Submit GillesPy2 1.6.4 - Githubissues

biosimulators-daemon commented 3 years ago

id: gillespy2 version: 1.6.4 specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_GillesPy2/12d459c0d7ba21ac5ec66ab8ff63e621ad74c2d3/biosimulators.json specificationsPatch: version: 1.6.4 image: url: ghcr.io/biosimulators/biosimulators_gillespy2/gillespy2:1.6.4 validateImage: true commitSimulator: true

biosimulators-daemon commented 3 years ago

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

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

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

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

biosimulators-daemon commented 3 years ago

The specifications of your simulator is valid!

biosimulators-daemon commented 3 years ago

Summary of tests

Executed 73 test cases
Passed 46 test cases:
- cli.CliDescribesSupportedEnvironmentVariablesInline
- cli.CliDisplaysHelpInline
- cli.CliDisplaysVersionInformationInline
- combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
- combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
- combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
- combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
- docker_image.DeclaresSupportedEnvironmentVariables
- docker_image.DefaultUserIsRoot
- docker_image.HasBioContainersLabels
- docker_image.HasOciLabels
- docker_image.SingularityImageExecutesSimulationsSuccessfully
- 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.SimulatorSupportsAddReplaceRemoveModelElementChanges
- sedml.SimulatorSupportsAlgorithmParameters
- sedml.SimulatorSupportsComputeModelChanges
- sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
- sedml.SimulatorSupportsDataSetsWithDifferentShapes
- sedml.SimulatorSupportsModelAttributeChanges
- sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
- sedml.SimulatorSupportsMultipleReportsPerSedDocument
- sedml.SimulatorSupportsMultipleTasksPerSedDocument
- sedml.SimulatorSupportsRepeatedTasksWithChanges
- sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
- sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
- sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges
- sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
- sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
- sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
- sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
- sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
- sedml.SimulatorSupportsRepeatedTasksWithVectorRanges
- sedml.SimulatorSupportsSubstitutingAlgorithms
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes
Failed 0 test cases
Skipped 27 test cases:
- published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
- published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
- published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator
- published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
- published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism
- published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE
- published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler
- published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT
- 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-Fehlberg
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator
- 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:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle
- published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra
- published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells
- sedml.SimulatorProducesLinear3DPlots
- sedml.SimulatorProducesLogarithmic3DPlots
- sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions

biosimulators-daemon commented 3 years ago

Warnings

`cli.CliDescribesSupportedEnvironmentVariablesInline` (3.0 s)

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

Warnings:

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

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

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

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

Log:

`docker_image.DeclaresSupportedEnvironmentVariables` (0.4 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'
    - 'BUNDLE_OUTPUTS'
    - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
    - 'COLLECT_SED_DOCUMENT_RESULTS'
    - 'DEBUG'
    - 'H5_REPORTS_PATH'
    - 'KEEP_INDIVIDUAL_OUTPUTS'
    - 'LOG_PATH'
    - 'PLOTS_PATH'
    - 'REPORTS_PATH'
    - 'REPORT_FORMATS'
    - 'SAVE_PLOT_DATA'
    - 'VALIDATE_IMAGES'
    - 'VALIDATE_OMEX_MANIFESTS'
    - 'VALIDATE_OMEX_METADATA'
    - 'VALIDATE_RESULTS'
    - 'VALIDATE_SEDML'
    - 'VALIDATE_SEDML_MODELS'
    - 'VIZ_FORMATS'

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

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

Log:

`docker_image.HasBioContainersLabels` (0.3 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` (4.1 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: [33mThe 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.

      [0m

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

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe 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.

        [0m

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

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

BIOMD0000000002_sim.sedml:

  Tasks (1):

    BIOMD0000000002_task

  Reports (1):

    report: 14 data sets

  Plots (1):

    Figure_4b: 5 curves

Executing SED-ML file 1: 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` (8.4 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: [33mThe 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 ...

biosimulators-daemon commented 3 years ago

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/Elowitz-Nature-2000-Repressilator (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: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:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (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: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:rba/Escherichia-coli-K12-WT (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_9012 Algorithm: KISAO_0000669

Reason for skip:
```
Case requires model formats format_9012 and simulation algorithms KISAO_0000669
```
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-Fehlberg (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000086

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000086
```
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/Elowitz-Nature-2000-Repressilator (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

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000019
```
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:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (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:
published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_9010 Algorithm: KISAO_0000019

Reason for skip:
```
Case requires model formats format_9010 and simulation algorithms KISAO_0000019
```
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.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.1 s)

Test that that the curated number of output dimensions matches the actual number of output dimensions

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

biosimulators-daemon commented 3 years ago

The image for your simulator is valid!

biosimulators-daemon commented 3 years ago

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.

biosimulators / Biosimulators

Submit GillesPy2 1.6.4 #429

Summary of tests

Warnings

`cli.CliDescribesSupportedEnvironmentVariablesInline` (3.0 s)

`docker_image.DeclaresSupportedEnvironmentVariables` (0.4 s)

`docker_image.HasBioContainersLabels` (0.3 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation` (4.1 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA` (8.4 s)

Skips

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

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

`published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator` (0.0 s)

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

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

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

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

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

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

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

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

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

`published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells` (0.0 s)

`sedml.SimulatorProducesLinear3DPlots` (0.1 s)

`sedml.SimulatorProducesLogarithmic3DPlots` (0.1 s)

`sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions` (0.1 s)

biosimulators / Biosimulators

Submit GillesPy2 1.6.4 #429

Summary of tests

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (3.0 s)

docker_image.DeclaresSupportedEnvironmentVariables (0.4 s)

docker_image.HasBioContainersLabels (0.3 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (4.1 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (8.4 s)

Skips

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

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

published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (0.0 s)

published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system (0.0 s)

published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (0.0 s)

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)

published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator (0.0 s)

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

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

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

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

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

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

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

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

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

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (0.0 s)

published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (0.0 s)

published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)

sedml.SimulatorProducesLinear3DPlots (0.1 s)

sedml.SimulatorProducesLogarithmic3DPlots (0.1 s)

sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.1 s)

`cli.CliDescribesSupportedEnvironmentVariablesInline` (3.0 s)

`docker_image.DeclaresSupportedEnvironmentVariables` (0.4 s)

`docker_image.HasBioContainersLabels` (0.3 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation` (4.1 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA` (8.4 s)

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

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

`published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator` (0.0 s)

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

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

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

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

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

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

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

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

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

`published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells` (0.0 s)

`sedml.SimulatorProducesLinear3DPlots` (0.1 s)

`sedml.SimulatorProducesLogarithmic3DPlots` (0.1 s)

`sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions` (0.1 s)