_effector_cells_to_the_tumor_site(p1, I, g1, E, c, T, V, s1)' 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 <kineticLaw> <math> expression 'compartment * Function_for_deactivation_and_removal_of_effector_cells_from_the_site_of_tumor(mu2, E)' 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 <kineticLaw> <math> expression 'compartment * Function_for_activation_of_interleukin_2(p2, V, T, E, g3, s2)' 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 <kineticLaw> <math> expression 'compartment * Function_for_deactivation_of_interleukin_2(mu3, I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

          - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.

             The <parameter> with the id 'r2' does not have a 'units' attribute.

          - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.

             The <parameter> with the id 'b' does not have a 'units' attribute.

          - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.

             The <parameter> with the id 'a' does not have a 'units' attribute.

          - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.

             The <parameter> with the id 'g2' does not have a 'units' attribute.

          - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.

             The <parameter> with the id 'p1' does not have a 'units' attribute.

          - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.

             The <parameter> with the id 'g1' does not have a 'units' attribute.

          - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.

             The <parameter> with the id 'mu2' does not have a 'units' attribute.

          - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.

             The <parameter> with the id 'c' does not have a 'units' attribute.

          - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.

             The <parameter> with the id 'p2' does not have a 'units' attribute.

          - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.

             The <parameter> with the id 'g3' does not have a 'units' attribute.

          - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.

             The <parameter> with the id 'mu3' does not have a 'units' attribute.

          - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.

             The <parameter> with the id 'V' does not have a 'units' attribute.

          - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.

             The <parameter> with the id 's1' does not have a 'units' attribute.

          - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.

             The <parameter> with the id 's2' does not have a 'units' attribute.

            [0m

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

  [31mThe COMBINE/OMEX archive is invalid.

    - The SED-ML file at location `./BIOMD0000000912_sim.sedml` is invalid.

      - Each identified SED object must have a unique id. Multiple objects have the following ids:

        - __single_var_output_el__1[0m

Warnings

`cli.CliDescribesSupportedEnvironmentVariablesInline` (6.4 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'

  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:

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations` (5.4 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

Plots were not produced:
BIOMD0000000912_sim.sedml/plot_1

Extra plots were produced:
BIOMD0000000912_sim.sedml/Figure_1

Log:


Cannot load backend 'TkAgg' which requires the 'tk' interactive framework, as 'headless' is currently running

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)

Pitcon routines available

NLEQ2 routines available

SBML support available

You are using NumPy (1.20.2) with SciPy (1.6.3)

/opt/conda/envs/py/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

Assimulo CVode available

RateChar is available

Parallel scanner is 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 *

/opt/conda/envs/py/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe 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 $expression 'compartment * Function_for_induction_of_tumor(r2, T, b, V)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'compartment * Function_for_removal_of_the_tumor(a, T, g2, V, E)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'compartment * Function_for_activation_and_transfer_of_effector_cells_to_the_tumor_site(p1, I, g1, E, c, T, V, s1)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'compartment * Function_for_deactivation_and_removal_of_effector_cells_from_the_site_of_tumor(mu2, E)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'compartment * Function_for_activation_of_interleukin_2(p2, V, T, E, g3, s2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'compartment * Function_for_deactivation_of_interleukin_2(mu3, I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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.
    
    [0m
warnings.warn(termcolor.colored(message, Colors.warning.value), category)

/opt/conda/envs/py/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe 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 $expression 'compartment * Function_for_induction_of_tumor(r2, T, b, V)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
    - 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 $expression 'compartment * Function_for_removal_of_the_tumor(a, T, g2, V, E)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
    - 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 $expression 'compartment * Function_for_activation_and_transfer_of_effector_cells_to_the_tumor_site(p1, I, g1, E, c, T, V, s1)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
    - 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 $expression 'compartment * Function_for_deactivation_and_removal_of_effector_cells_from_the_site_of_tumor(mu2, E)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
    - 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 $expression 'compartment * Function_for_activation_of_interleukin_2(p2, V, T, E, g3, s2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
    - 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 $expression 'compartment * Function_for_deactivation_of_interleukin_2(mu3, I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
    - 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.
    [0m
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: 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/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous` (6.3 s)

Required model formats and simulation algorithms for SED tasks:
```

Format: format_2585 Algorithm: KISAO_0000019

Warnings:

Unexpected reports were produced:
simulation_1.sedml/Figure_3a
simulation_1.sedml/Figure_3b
simulation_1.sedml/Figure_3c
simulation_1.sedml/Figure_3d

Plots were not produced:
simulation.sedml/Figure_3a
simulation.sedml/Figure_3b
simulation.sedml/Figure_3c
simulation.sedml/Figure_3d

Extra plots were produced:
simulation_1.sedml/Figure_3a
simulation_1.sedml/Figure_3b
simulation_1.sedml/Figure_3c
simulation_1.sedml/Figure_3d

Log:


Cannot load backend 'TkAgg' which requires the 'tk' interactive framework, as 'headless' is currently running

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)

Pitcon routines available

NLEQ2 routines available

SBML support available

You are using NumPy (1.20.2) with SciPy (1.6.3)

/opt/conda/envs/py/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

Assimulo CVode available

RateChar is available

Parallel scanner is 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 *

/opt/conda/envs/py/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe SED document is potentially incorrect.
- Model Ciliberto2003_Morphogenesis may be invalid.
  - The model file BIOMD0000000297_url.xml may be invalid.
  - The value of the 'sboTerm' attribute on a is expected to be an SBO identifier (http://www.biomodels.net/SBO/). In SBML Level 2 prior to Version 4 it is expected to refer to a participant physical type (i.e., terms derived from SBO:0000236, "participant physical type"); in Versions 4 and above it is expected to refer to a material entity (i.e., terms derived from SBO:0000240, "material entity").
    
    Reference: L2V4 Section 5
    
    SBO term 'SBO:0000014' on the is not in the appropriate branch.
  - The value of the 'sboTerm' attribute on a is expected to be an SBO identifier (http://www.biomodels.net/SBO/). In SBML Level 2 prior to Version 4 it is expected to refer to a participant physical type (i.e., terms derived from SBO:0000236, "participant physical type"); in Versions 4 and above it is expected to refer to a material entity (i.e., terms derived from SBO:0000240, "material entity").
    
    Reference: L2V4 Section 5
    
    SBO term 'SBO:0000236' on the is not in the appropriate branch.
  - The value of the 'sboTerm' attribute on a is expected to be an SBO identifier (http://www.biomodels.net/SBO/). In SBML Level 2 prior to Version 4 it is expected to refer to a participant physical type (i.e., terms derived from SBO:0000236, "participant physical type"); in Versions 4 and above it is expected to refer to a material entity (i.e., terms derived from SBO:0000240, "material entity").
    
    Reference: L2V4 Section 5
    
    SBO term 'SBO:0000236' on the is not in the appropriate branch.
  - The value of the 'sboTerm' attribute on a is expected to be an SBO identifier (http://www.biomodels.net/SBO/) referring to a quantitative parameter defined in SBO (i.e., terms derived from SBO:0000002, "quantitative systems description parameter").
    
    Reference: L2V4 Sections 4.9.5 and 5
    
    SBO term 'SBO:0000336' on the is not in the appropriate branch.
  - The value of the 'sboTerm' attribute on a is expected to be an SBO identifier (http://www.biomodels.net/SBO/) referring to a quantitative parameter defined in SBO (i.e., terms derived from SBO:0000002, "quantitative systems description parameter").
    
    Reference: L2V4 Sections 4.9.5 and 5
    
    SBO term 'SBO:0000336' on the is not in the appropriate branch.
  - The value of the 'sboTerm' attribute on a is expected to be an SBO identifier (http://www.biomodels.net/SBO/) referring to a quantitative parameter defined in SBO (i.e., terms derived from SBO:0000002, "quantitative systems description parameter").
    
    Reference: L2V4 Sections 4.9.5 and 5
    
    SBO term 'SBO:0000393' on the is not in the appropriate branch.
  - The value of the 'sboTerm' attribute on a is expected to be an SBO identifier (http://www.biomodels.net/SBO/) referring to a quantitative parameter defined in SBO (i.e., terms derived from SBO:0000002, "quantitative systems description parameter").
    
    Reference: L2V4 Sections 4.9.5 and 5
    
    SBO term 'SBO:0000393' on the is not in the appropriate branch.
  - The value of the 'sboTerm' attribute on a is expected to be an SBO identifier (http://www.biomodels.net/SBO/) referring to a quantitative parameter defined in SBO (i.e., terms derived from SBO:0000002, "quantitative systems description parameter").
    
    Reference: L2V4 Sections 4.9.5 and 5
    
    SBO term 'SBO:0000393' on the is not in the appropriate branch.
  - The value of the 'sboTerm' attribute on a is expected to be an SBO identifier (http://www.biomodels.net/SBO/) referring to a quantitative parameter defined in SBO (i.e., terms derived from SBO:0000002, "quantitative systems description parameter").
    
    Reference: L2V4 Sections 4.9.5 and 5
    
    SBO term 'SBO:0000393' on the is not in the appropriate branch.
  - The value of the 'sboTerm' attribute on a is expected to be an SBO identifier (http://www.biomodels.net/SBO/) referring to a quantitative parameter defined in SBO (i.e., terms derived from SBO:0000002, "quantitative systems description parameter").
    
    Reference: L2V4 Sections 4.9.5 and 5
    
    SBO term 'SBO:0000393' on the is not in the appropriate branch.
  - The value of the 'sboTerm' attribute on a is expected to be an SBO identifier (http://www.biomodels.net/SBO/) referring to a quantitative parameter defined in SBO (i.e., terms derived from SBO:0000002, "quantitative systems description parameter").
    
    Reference: L2V4 Sections 4.9.5 and 5
    
    SBO term 'SBO:0000393' on the is not in the appropriate branch.
  - The value of the 'sboTerm' attribute on a is expected to be an SBO identifier (http://www.biomodels.net/SBO/) referring to a quantitative parameter defined in SBO (i.e., terms derived from SBO:0000002, "quantitative systems description parameter").
    
    Reference: L2V4 Sections 4.9.5 and 5
    
    SBO term 'SBO:0000393' on the is not in the appropriate branch.
  - 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 $expression 'kswe_prime$ Swe1 + kswe_doubleprime Swe1M + kswe_tripleprime * PSwe1' 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 $expression 'kmih_prime$ Mih_ast + kmih_doubleprime Mih' 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 $expression 'IEtot - IE' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'Cdh1tot - Cdh1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'Mih1tot - Mih1a' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'Mcmtot - Mcm' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'SBFtot - SBF' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'kdiss * Trim' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'Trim$ (kdsic_prime Cln + kdsic_doubleprime * Clb + kdsic)' 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 $expression 'Trim$ (kdclb_doubleprime Cdh1 + kdclb_tripleprime * Cdc20a + kdclb_prime)' 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 $expression 'Trim * kswe' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'kass$ Sic Clb' 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 $expression 'PTrim * kmih' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'Clb$ (kdclb_doubleprime Cdh1 + kdclb_tripleprime * Cdc20a + kdclb_prime)' 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 $expression 'kswe * Clb' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'ksclb$ mass Jm * (eps + Mcm) / (mass + Jm)' 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 $expression 'kmih * PClb' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'SBF$ (kisbf_prime + kisbf_doubleprime Clb) / (jisbf + SBF)' 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 $expression 'SBFin$ (kasbf_prime mass + kasbf_doubleprime * Cln) / (jasbf + SBFin)' 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 $expression 'IE * kiie / (jiie + IE)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'kaie$ IEin Clb / (jaie + IEin)' 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 $expression 'Cdc20a * kicdc20 / (jicdc20 + Cdc20a)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'kdcdc20 * Cdc20a' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'kacdc20$ Cdc20 IE / (jacdc20 + Cdc20)' 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 $expression 'Cdh1$ (kicdh Clb + kicdh_prime * Cln) / (jicdh + Cdh1)' 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 $expression 'Cdh1in$ (Kacdh_prime + Kacdh_doubleprime Cdc20a) / (jacdh + Cdh1in)' 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 $expression 'khsl1$ BUD Swe1' 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 $expression 'khsl1$ BUD PSwe1' 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 $expression 'Viwee$ Swe1 Clb / (Jiwee + Swe1)' 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 $expression 'Viwee$ Swe1M Clb / (Jiwee + Swe1M)' 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 $expression 'kdswe_prime * Swe1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'khsl1r * Swe1M' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'khsl1r * PSwe1M' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'PSwe1 * Vawee / (Jawee + PSwe1)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'PSwe1M * Vawee / (Jawee + PSwe1M)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'ksswe * SBF' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'kssweC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'kdswe_prime * PSwe1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'kdiss * PTrim' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'PTrim$ (kdclb_doubleprime Cdh1 + kdclb_tripleprime * Cdc20a + kdclb_prime)' 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 $expression 'PTrim$ (kdsic_prime Cln + kdsic_doubleprime * Clb + kdsic)' 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 $expression 'kass$ PClb Sic' 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 $expression 'Mih1a * Vimih / (jimih + Mih1a)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'Vamih$ Mih1 Clb / (Jamih + Mih1)' 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 $expression 'Mcm * kimcm / (jimcm + Mcm)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'Mcmin$ Clb kamcm / (jamcm + Mcmin)' 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 $expression 'kdbud * BE' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'ksbud * Cln' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'Sic$ (kdsic_prime Cln + kdsic_doubleprime * Clb + kdsic)' 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 $expression 'kssic' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'kdcln * Cln' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'kscln * SBF' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'kdswe_prime * Swe1M' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'kdcdc20 * Cdc20' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'kscdc20_prime + kscdc20_doubleprime * pow(Clb, 4) / (pow(jscdc20, 4) + pow(Clb, 4))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'kdswe_doubleprime * PSwe1M' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'PClb$ (kdclb_doubleprime Cdh1 + kdclb_tripleprime * Cdc20a + kdclb_prime)' 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 $expression 'mu * mass' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 'gt(Clb, 0.2)' 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 $expression '1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 'and(lt(Clb, 0.2), gt(flag, 0))' 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 $expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression '0.5 * mass' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 'or(geq(Clb, 0.2), geq(BE, 0.6))' 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 $expression '1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 'and(lt(Clb, 0.2), lt(BE, 0.6))' 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 $expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 'kswe' 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 'kswe_prime' 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 'kswe_doubleprime' 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 'kswe_tripleprime' 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 'kmih' 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 'kmih_prime' 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 'Mih_ast' 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 'kmih_doubleprime' 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 'Mih' 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 'IEin' does not have a 'units' attribute.
    
    ...

Skips

`published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ` (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_3972 Algorithm: KISAO_0000263

Reason for skip:
```
Case requires model formats format_3972 and simulation algorithms KISAO_0000263
```
Log:
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_3972 Algorithm: KISAO_0000019

Reason for skip:
```
Case requires model formats format_3972 and simulation algorithms KISAO_0000019
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_000019

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_000019
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000496

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000496
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000560

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000560
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000560

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000560
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000019
Format: format_2585 Algorithm: KISAO_0000027
Format: format_2585 Algorithm: KISAO_0000030

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000019, KISAO_0000027, KISAO_0000030
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000019
Format: format_2585 Algorithm: KISAO_0000030

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000019, KISAO_0000030
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000027

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000027
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000029

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000029
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000437

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000437
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000449

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000449
```
Log:
sedml.SimulatorProducesLinear3DPlots (0.1 s)

Test that a simulator produces linear 3D plots

Reason for skip:
```
No curated COMBINE/OMEX archives are available to generate archives for testing
```
Log:
sedml.SimulatorProducesLogarithmic3DPlots (0.1 s)

Test that a simulator produces logarithmic 3D plots

Reason for skip:
```
No curated COMBINE/OMEX archives are available to generate archives for testing
```
Log:

- 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 [here](https://github.com/biosimulators/Biosimulators/actions/runs/808424046). 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/808424046).

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.

The specifications of your simulator is valid!

Summary of tests

Executed 61 test cases
Passed 47 test cases:
- cli.CliDescribesSupportedEnvironmentVariablesInline
- cli.CliDisplaysHelpInline
- cli.CliDisplaysVersionInformationInline
- combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
- combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
- combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
- combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
- docker_image.DeclaresSupportedEnvironmentVariables
- docker_image.DefaultUserIsRoot
- docker_image.HasBioContainersLabels
- docker_image.HasOciLabels
- log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
- log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
- log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
- log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
- results_report.SimulatorGeneratesReportsOfSimulationResults
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
- sedml.SimulatorProducesLinear2DPlots
- sedml.SimulatorProducesLogarithmic2DPlots
- sedml.SimulatorProducesMultiplePlots
- sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
- sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
- sedml.SimulatorSupportsAlgorithmParameters
- sedml.SimulatorSupportsComputeModelChanges
- sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
- sedml.SimulatorSupportsDataSetsWithDifferentShapes
- sedml.SimulatorSupportsModelAttributeChanges
- sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
- sedml.SimulatorSupportsMultipleReportsPerSedDocument
- sedml.SimulatorSupportsMultipleTasksPerSedDocument
- sedml.SimulatorSupportsRepeatedTasksWithChanges
- sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
- sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
- sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges
- sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
- sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
- sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
- sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
- sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
- sedml.SimulatorSupportsRepeatedTasksWithVectorRanges
- sedml.SimulatorSupportsSubstitutingAlgorithms
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes
Failed 0 test cases
Skipped 14 test cases:
- published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
- published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
- 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
- sedml.SimulatorProducesLinear3DPlots
- sedml.SimulatorProducesLogarithmic3DPlots

Warnings

`cli.CliDescribesSupportedEnvironmentVariablesInline` (6.5 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'

  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:

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations` (5.7 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

Plots were not produced:
BIOMD0000000912_sim.sedml/plot_1

Extra plots were produced:
BIOMD0000000912_sim.sedml/Figure_1

Log:


Cannot load backend 'TkAgg' which requires the 'tk' interactive framework, as 'headless' is currently running

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)

Pitcon routines available

NLEQ2 routines available

SBML support available

You are using NumPy (1.20.2) with SciPy (1.6.3)

/opt/conda/envs/py/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

Assimulo CVode available

RateChar is available

Parallel scanner is 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 *

/opt/conda/envs/py/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe 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 $expression 'compartment * Function_for_induction_of_tumor(r2, T, b, V)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'compartment * Function_for_removal_of_the_tumor(a, T, g2, V, E)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'compartment * Function_for_activation_and_transfer_of_effector_cells_to_the_tumor_site(p1, I, g1, E, c, T, V, s1)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'compartment * Function_for_deactivation_and_removal_of_effector_cells_from_the_site_of_tumor(mu2, E)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'compartment * Function_for_activation_of_interleukin_2(p2, V, T, E, g3, s2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'compartment * Function_for_deactivation_of_interleukin_2(mu3, I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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.
    
    [0m
warnings.warn(termcolor.colored(message, Colors.warning.value), category)

/opt/conda/envs/py/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe 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 $expression 'compartment * Function_for_induction_of_tumor(r2, T, b, V)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
    - 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 $expression 'compartment * Function_for_removal_of_the_tumor(a, T, g2, V, E)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
    - 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 $expression 'compartment * Function_for_activation_and_transfer_of_effector_cells_to_the_tumor_site(p1, I, g1, E, c, T, V, s1)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
    - 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 $expression 'compartment * Function_for_deactivation_and_removal_of_effector_cells_from_the_site_of_tumor(mu2, E)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
    - 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 $expression 'compartment * Function_for_activation_of_interleukin_2(p2, V, T, E, g3, s2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
    - 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 $expression 'compartment * Function_for_deactivation_of_interleukin_2(mu3, I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
    - 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.
    [0m
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: 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/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous` (6.8 s)

Required model formats and simulation algorithms for SED tasks:
```

Format: format_2585 Algorithm: KISAO_0000019

Warnings:

Unexpected reports were produced:
simulation_1.sedml/Figure_3a
simulation_1.sedml/Figure_3b
simulation_1.sedml/Figure_3c
simulation_1.sedml/Figure_3d

Plots were not produced:
simulation.sedml/Figure_3a
simulation.sedml/Figure_3b
simulation.sedml/Figure_3c
simulation.sedml/Figure_3d

Extra plots were produced:
simulation_1.sedml/Figure_3a
simulation_1.sedml/Figure_3b
simulation_1.sedml/Figure_3c
simulation_1.sedml/Figure_3d

Log:


Cannot load backend 'TkAgg' which requires the 'tk' interactive framework, as 'headless' is currently running

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)

Pitcon routines available

NLEQ2 routines available

SBML support available

You are using NumPy (1.20.2) with SciPy (1.6.3)

/opt/conda/envs/py/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

Assimulo CVode available

RateChar is available

Parallel scanner is 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 *

/opt/conda/envs/py/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe SED document is potentially incorrect.
- Model Ciliberto2003_Morphogenesis may be invalid.
  - The model file BIOMD0000000297_url.xml may be invalid.
  - The value of the 'sboTerm' attribute on a is expected to be an SBO identifier (http://www.biomodels.net/SBO/). In SBML Level 2 prior to Version 4 it is expected to refer to a participant physical type (i.e., terms derived from SBO:0000236, "participant physical type"); in Versions 4 and above it is expected to refer to a material entity (i.e., terms derived from SBO:0000240, "material entity").
    
    Reference: L2V4 Section 5
    
    SBO term 'SBO:0000014' on the is not in the appropriate branch.
  - The value of the 'sboTerm' attribute on a is expected to be an SBO identifier (http://www.biomodels.net/SBO/). In SBML Level 2 prior to Version 4 it is expected to refer to a participant physical type (i.e., terms derived from SBO:0000236, "participant physical type"); in Versions 4 and above it is expected to refer to a material entity (i.e., terms derived from SBO:0000240, "material entity").
    
    Reference: L2V4 Section 5
    
    SBO term 'SBO:0000236' on the is not in the appropriate branch.
  - The value of the 'sboTerm' attribute on a is expected to be an SBO identifier (http://www.biomodels.net/SBO/). In SBML Level 2 prior to Version 4 it is expected to refer to a participant physical type (i.e., terms derived from SBO:0000236, "participant physical type"); in Versions 4 and above it is expected to refer to a material entity (i.e., terms derived from SBO:0000240, "material entity").
    
    Reference: L2V4 Section 5
    
    SBO term 'SBO:0000236' on the is not in the appropriate branch.
  - The value of the 'sboTerm' attribute on a is expected to be an SBO identifier (http://www.biomodels.net/SBO/) referring to a quantitative parameter defined in SBO (i.e., terms derived from SBO:0000002, "quantitative systems description parameter").
    
    Reference: L2V4 Sections 4.9.5 and 5
    
    SBO term 'SBO:0000336' on the is not in the appropriate branch.
  - The value of the 'sboTerm' attribute on a is expected to be an SBO identifier (http://www.biomodels.net/SBO/) referring to a quantitative parameter defined in SBO (i.e., terms derived from SBO:0000002, "quantitative systems description parameter").
    
    Reference: L2V4 Sections 4.9.5 and 5
    
    SBO term 'SBO:0000336' on the is not in the appropriate branch.
  - The value of the 'sboTerm' attribute on a is expected to be an SBO identifier (http://www.biomodels.net/SBO/) referring to a quantitative parameter defined in SBO (i.e., terms derived from SBO:0000002, "quantitative systems description parameter").
    
    Reference: L2V4 Sections 4.9.5 and 5
    
    SBO term 'SBO:0000393' on the is not in the appropriate branch.
  - The value of the 'sboTerm' attribute on a is expected to be an SBO identifier (http://www.biomodels.net/SBO/) referring to a quantitative parameter defined in SBO (i.e., terms derived from SBO:0000002, "quantitative systems description parameter").
    
    Reference: L2V4 Sections 4.9.5 and 5
    
    SBO term 'SBO:0000393' on the is not in the appropriate branch.
  - The value of the 'sboTerm' attribute on a is expected to be an SBO identifier (http://www.biomodels.net/SBO/) referring to a quantitative parameter defined in SBO (i.e., terms derived from SBO:0000002, "quantitative systems description parameter").
    
    Reference: L2V4 Sections 4.9.5 and 5
    
    SBO term 'SBO:0000393' on the is not in the appropriate branch.
  - The value of the 'sboTerm' attribute on a is expected to be an SBO identifier (http://www.biomodels.net/SBO/) referring to a quantitative parameter defined in SBO (i.e., terms derived from SBO:0000002, "quantitative systems description parameter").
    
    Reference: L2V4 Sections 4.9.5 and 5
    
    SBO term 'SBO:0000393' on the is not in the appropriate branch.
  - The value of the 'sboTerm' attribute on a is expected to be an SBO identifier (http://www.biomodels.net/SBO/) referring to a quantitative parameter defined in SBO (i.e., terms derived from SBO:0000002, "quantitative systems description parameter").
    
    Reference: L2V4 Sections 4.9.5 and 5
    
    SBO term 'SBO:0000393' on the is not in the appropriate branch.
  - The value of the 'sboTerm' attribute on a is expected to be an SBO identifier (http://www.biomodels.net/SBO/) referring to a quantitative parameter defined in SBO (i.e., terms derived from SBO:0000002, "quantitative systems description parameter").
    
    Reference: L2V4 Sections 4.9.5 and 5
    
    SBO term 'SBO:0000393' on the is not in the appropriate branch.
  - The value of the 'sboTerm' attribute on a is expected to be an SBO identifier (http://www.biomodels.net/SBO/) referring to a quantitative parameter defined in SBO (i.e., terms derived from SBO:0000002, "quantitative systems description parameter").
    
    Reference: L2V4 Sections 4.9.5 and 5
    
    SBO term 'SBO:0000393' on the is not in the appropriate branch.
  - 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 $expression 'kswe_prime$ Swe1 + kswe_doubleprime Swe1M + kswe_tripleprime * PSwe1' 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 $expression 'kmih_prime$ Mih_ast + kmih_doubleprime Mih' 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 $expression 'IEtot - IE' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'Cdh1tot - Cdh1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'Mih1tot - Mih1a' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'Mcmtot - Mcm' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'SBFtot - SBF' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'kdiss * Trim' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'Trim$ (kdsic_prime Cln + kdsic_doubleprime * Clb + kdsic)' 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 $expression 'Trim$ (kdclb_doubleprime Cdh1 + kdclb_tripleprime * Cdc20a + kdclb_prime)' 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 $expression 'Trim * kswe' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'kass$ Sic Clb' 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 $expression 'PTrim * kmih' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'Clb$ (kdclb_doubleprime Cdh1 + kdclb_tripleprime * Cdc20a + kdclb_prime)' 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 $expression 'kswe * Clb' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'ksclb$ mass Jm * (eps + Mcm) / (mass + Jm)' 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 $expression 'kmih * PClb' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'SBF$ (kisbf_prime + kisbf_doubleprime Clb) / (jisbf + SBF)' 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 $expression 'SBFin$ (kasbf_prime mass + kasbf_doubleprime * Cln) / (jasbf + SBFin)' 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 $expression 'IE * kiie / (jiie + IE)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'kaie$ IEin Clb / (jaie + IEin)' 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 $expression 'Cdc20a * kicdc20 / (jicdc20 + Cdc20a)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'kdcdc20 * Cdc20a' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'kacdc20$ Cdc20 IE / (jacdc20 + Cdc20)' 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 $expression 'Cdh1$ (kicdh Clb + kicdh_prime * Cln) / (jicdh + Cdh1)' 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 $expression 'Cdh1in$ (Kacdh_prime + Kacdh_doubleprime Cdc20a) / (jacdh + Cdh1in)' 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 $expression 'khsl1$ BUD Swe1' 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 $expression 'khsl1$ BUD PSwe1' 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 $expression 'Viwee$ Swe1 Clb / (Jiwee + Swe1)' 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 $expression 'Viwee$ Swe1M Clb / (Jiwee + Swe1M)' 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 $expression 'kdswe_prime * Swe1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'khsl1r * Swe1M' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'khsl1r * PSwe1M' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'PSwe1 * Vawee / (Jawee + PSwe1)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'PSwe1M * Vawee / (Jawee + PSwe1M)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'ksswe * SBF' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'kssweC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'kdswe_prime * PSwe1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'kdiss * PTrim' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'PTrim$ (kdclb_doubleprime Cdh1 + kdclb_tripleprime * Cdc20a + kdclb_prime)' 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 $expression 'PTrim$ (kdsic_prime Cln + kdsic_doubleprime * Clb + kdsic)' 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 $expression 'kass$ PClb Sic' 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 $expression 'Mih1a * Vimih / (jimih + Mih1a)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'Vamih$ Mih1 Clb / (Jamih + Mih1)' 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 $expression 'Mcm * kimcm / (jimcm + Mcm)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'Mcmin$ Clb kamcm / (jamcm + Mcmin)' 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 $expression 'kdbud * BE' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'ksbud * Cln' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'Sic$ (kdsic_prime Cln + kdsic_doubleprime * Clb + kdsic)' 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 $expression 'kssic' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'kdcln * Cln' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'kscln * SBF' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'kdswe_prime * Swe1M' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'kdcdc20 * Cdc20' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'kscdc20_prime + kscdc20_doubleprime * pow(Clb, 4) / (pow(jscdc20, 4) + pow(Clb, 4))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'kdswe_doubleprime * PSwe1M' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression 'PClb$ (kdclb_doubleprime Cdh1 + kdclb_tripleprime * Cdc20a + kdclb_prime)' 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 $expression 'mu * mass' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 'gt(Clb, 0.2)' 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 $expression '1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 'and(lt(Clb, 0.2), gt(flag, 0))' 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 $expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 $expression '0.5 * mass' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 'or(geq(Clb, 0.2), geq(BE, 0.6))' 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 $expression '1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 'and(lt(Clb, 0.2), lt(BE, 0.6))' 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 $expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.$
  - 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 'kswe' 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 'kswe_prime' 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 'kswe_doubleprime' 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 'kswe_tripleprime' 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 'kmih' 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 'kmih_prime' 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 'Mih_ast' 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 'kmih_doubleprime' 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 'Mih' 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 'IEin' does not have a 'units' attribute.
    
    ...

Skips

`published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ` (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_3972 Algorithm: KISAO_0000263

Reason for skip:
```
Case requires model formats format_3972 and simulation algorithms KISAO_0000263
```
Log:
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_3972 Algorithm: KISAO_0000019

Reason for skip:
```
Case requires model formats format_3972 and simulation algorithms KISAO_0000019
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_000019

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_000019
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000496

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000496
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000560

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000560
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000560

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000560
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000019
Format: format_2585 Algorithm: KISAO_0000027
Format: format_2585 Algorithm: KISAO_0000030

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000019, KISAO_0000027, KISAO_0000030
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000019
Format: format_2585 Algorithm: KISAO_0000030

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000019, KISAO_0000030
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000027

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000027
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000029

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000029
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000437

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000437
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000449

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000449
```
Log:
sedml.SimulatorProducesLinear3DPlots (0.1 s)

Test that a simulator produces linear 3D plots

Reason for skip:
```
No curated COMBINE/OMEX archives are available to generate archives for testing
```
Log:
sedml.SimulatorProducesLogarithmic3DPlots (0.1 s)

Test that a simulator produces logarithmic 3D plots

Reason for skip:
```
No curated COMBINE/OMEX archives are available to generate archives for testing
```
Log:

The image for your simulator is valid!

Your submission was committed to the BioSimulators registry. Thank you!

Future submissions of subsequent versions of pysces to the BioSimulators registry will be automatically validated. These submissions will not require manual review by the BioSimulators Team.

biosimulators / Biosimulators

Submit PySceS 0.9.9 #207

Summary of tests

Failures

sedml.SimulatorSupportsMultipleReportsPerSedDocument (3.5 s)

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (6.4 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (5.4 s)

Skips

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)

published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)

sedml.SimulatorProducesLinear3DPlots (0.1 s)

sedml.SimulatorProducesLogarithmic3DPlots (0.1 s)

Summary of tests

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (6.5 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (5.7 s)

Skips

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)

published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)

sedml.SimulatorProducesLinear3DPlots (0.1 s)

sedml.SimulatorProducesLogarithmic3DPlots (0.1 s)

`sedml.SimulatorSupportsMultipleReportsPerSedDocument` (3.5 s)

`cli.CliDescribesSupportedEnvironmentVariablesInline` (6.4 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations` (5.4 s)

`published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling` (0.0 s)

`sedml.SimulatorProducesLinear3DPlots` (0.1 s)

`sedml.SimulatorProducesLogarithmic3DPlots` (0.1 s)

`cli.CliDescribesSupportedEnvironmentVariablesInline` (6.5 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations` (5.7 s)

`published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling` (0.0 s)

`sedml.SimulatorProducesLinear3DPlots` (0.1 s)

`sedml.SimulatorProducesLogarithmic3DPlots` (0.1 s)