Submit GillesPy2 1.5.11

id: gillespy2
version: 1.5.11
specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_GillesPy2/591b17d538f07704db5a13ef48667c940807bd98/biosimulators.json
specificationsPatch:
version: 1.5.11
image:
url: ghcr.io/biosimulators/biosimulators_gillespy2/gillespy2:1.5.11
validateImage: true
commitSimulator: true

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 65 test cases

Passed 45 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/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA
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.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

Failed 0 test cases

Skipped 20 test cases:

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler
published_project.SimulatorCanExecutePublishedProject:sbml-core/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/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-fbc/Escherichia-coli-core-metabolism
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling
published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra
sedml.SimulatorProducesLinear3DPlots
sedml.SimulatorProducesLogarithmic3DPlots
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes

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:

docker_image.DeclaresSupportedEnvironmentVariables (0.8 s)
Test if a Docker image declares the environment variables that is supports
Warnings:
Docker images for simulation tools should declare the environment variables that they support.

The Docker image does not declare the following standard environment variables recognized by BioSimulators:
  - 'ALGORITHM_SUBSTITUTION_POLICY'

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

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

Log:

docker_image.HasBioContainersLabels (0.6 s)
Test that a Docker image has BioContainers labels with metadata about the image
Warnings:
The Docker image should have the following BioContainers labels:
  extra.identifiers.biotools

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (4.4 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000088

Warnings:
Unexpected reports were produced:
  BIOMD0000000002_sim.sedml/Figure_4b

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

  - Model `BIOMD0000000002` may be invalid.

    - The model file `BIOMD0000000002_url.xml` may be invalid.

      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

         The units of the <kineticLaw> <math> expression 'comp1 * (kf_0 * B * L - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

         The units of the <kineticLaw> <math> expression 'comp1 * (kf_1 * BL * L - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

         The units of the <kineticLaw> <math> expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

         The units of the <kineticLaw> <math> expression 'comp1 * (kf_3 * A * L - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

         The units of the <kineticLaw> <math> expression 'comp1 * (kf_4 * AL * L - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

         The units of the <kineticLaw> <math> expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

         The units of the <kineticLaw> <math> expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

         The units of the <kineticLaw> <math> expression 'comp1 * (kf_7 * I * L - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

         The units of the <kineticLaw> <math> expression 'comp1 * (kf_8 * IL * L - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

         The units of the <kineticLaw> <math> expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

         The units of the <kineticLaw> <math> expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

         The units of the <kineticLaw> <math> expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

         The units of the <kineticLaw> <math> expression 'comp1 * (kf_12 * D * L - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

         The units of the <kineticLaw> <math> expression 'comp1 * (kf_13 * DL * L - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

         The units of the <kineticLaw> <math> expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

         The units of the <kineticLaw> <math> expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

         The units of the <kineticLaw> <math> expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

      - As a principle of best modeling practice, the units of a <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 'kf_0' 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 'kr_0' 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 'kf_1' 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 'kr_1' 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 'kf_2' 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 'kr_2' 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 'kf_3' 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 'kr_3' 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 'kf_4' 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 'kr_4' 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 'kf_5' 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 'kr_5' 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 'kf_6' 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 'kr_6' 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 'kf_7' 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 'kr_7' 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 'kf_8' 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 'kr_8' 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 'kf_9' 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 'kr_9' 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 'kf_10' 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 'kr_10' 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 'kf_11' 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 'kr_11' 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 'kf_12' 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 'kr_12' 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 'kf_13' 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 'kr_13' 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 'kf_14' 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 'kr_14' 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 'kf_15' 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 'kr_15' 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 'kf_16' 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 'kr_16' does not have a 'units' attribute.

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

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

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

    - Model `BIOMD0000000002` may be invalid.

      - The model file `BIOMD0000000002_url.xml` may be invalid.

        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

           The units of the <kineticLaw> <math> expression 'comp1 * (kf_0 * B * L - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

           The units of the <kineticLaw> <math> expression 'comp1 * (kf_1 * BL * L - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

           The units of the <kineticLaw> <math> expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

           The units of the <kineticLaw> <math> expression 'comp1 * (kf_3 * A * L - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

           The units of the <kineticLaw> <math> expression 'comp1 * (kf_4 * AL * L - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

           The units of the <kineticLaw> <math> expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

           The units of the <kineticLaw> <math> expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

           The units of the <kineticLaw> <math> expression 'comp1 * (kf_7 * I * L - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

           The units of the <kineticLaw> <math> expression 'comp1 * (kf_8 * IL * L - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

           The units of the <kineticLaw> <math> expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

           The units of the <kineticLaw> <math> expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

           The units of the <kineticLaw> <math> expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

           The units of the <kineticLaw> <math> expression 'comp1 * (kf_12 * D * L - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

           The units of the <kineticLaw> <math> expression 'comp1 * (kf_13 * DL * L - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

           The units of the <kineticLaw> <math> expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

           The units of the <kineticLaw> <math> expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

           The units of the <kineticLaw> <math> expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - As a principle of best modeling practice, the units of a <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 'kf_0' 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 'kr_0' 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 'kf_1' 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 'kr_1' 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 'kf_2' 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 'kr_2' 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 'kf_3' 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 'kr_3' 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 'kf_4' 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 'kr_4' 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 'kf_5' 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 'kr_5' 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 'kf_6' 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 'kr_6' 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 'kf_7' 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 'kr_7' 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 'kf_8' 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 'kr_8' 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 'kf_9' 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 'kr_9' 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 'kf_10' 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 'kr_10' 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 'kf_11' 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 'kr_11' 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 'kf_12' 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 'kr_12' 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 'kf_13' 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 'kr_13' 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 'kf_14' 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 'kr_14' 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 'kf_15' 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 'kr_15' 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 'kf_16' 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 'kr_16' does not have a 'units' attribute.

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

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

  BIOMD0000000002_sim.sedml:

    Tasks (1):

      BIOMD0000000002_task

    Reports (1):

      report: 14 data sets

    Plots (1):

      Figure_4b: 5 curves

Executing SED-ML file 0: BIOMD0000000002_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/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (5.8 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000029

Warnings:
Unexpected reports were produced:
  simulation.sedml/plot2d_Fig_1_c
  simulation.sedml/plot2d_low_delta_R_stoch

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

  - Model `ODE_stochastic` may be invalid.

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

      - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function.

        Reference: L3V1 Section 3.4

         The formula '-(C * Kr_AR_binding) + A * Kf_AR_binding * R' in the math element of the <kineticLaw> can only act on variables with the same units.

      - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function.

        Reference: L3V1 Section 3.4

         The formula 'Kf_A_trnscr * PrmA - Kr_A_trnscr * PrmA * mRNA_A_' in the math element of the <kineticLaw> can only act on variables with the same units.

      - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function.

        Reference: L3V1 Section 3.4

         The formula 'Kf_active_A_trnscr * PrmA_bound - Kr_active_A_trnscr * PrmA_bound * mRNA_A_' in the math element of the <kineticLaw> can only act on variables with the same units.

      - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function.

        Reference: L3V1 Section 3.4

         The formula 'Kf_R_trnsc * PrmR - Kr_R_trnsc * PrmR * mRNA_R' in the math element of the <kineticLaw> can only act on variables with the same units.

      - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function.

        Reference: L3V1 Section 3.4

         The formula 'Kf_active_R_trnsc * PrmR_bound - Kr_active_R_trnsc * PrmR_bound * mRNA_R' in the math element of the <kineticLaw> can only act on variables with the same units.

      - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function.

        Reference: L3V1 Section 3.4

         The formula 'A * Kf_PrmA_activation * PrmA - Kr_PrmA_activation * PrmA_bound' in the math element of the <kineticLaw> can only act on variables with the same units.

      - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function.

        Reference: L3V1 Section 3.4

         The formula 'A * Kf_PrmR_activation * PrmR - Kr_PrmR_activation * PrmR_bound' in the math element of the <kineticLaw> can only act on variables with the same units.

      - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function.

        Reference: L3V1 Section 3.4

         The formula 'Kf_R_trnsl * mRNA_R - Kr_R_trnsl * R * mRNA_R' in the math element of the <kineticLaw> can only act on variables with the same units.

      - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function.

        Reference: L3V1 Section 3.4

         The formula 'Kf_A_trnsl * mRNA_A_ - A * Kr_A_trnsl * mRNA_A_' in the math element of the <kineticLaw> can only act on variables with the same units.

      - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model.

        Reference: L3V1 Section 3.4

         The formula '(-(C * Kr_AR_binding) + A * Kf_AR_binding * R) * cell' in the <kineticLaw> element of the <reaction> with id 'AR_binding' produces units that are inconsistent with units of earlier KineticLaw elements.

      - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model.

        Reference: L3V1 Section 3.4

         The formula '(Kf_A_trnscr * PrmA - Kr_A_trnscr * PrmA * mRNA_A_) * cell' in the <kineticLaw> element of the <reaction> with id 'A_trnscr' produces units that are inconsistent with units of earlier KineticLaw elements.

      - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model.

        Reference: L3V1 Section 3.4

         The formula '(Kf_active_A_trnscr * PrmA_bound - Kr_active_A_trnscr * PrmA_bound * mRNA_A_) * cell' in the <kineticLaw> element of the <reaction> with id 'active_A_trnscr' produces units that are inconsistent with units of earlier KineticLaw elements.

      - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model.

        Reference: L3V1 Section 3.4

         The formula '(Kf_R_trnsc * PrmR - Kr_R_trnsc * PrmR * mRNA_R) * cell' in the <kineticLaw> element of the <reaction> with id 'R_trnsc' produces units that are inconsistent with units of earlier KineticLaw elements.

      - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model.

        Reference: L3V1 Section 3.4

         The formula '(Kf_active_R_trnsc * PrmR_bound - Kr_active_R_trnsc * PrmR_bound * mRNA_R) * cell' in the <kineticLaw> element of the <reaction> with id 'active_R_trnsc' produces units that are inconsistent with units of earlier KineticLaw elements.

      - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model.

        Reference: L3V1 Section 3.4

         The formula '(A * Kf_PrmA_activation * PrmA - Kr_PrmA_activation * PrmA_bound) * cell' in the <kineticLaw> element of the <reaction> with id 'PrmA_activation' produces units that are inconsistent with units of earlier KineticLaw elements.

      - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model.

        Reference: L3V1 Section 3.4

         The formula '(A * Kf_PrmR_activation * PrmR - Kr_PrmR_activation * PrmR_bound) * cell' in the <kineticLaw> element of the <reaction> with id 'PrmR_activation' produces units that are inconsistent with units of earlier KineticLaw elements.

      - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model.

        Reference: L3V1 Section 3.4

         The formula '(Kf_R_trnsl * mRNA_R - Kr_R_trnsl * R * mRNA_R) * cell' in the <kineticLaw> element of the <reaction> with id 'R_trnsl' produces units that are inconsistent with units of earlier KineticLaw elements.

      - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model.

        Reference: L3V1 Section 3.4

         The formula '(Kf_A_trnsl * mRNA_A_ - A * Kr_A_trnsl * mRNA_A_) * cell' in the <kineticLaw> element of the <reaction> with id 'A_trnsl' produces units that are inconsistent with units of earlier KineticLaw elements.

      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

         The units of the <assignmentRule> <math> expression '0.00332107756632545 / KMOLE' 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 <assignmentRule> <math> expression '0.00166053878316273 / KMOLE' 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 <assignmentRule> <math> expression '0.00166053878316273 / KMOLE' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

      - The units of the 'math' formula in a <kineticLaw> definition are expected to be the equivalent of _substance per time_.

        Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4

         In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the <math> expression in the <kineticLaw> (from the <reaction> with id 'C_decay') are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0), metre (exponent = 3, multiplier = 1, scale = -6).

      - The units of the 'math' formula in a <kineticLaw> definition are expected to be the equivalent of _substance per time_.

        Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4

         In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the <math> expression in the <kineticLaw> (from the <reaction> with id 'A_decay') are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0), metre (exponent = 3, multiplier = 1, scale = -6).

      - The units of the 'math' formula in a <kineticLaw> definition are expected to be the equivalent of _substance per time_.

        Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4

         In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the <math> expression in the <kineticLaw> (from the <reaction> with id 'mRNA_A_decay') are second (exponent = -1, multiplier = 1, scale = 0), item (exponent = 1, multiplier = 1, scale = 0), metre (exponent = 3, multiplier = 1, scale = -6).

      - The units of the 'math' formula in a <kineticLaw> definition are expected to be the equivalent of _substance per time_.

        Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4

         In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the <math> expression in the <kineticLaw> (from the <reaction> with id 'mRNA_R_decay') are second (exponent = -1, multiplier = 1, scale = 0), item (exponent = 1, multiplier = 1, scale = 0), metre (exponent = 3, multiplier = 1, scale = -6).

      - The units of the 'math' formula in a <kineticLaw> definition are expected to be the equivalent of _substance per time_.

        Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4

         In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the <math> expression in the <kineticLaw> (from the <reaction> with id 'AR_binding') are metre (exponent = 3, multiplier = 1, scale = -6).

      - The units of the 'math' formula in a <kineticLaw> definition are expected to be the equivalent of _substance per time_.

        Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4

         In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the <math> expression in the <kineticLaw> (from the <reaction> with id 'R_decay') are second (exponent = -1, multiplier = 1, scale = 0), item (exponent = 1, multiplier = 1, scale = 0), metre (exponent = 3, multiplier = 1, scale = -6).

      - The units of the 'math' formula in a <kineticLaw> definition are expected to be the equivalent of _substance per time_.

        Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4

         In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the <math> expression in the <kineticLaw> (from the <reaction> with id 'A_trnscr') are metre (exponent = 3, multiplier = 1, scale = -6).

      - The units of the 'math' formula in a <kineticLaw> definition are expected to be the equivalent of _substance per time_.

        Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4

         In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the <math> expression in the <kineticLaw> (from the <reaction> with id 'active_A_trnscr') are metre (exponent = 3, multiplier = 1, scale = -6).

      - The units of the 'math' formula in a <kineticLaw> definition are expected to be the equivalent of _substance per time_.

        Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4

         In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the <math> expression in the <kineticLaw> (from the <reaction> with id 'R_trnsc') are metre (exponent = 3, multiplier = 1, scale = -6).

      - The units of the 'math' formula in a <kineticLaw> definition are expected to be the equivalent of _substance per time_.

        Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4

         In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the <math> expression in the <kineticLaw> (from the <reaction> with id 'active_R_trnsc') are metre (exponent = 3, multiplier = 1, scale = -6).

      - The units of the 'math' formula in a <kineticLaw> definition are expected to be the equivalent of _substance per time_.

        Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4

         In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the <math> expression in the <kineticLaw> (from the <reaction> with id 'PrmA_activation') are metre (exponent = 3, multiplier = 1, scale = -6).

      - The units of the 'math' formula in a <kineticLaw> definition are expected to be the equivalent of _substance per time_.

        Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4

         In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the <math> expression in the <kineticLaw> (from the <reaction> with id 'PrmR_activation') are metre (exponent = 3, multiplier = 1, scale = -6).

      - The units of the 'math' formula in a <kineticLaw> definition are expected to be the equivalent of _substance per time_.

        Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4

         In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the <math> expression in the <kineticLaw> (from the <reaction> with id 'R_trnsl') are metre (exponent = 3, multiplier = 1, scale = -6).

      - The units of the 'math' formula in a <kineticLaw> definition are expected to be the equivalent of _substance per time_.

        Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4

         In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the <math> expression in the <kineticLaw> (from the <reaction> with id 'A_trnsl') are metre (exponent = 3, multiplier = 1, scale = -6).

  - Model `ODE_stochastic_0` may be invalid.

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

      - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function.

        Reference: L3V1 Section 3.4

         The formula '-(C * Kr_AR_binding) + A * Kf_AR_binding * R' in the math element of the <kineticLaw> can only act on variables with the same units.

      - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function.

        Reference: L3V1 Section 3.4

         The formula 'Kf_A_trnscr * PrmA - Kr_A_trnscr * PrmA * mRNA_A_' in the math element of the <kineticLaw> can only act on variables with the same units.

      - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function.

        Reference: L3V1 Section 3.4

         The formula 'Kf_active_A_trnscr * PrmA_bound - Kr_active_A_trnscr * PrmA_bound * mRNA_A_' in the math element of the <kineticLaw> can only act on variables with the same units.

      - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function.

        Reference: L3V1 Section 3.4

         The formula 'Kf_R_trnsc * PrmR  ...

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:cellml/Lorenz-system (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_3240
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_3240 and simulation algorithms KISAO_0000019

Log:

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_9004 and simulation algorithms KISAO_0000019

Log:

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000030

Reason for skip:
Case requires model formats format_9004 and simulation algorithms KISAO_0000030

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_2585 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-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:

published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_9001
Algorithm: KISAO_0000057

Reason for skip:
Case requires model formats format_9001 and simulation algorithms KISAO_0000057

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:

sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (3.7 s)
Test that a simulator supports multiple time courses with non-zero initial times
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_gillespy2/gillespy2:1.5.11' could not execute the archive:

  Unknown error

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

  - Model `BIOMD0000000002` may be invalid.

    - The model file `BIOMD0000000002_url.xml` may be invalid.

      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

         The units of the <kineticLaw> <math> expression 'comp1 * (kf_0 * B * L - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

         The units of the <kineticLaw> <math> expression 'comp1 * (kf_1 * BL * L - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

         The units of the <kineticLaw> <math> expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

         The units of the <kineticLaw> <math> expression 'comp1 * (kf_3 * A * L - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

         The units of the <kineticLaw> <math> expression 'comp1 * (kf_4 * AL * L - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

         The units of the <kineticLaw> <math> expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

         The units of the <kineticLaw> <math> expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

         The units of the <kineticLaw> <math> expression 'comp1 * (kf_7 * I * L - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

         The units of the <kineticLaw> <math> expression 'comp1 * (kf_8 * IL * L - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

         The units of the <kineticLaw> <math> expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

         The units of the <kineticLaw> <math> expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

         The units of the <kineticLaw> <math> expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

         The units of the <kineticLaw> <math> expression 'comp1 * (kf_12 * D * L - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

         The units of the <kineticLaw> <math> expression 'comp1 * (kf_13 * DL * L - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

         The units of the <kineticLaw> <math> expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

         The units of the <kineticLaw> <math> expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

         The units of the <kineticLaw> <math> expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

      - As a principle of best modeling practice, the units of a <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 'kf_0' 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 'kr_0' 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 'kf_1' 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 'kr_1' 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 'kf_2' 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 'kr_2' 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 'kf_3' 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 'kr_3' 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 'kf_4' 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 'kr_4' 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 'kf_5' 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 'kr_5' 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 'kf_6' 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 'kr_6' 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 'kf_7' 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 'kr_7' 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 'kf_8' 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 'kr_8' 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 'kf_9' 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 'kr_9' 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 'kf_10' 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 'kr_10' 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 'kf_11' 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 'kr_11' 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 'kf_12' 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 'kr_12' 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 'kf_13' 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 'kr_13' 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 'kf_14' 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 'kr_14' 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 'kf_15' 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 'kr_15' 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 'kf_16' 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 'kr_16' does not have a 'units' attribute.

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

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

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

    - Model `BIOMD0000000002` may be invalid.

      - The model file `BIOMD0000000002_url.xml` may be invalid.

        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

           The units of the <kineticLaw> <math> expression 'comp1 * (kf_0 * B * L - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

           The units of the <kineticLaw> <math> expression 'comp1 * (kf_1 * BL * L - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

           The units of the <kineticLaw> <math> expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

           The units of the <kineticLaw> <math> expression 'comp1 * (kf_3 * A * L - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

           The units of the <kineticLaw> <math> expression 'comp1 * (kf_4 * AL * L - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

           The units of the <kineticLaw> <math> expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

           The units of the <kineticLaw> <math> expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

           The units of the <kineticLaw> <math> expression 'comp1 * (kf_7 * I * L - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

           The units of the <kineticLaw> <math> expression 'comp1 * (kf_8 * IL * L - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

           The units of the <kineticLaw> <math> expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

           The units of the <kineticLaw> <math> expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

           The units of the <kineticLaw> <math> expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

           The units of the <kineticLaw> <math> expression 'comp1 * (kf_12 * D * L - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

           The units of the <kineticLaw> <math> expression 'comp1 * (kf_13 * DL * L - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

           The units of the <kineticLaw> <math> expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

           The units of the <kineticLaw> <math> expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression.

           The units of the <kineticLaw> <math> expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - As a principle of best modeling practice, the units of a <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 'kf_0' 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 'kr_0' 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 'kf_1' 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 'kr_1' 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 'kf_2' 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 'kr_2' 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 'kf_3' 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 'kr_3' 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 'kf_4' 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 'kr_4' 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 'kf_5' 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 'kr_5' 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 'kf_6' 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 'kr_6' 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 'kf_7' 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 'kr_7' 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 'kf_8' 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 'kr_8' 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 'kf_9' 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 'kr_9' 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 'kf_10' 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 'kr_10' 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 'kf_11' 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 'kr_11' 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 'kf_12' 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 'kr_12' 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 'kf_13' 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 'kr_13' 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 'kf_14' 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 'kr_14' 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 'kf_15' 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 'kr_15' 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 'kf_16' 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 'kr_16' does not have a 'units' attribute.

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

Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  BIOMD0000000002_sim.sedml:

    Tasks (1):

      BIOMD0000000002_task

    Reports (1):

      report: 14 data sets

Executing SED-ML file 0: BIOMD0000000002_sim.sedml ...

Bundling outputs ...

Cleaning up ...

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

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Initial simulation time 0.5 is not supported. Initial time must be 0.

The image for your simulator is valid!

Your submission was committed to the BioSimulators registry. Thank you!
Future submissions of subsequent versions of gillespy2 to the BioSimulators registry will be automatically validated. These submissions will not require manual review by the BioSimulators Team.