Submit RBApy 1.0.2

[biosimulators-daemon]

---

id: rbapy version: "1.0.2" specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_RBApy/3fcd56ecf025852d2c326efdbbb0d4789c58c98e/biosimulators.json specificationsPatch: version: "1.0.2" image: url: ghcr.io/biosimulators/biosimulators_rbapy/rbapy:1.0.2 validateImage: true commitSimulator: true

---

Changelog

• Changed commit hash
• Granted access to RBApy team to BioSimulators-daemon
• Added example RBA model
• Sped up tests by limiting data sets

[biosimulators-daemon]

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

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

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

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

[biosimulators-daemon]

The validation/submission of your simulator failed.

- Simulator specifications could not be retrieved from https://raw.githubusercontent.com/biosimulators/Biosimulators_RBApy/4ecba8c5188998ee9357198b9bc7e6dfa14ace37/biosimulators.json.
- 
-   404 Client Error: Not Found for url: https://raw.githubusercontent.com/biosimulators/Biosimulators_RBApy/4ecba8c5188998ee9357198b9bc7e6dfa14ace37/biosimulators.json

The complete log of your validation/submission job, including further information about the failure, is available for 90 days here.

If you chose to validate your Docker image, the results of the validation of your image will be available shortly 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.

Once you have fixed the problem, edit the first block of this issue to re-initiate this validation.

The BioSimulators Team is happy to help. Questions and feedback can be directed to the BioSimulators Team by posting comments to this issues that reference the GitHub team @biosimulators/biosimulators (without the backticks).

[biosimulators-daemon]

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

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

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

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

[biosimulators-daemon]

- You (@biosimulators-daemon) do not have permissions to update the specifications of RBApy. Only the members of @biosimulators/rbapy can update the specifications of RBApy. Please contact the members of this group to request permissions to update RBApy.

[biosimulators-daemon]

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

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

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

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

[biosimulators-daemon]

- You (@biosimulators-daemon) do not have permissions to update the specifications of RBApy. Only the members of @biosimulators/rbapy can update the specifications of RBApy. Please contact the members of this group to request permissions to update RBApy.

[biosimulators-daemon]

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

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

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

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

[biosimulators-daemon]

The specifications of your simulator is valid!

[biosimulators-daemon]

Summary of tests

• Executed 72 test cases

• Passed 7 test cases:

  • cli.CliDescribesSupportedEnvironmentVariablesInline
  • cli.CliDisplaysHelpInline
  • cli.CliDisplaysVersionInformationInline
  • docker_image.DeclaresSupportedEnvironmentVariables
  • docker_image.DefaultUserIsRoot
  • docker_image.HasBioContainersLabels
  • docker_image.HasOciLabels

• Failed 0 test cases

• Skipped 65 test cases:

  • combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
  • combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
  • combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
  • combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
  • docker_image.SingularityImageExecutesSimulationsSuccessfully
  • log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
  • log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
  • log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
  • log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
  • published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
  • published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
  • published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator
  • published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
  • published_project.SimulatorCanExecutePublishedProject: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: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/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
  • 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-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA
  • published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism
  • published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling
  • published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle
  • published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra
  • published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells
  • results_report.SimulatorGeneratesReportsOfSimulationResults
  • sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
  • sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
  • sedml.SimulatorProducesLinear2DPlots
  • sedml.SimulatorProducesLinear3DPlots
  • sedml.SimulatorProducesLogarithmic2DPlots
  • sedml.SimulatorProducesLogarithmic3DPlots
  • sedml.SimulatorProducesMultiplePlots
  • sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
  • sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
  • sedml.SimulatorSupportsAlgorithmParameters
  • sedml.SimulatorSupportsComputeModelChanges
  • sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
  • sedml.SimulatorSupportsDataSetsWithDifferentShapes
  • sedml.SimulatorSupportsModelAttributeChanges
  • sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
  • sedml.SimulatorSupportsMultipleReportsPerSedDocument
  • sedml.SimulatorSupportsMultipleTasksPerSedDocument
  • sedml.SimulatorSupportsRepeatedTasksWithChanges
  • sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
  • sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
  • sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges
  • sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
  • sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
  • sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
  • sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
  • sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
  • sedml.SimulatorSupportsRepeatedTasksWithVectorRanges
  • sedml.SimulatorSupportsSubstitutingAlgorithms
  • sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes
  • sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

[biosimulators-daemon]

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (6.1 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'
    - '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_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 (1.5 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'
    - '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_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:

[biosimulators-daemon]

Skips

combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories (0.0 s)

Test that SED documents in nested directories can be executed

Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

Log:

combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories (0.0 s)

Test that SED documents with the same names in nested directories can be executed and their outputs are saved to distinct paths

Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

Log:

combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile (0.0 s)

Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file.

Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

Log:

combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments (0.0 s)

Test that when a COMBINE/OMEX archive does not have a defined master file, the simulator executes all SED-ML files.

Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

Log:

docker_image.SingularityImageExecutesSimulationsSuccessfully (0.0 s)

Test that the Singularity version of a Docker image can sucessfully execute COMBINE archives

Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

Log:

log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (0.0 s)

Test that simulator logs the execution of COMBINE/OMEX archives

Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

Log:

log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments (0.0 s)

Test that simulator logs the execution of individual SED document in COMBINE/OMEX archives

Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

Log:

log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs (0.0 s)

Test that simulator logs the execution of individual SED outputs in COMBINE/OMEX archives

Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

Log:

log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks (0.0 s)

Test that simulator logs the execution of individual SED tasks in COMBINE/OMEX archives

Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

Log:

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: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/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000088

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_0000088

  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-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000029

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_0000029

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000437

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_0000437

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000449

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_0000449

  Log:

  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:

  results_report.SimulatorGeneratesReportsOfSimulationResults (0.0 s)

  Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file.

  Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

  Log:

  sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments (0.0 s)

  Test that a simulator can resolve model sources defined by URI fragments (e.g., #model1).

  Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

  Log:

  sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (0.0 s)

  Test that a simulator can resolve model sources defined by URI fragments (e.g., #model1) and inherit the changes of the model.

  Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

  Log:

  sedml.SimulatorProducesLinear2DPlots (0.0 s)

  Test that a simulator produces linear 2D plots

  Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

  Log:

  sedml.SimulatorProducesLinear3DPlots (0.0 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.SimulatorProducesLogarithmic2DPlots (0.0 s)

  Test that a simulator produces logarithmic 2D plots

  Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

  Log:

  sedml.SimulatorProducesLogarithmic3DPlots (0.0 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.SimulatorProducesMultiplePlots (0.0 s)

  Test that a simulator produces multiple plots

  Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

  Log:

  sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.0 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:

  sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (0.0 s)

  Test that a simulator supports model changes that involve adding, replacing, and removing model elements.

  Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

  Log:

  sedml.SimulatorSupportsAlgorithmParameters (0.0 s)

  Test that a simulator supports setting the values of parameters of algorithms

  Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

  Log:

  sedml.SimulatorSupportsComputeModelChanges (0.0 s)

  Test that a simulator supports compute model changes

  Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

  Log:

  sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes (0.0 s)

  Test that a simulator supports data generators with different shapes

  Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

  Log:

  sedml.SimulatorSupportsDataSetsWithDifferentShapes (0.0 s)

  Test that a simulator supports data generators with different shapes

  Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

  Log:

  sedml.SimulatorSupportsModelAttributeChanges (0.0 s)

  Test that a simulator supports changes to the attributes of model elements

  Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

  Log:

  sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports (0.0 s)

  Test that a simulator supports the core elements of SED: models, simulations, tasks, data generators for individual variables, and reports

  Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

  Log:

  sedml.SimulatorSupportsMultipleReportsPerSedDocument (0.0 s)

  Test that a simulator supports multiple reports per SED document

  Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

  Log:

  sedml.SimulatorSupportsMultipleTasksPerSedDocument (0.0 s)

  Test that a simulator supports multiple tasks per SED document

  Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

  Log:

  sedml.SimulatorSupportsRepeatedTasksWithChanges (0.0 s)

  Test that a simulator supports repeated tasks with multiple subtasks

  Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

  Log:

  sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (0.0 s)

  Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables

  Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

  Log:

  sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (0.0 s)

  Test that a simulator supports repeated tasks over functional ranges

  Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

  Log:

  sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (0.0 s)

  Test that a simulator supports repeated tasks over uniform ranges

  Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

  Log:

  sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (0.0 s)

  Test that a simulator supports repeated tasks over uniform ranges

  Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

  Log:

  sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (0.0 s)

  Test that a simulator supports repeated tasks with multiple subtasks

  Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

  Log:

  sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges (0.0 s)

  Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables

  Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

  Log:

  sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks (0.0 s)

  Test that a simulator supports nested repeated tasks

  Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

  Log:

  sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes (0.0 s)

  Test that a simulator supports repeated tasks whose sub-tasks have mixed types. Also tests that sub-types executed in order of the values of their order attributes and that reports of the results of repeated tasks handle sub-tasks to produce results of different shapes.

  Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

  Log:

  sedml.SimulatorSupportsRepeatedTasksWithVectorRanges (0.0 s)

  Test that a simulator supports repeated tasks over vector ranges

  Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

  Log:

  sedml.SimulatorSupportsSubstitutingAlgorithms (0.0 s)

  Check that a simulator can substitute algorithms that it doesn't implement with similar algorithms when the algorithm substitution policy is less restrictive than :obj:AlgorithmSubstitutionPolicy.SAME_METHOD. Also check that a simulator ignores unsupported algorithm parameters when the algorithm substitution policy is less restrictive than :obj:AlgorithmSubstitutionPolicy.NONE.

  Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

  Log:

  sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (0.0 s)

  Test that a simulator supports multiple time courses with non-zero initial times

  Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

  Log:

  sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes (0.0 s)

  Test that a simulator supports time courses with non-zero output start times

  Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

  Log:

[biosimulators-daemon]

No test cases are applicable to your simulator. Please use this issue to share appropriate test COMBINE/OMEX files. The BioSimulators Team will add these files to this validation program and then re-review your simulator.

[biosimulators-daemon]

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

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

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

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

[biosimulators-daemon]

The specifications of your simulator is valid!

[biosimulators-daemon]

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

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

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

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

[biosimulators-daemon]

The specifications of your simulator is valid!

[biosimulators-daemon]

Summary of tests

• Executed 73 test cases

• Passed 31 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:rba/Escherichia-coli-K12-WT
  • results_report.SimulatorGeneratesReportsOfSimulationResults
  • sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
  • sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
  • sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
  • sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
  • sedml.SimulatorSupportsMultipleReportsPerSedDocument
  • sedml.SimulatorSupportsMultipleTasksPerSedDocument
  • sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
  • sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges
  • sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
  • sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
  • sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
  • sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
  • sedml.SimulatorSupportsRepeatedTasksWithVectorRanges

• Failed 0 test cases

• Skipped 42 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: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/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
  • 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-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA
  • published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism
  • published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling
  • published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle
  • published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra
  • published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells
  • sedml.SimulatorProducesLinear2DPlots
  • sedml.SimulatorProducesLinear3DPlots
  • sedml.SimulatorProducesLogarithmic2DPlots
  • sedml.SimulatorProducesLogarithmic3DPlots
  • sedml.SimulatorProducesMultiplePlots
  • sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
  • sedml.SimulatorSupportsAlgorithmParameters
  • sedml.SimulatorSupportsComputeModelChanges
  • sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
  • sedml.SimulatorSupportsDataSetsWithDifferentShapes
  • sedml.SimulatorSupportsModelAttributeChanges
  • sedml.SimulatorSupportsRepeatedTasksWithChanges
  • sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
  • sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
  • sedml.SimulatorSupportsSubstitutingAlgorithms
  • sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes
  • sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

[biosimulators-daemon]

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (3.9 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'
    - '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_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 (1.3 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'
    - '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_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:

[biosimulators-daemon]

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: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/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000088

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_0000088

  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-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000029

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_0000029

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000437

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_0000437

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000449

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_0000449

  Log:

  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.SimulatorProducesLinear2DPlots (4.3 s)

  Test that a simulator produces linear 2D plots

  Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

  Log:

  sedml.SimulatorProducesLinear3DPlots (4.0 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.SimulatorProducesLogarithmic2DPlots (3.9 s)

  Test that a simulator produces logarithmic 2D plots

  Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

  Log:

  sedml.SimulatorProducesLogarithmic3DPlots (4.1 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.SimulatorProducesMultiplePlots (3.9 s)

  Test that a simulator produces multiple plots

  Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

  Log:

  sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (4.0 s)

  Test that a simulator supports model changes that involve adding, replacing, and removing model elements.

  Reason for skip:

  This test is only implemented for XML-based model languages. Please contact the BioSimulators Team to discuss implementing tests for additional languages.

  Log:

  sedml.SimulatorSupportsAlgorithmParameters (4.3 s)

  Test that a simulator supports setting the values of parameters of algorithms

  Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

  Log:

  sedml.SimulatorSupportsComputeModelChanges (4.0 s)

  Test that a simulator supports compute model changes

  Reason for skip:

  This test is only implemented for XML-based model languages. Please contact the BioSimulators Team to discuss implementing tests for additional languages.

  Log:

  sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes (4.1 s)

  Test that a simulator supports data generators with different shapes

  Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

  Log:

  sedml.SimulatorSupportsDataSetsWithDifferentShapes (4.1 s)

  Test that a simulator supports data generators with different shapes

  Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

  Log:

  sedml.SimulatorSupportsModelAttributeChanges (3.9 s)

  Test that a simulator supports changes to the attributes of model elements

  Reason for skip:

  This test is only implemented for XML-based model languages. Please contact the BioSimulators Team to discuss implementing tests for additional languages.

  Log:

  sedml.SimulatorSupportsRepeatedTasksWithChanges (4.1 s)

  Test that a simulator supports repeated tasks with multiple subtasks

  Reason for skip:

  This test is only implemented for XML-based model languages. Please contact the BioSimulators Team to discuss implementing tests for additional languages.

  Log:

  sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (4.2 s)

  Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables

  Reason for skip:

  This test is only implemented for XML-based model languages. Please contact the BioSimulators Team to discuss implementing tests for additional languages.

  Log:

  sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes (467.0 s)

  Test that a simulator supports repeated tasks whose sub-tasks have mixed types. Also tests that sub-types executed in order of the values of their order attributes and that reports of the results of repeated tasks handle sub-tasks to produce results of different shapes.

  Reason for skip:

  The image 'ghcr.io/biosimulators/biosimulators_rbapy/rbapy:1.0.2' could not execute the archive:
  
  [Errno 1] Operation not permitted

  Log:

  /usr/local/lib/python3.8/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect.
  
  - Task `__repeated_task_1` may be invalid.
  
    - The outputs of the sub-tasks have different shapes.
  
  - Output `__repeated_task_report` may be invalid.
  
    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.
  
  warnings.warn(termcolor.colored(message, Colors.warning.value), category)
  
  /usr/local/lib/python3.8/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid.
  
  - The SED-ML file at location `simulation.sedml` may be invalid.
  
    - Task `__repeated_task_1` may be invalid.
  
      - The outputs of the sub-tasks have different shapes.
  
    - Output `__repeated_task_report` may be invalid.
  
      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.
  
  warnings.warn(termcolor.colored(message, Colors.warning.value), category)
  
  Archive contains 1 SED-ML documents with 1 models, 1 simulations, 3 tasks, 2 reports, and 0 plots:
  
  simulation.sedml:
  
    Tasks (3):
  
      __repeated_task_0
  
      __repeated_task_1
  
      task
  
    Reports (2):
  
      __repeated_task_report: 1 data sets
  
      task_report: 1 data sets
  
  Executing SED-ML file 0: simulation.sedml ...
  
  Bundling outputs ...
  
  Cleaning up ...
  
  ============= SUMMARY =============
  
  Executed 1 SED documents:
  
  SED documents (1):
  
    Succeeded: 1
  
    Skipped: 0
  
    Failed: 0
  
  Tasks (3):
  
    Succeeded: 3
  
    Skipped: 0
  
    Failed: 0
  
  Outputs (2):
  
    Succeeded: 2
  
    Skipped: 0
  
    Failed: 0
  

  sedml.SimulatorSupportsSubstitutingAlgorithms (4.3 s)

  Check that a simulator can substitute algorithms that it doesn't implement with similar algorithms when the algorithm substitution policy is less restrictive than :obj:AlgorithmSubstitutionPolicy.SAME_METHOD. Also check that a simulator ignores unsupported algorithm parameters when the algorithm substitution policy is less restrictive than :obj:AlgorithmSubstitutionPolicy.NONE.

  Reason for skip:

  Algorithm substitution for "Resource Balance Analysis" (http://www.biomodels.net/kisao/KISAO#KISAO_0000669) for policy SIMILAR_VARIABLES is not supported.

  Log:

  sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (4.0 s)

  Test that a simulator supports multiple time courses with non-zero initial times

  Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

  Log:

  sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes (4.0 s)

  Test that a simulator supports time courses with non-zero output start times

  Reason for skip:

  No curated COMBINE/OMEX archives are available to generate archives for testing

  Log:

[biosimulators-daemon]

The image for your simulator is valid!

[biosimulators-daemon]

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

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