Submit GillesPy2 1.5.7

[biosimulators-daemon]

---

id: gillespy2 version: 1.5.7 specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_GillesPy2/be85eb4ef475ea961079fc06adc7035399a288e6/biosimulators.json specificationsPatch: version: 1.5.7 image: url: ghcr.io/biosimulators/biosimulators_gillespy2/gillespy2:1.5.7 validateImage: true commitSimulator: true

---

Changelog

• Rerunning with fixed test suite (added missing requirement)

[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 here. The results of the validation of your tool will also be saved as a JSON file.A link to this file will be available from the "Artifacts" section at the bottom of this page.

[biosimulators-daemon]

The specifications of your simulator is valid!

[biosimulators-daemon]

Summary of tests

• Executed 60 test cases

• Passed 9 test cases:

  • cli.CliDescribesSupportedEnvironmentVariablesInline
  • cli.CliDisplaysHelpInline
  • cli.CliDisplaysVersionInformationInline
  • docker_image.DeclaresSupportedEnvironmentVariables
  • docker_image.DefaultUserIsRoot
  • docker_image.HasBioContainersLabels
  • docker_image.HasOciLabels
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA

• Failed 16 test cases:

  • combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
  • combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
  • combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
  • combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
  • results_report.SimulatorGeneratesReportsOfSimulationResults
  • sedml.SimulatorProducesLinear2DPlots
  • sedml.SimulatorProducesLinear3DPlots
  • sedml.SimulatorProducesLogarithmic2DPlots
  • sedml.SimulatorProducesLogarithmic3DPlots
  • sedml.SimulatorProducesMultiplePlots
  • sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
  • sedml.SimulatorSupportsAlgorithmParameters
  • sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
  • sedml.SimulatorSupportsMultipleReportsPerSedDocument
  • sedml.SimulatorSupportsMultipleTasksPerSedDocument
  • sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

• Skipped 35 test cases:

  • log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
  • log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
  • log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
  • log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
  • published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
  • published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM
  • published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism
  • published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling
  • sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
  • sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
  • sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
  • sedml.SimulatorSupportsComputeModelChanges
  • sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
  • sedml.SimulatorSupportsDataSetsWithDifferentShapes
  • sedml.SimulatorSupportsModelAttributeChanges
  • sedml.SimulatorSupportsRepeatedTasksWithChanges
  • sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
  • sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
  • sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges
  • sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
  • sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
  • sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
  • sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
  • sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
  • sedml.SimulatorSupportsRepeatedTasksWithVectorRanges
  • sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes

[biosimulators-daemon]

Failures

combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories (0.0 s)

Test that SED documents in nested directories can be executed

Exception:

  No module named 'libsbml'

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

Exception:

  No module named 'libsbml'

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.

Exception:

  No module named 'libsbml'

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.

Exception:

  No module named 'libsbml'

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.

Exception:

  No module named 'libsbml'

Log:

sedml.SimulatorProducesLinear2DPlots (0.0 s)

Test that a simulator produces linear 2D plots

Exception:

  No module named 'libsbml'

Log:

sedml.SimulatorProducesLinear3DPlots (0.0 s)

Test that a simulator produces linear 3D plots

Exception:

  No module named 'libsbml'

Log:

sedml.SimulatorProducesLogarithmic2DPlots (0.0 s)

Test that a simulator produces logarithmic 2D plots

Exception:

  No module named 'libsbml'

Log:

sedml.SimulatorProducesLogarithmic3DPlots (0.0 s)

Test that a simulator produces logarithmic 3D plots

Exception:

  No module named 'libsbml'

Log:

sedml.SimulatorProducesMultiplePlots (0.0 s)

Test that a simulator produces multiple plots

Exception:

  No module named 'libsbml'

Log:

sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.0 s)

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

Exception:

  No module named 'libsbml'

Log:

sedml.SimulatorSupportsAlgorithmParameters (0.0 s)

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

Exception:

  No module named 'libsbml'

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

Exception:

  No module named 'libsbml'

Log:

sedml.SimulatorSupportsMultipleReportsPerSedDocument (0.0 s)

Test that a simulator supports multiple reports per SED document

Exception:

  No module named 'libsbml'

Log:

sedml.SimulatorSupportsMultipleTasksPerSedDocument (0.0 s)

Test that a simulator supports multiple tasks per SED document

Exception:

  No module named 'libsbml'

Log:

sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes (0.0 s)

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

Exception:

  No module named 'libsbml'

Log:

[biosimulators-daemon]

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (5.8 s)

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

Warnings:

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

  The command-line interface does not describe the following standard environment variables recognized by BioSimulators:
    - 'ALGORITHM_SUBSTITUTION_POLICY'

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

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

Log:

docker_image.DeclaresSupportedEnvironmentVariables (0.6 s)

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

Warnings:

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

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

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

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

Log:

docker_image.HasBioContainersLabels (0.3 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 (4.2 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:

  Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:
  
  BIOMD0000000002_sim.sedml:
  
    Tasks (1):
  
      BIOMD0000000002_task
  
    Reports (1):
  
      report: 14 data sets
  
    Plots (1):
  
      Figure_4b: 5 curves
  
  Executing SED-ML file 0: BIOMD0000000002_sim.sedml ...
  
  Bundling outputs ...
  
  Cleaning up ...
  
  ============= SUMMARY =============
  
  Executed 1 SED documents:
  
  SED documents (1):
  
    Succeeded: 1
  
    Skipped: 0
  
    Failed: 0
  
  Tasks (1):
  
    Succeeded: 1
  
    Skipped: 0
  
    Failed: 0
  
  Outputs (2):
  
    Succeeded: 2
  
    Skipped: 0
  
    Failed: 0
  

  published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (5.4 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:

  Archive contains 1 SED-ML documents with 2 models, 2 simulations, 2 tasks, 2 reports, and 2 plots:
  
  simulation.sedml:
  
    Tasks (2):
  
      tsk_1_0
  
      tsk_1_1
  
    Reports (2):
  
      report_Fig_1_c: 10 data sets
  
      report_low_delta_R_stoch: 10 data sets
  
    Plots (2):
  
      plot2d_Fig_1_c: 9 curves
  
      plot2d_low_delta_R_stoch: 9 curves
  
  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 (2):
  
    Succeeded: 2
  
    Skipped: 0
  
    Failed: 0
  
  Outputs (4):
  
    Succeeded: 4
  
    Skipped: 0
  
    Failed: 0
  

[biosimulators-daemon]

Skips

log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (0.0 s)

Test that simulator logs the execution of COMBINE/OMEX archives

Reason for skip:

  No module named 'libsbml'

Log:

log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments (0.0 s)

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

Reason for skip:

  No module named 'libsbml'

Log:

log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs (0.0 s)

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

Reason for skip:

  No module named 'libsbml'

Log:

log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks (0.0 s)

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

Reason for skip:

  No module named 'libsbml'

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000019

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_0000019

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000019

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_0000019

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_000019

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_000019

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000496

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_0000496

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000560

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_0000560

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000560

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_0000560

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000019

• Format: format_2585 Algorithm: KISAO_0000027

• Format: format_2585 Algorithm: KISAO_0000030

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_0000019, KISAO_0000027, KISAO_0000030

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000019

• Format: format_2585 Algorithm: KISAO_0000030

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_0000019, KISAO_0000030

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000027

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_0000027

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000437

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_0000437

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000449

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_0000449

  Log:

  sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments (0.0 s)

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

  Reason for skip:

  No module named 'libsbml'

  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 module named 'libsbml'

  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 module named 'libsbml'

  Log:

  sedml.SimulatorSupportsComputeModelChanges (0.0 s)

  Test that a simulator supports compute model changes

  Reason for skip:

  No module named 'libsbml'

  Log:

  sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes (0.0 s)

  Test that a simulator supports data generators with different shapes

  Reason for skip:

  No module named 'libsbml'

  Log:

  sedml.SimulatorSupportsDataSetsWithDifferentShapes (0.0 s)

  Test that a simulator supports data generators with different shapes

  Reason for skip:

  No module named 'libsbml'

  Log:

  sedml.SimulatorSupportsModelAttributeChanges (0.0 s)

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

  Reason for skip:

  No module named 'libsbml'

  Log:

  sedml.SimulatorSupportsRepeatedTasksWithChanges (0.0 s)

  Test that a simulator supports repeated tasks with multiple subtasks

  Reason for skip:

  No module named 'libsbml'

  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 module named 'libsbml'

  Log:

  sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (0.0 s)

  Test that a simulator supports repeated tasks over functional ranges

  Reason for skip:

  No module named 'libsbml'

  Log:

  sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (0.0 s)

  Test that a simulator supports repeated tasks over uniform ranges

  Reason for skip:

  No module named 'libsbml'

  Log:

  sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (0.0 s)

  Test that a simulator supports repeated tasks over uniform ranges

  Reason for skip:

  No module named 'libsbml'

  Log:

  sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (0.0 s)

  Test that a simulator supports repeated tasks with multiple subtasks

  Reason for skip:

  No module named 'libsbml'

  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 module named 'libsbml'

  Log:

  sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks (0.0 s)

  Test that a simulator supports nested repeated tasks

  Reason for skip:

  No module named 'libsbml'

  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 module named 'libsbml'

  Log:

  sedml.SimulatorSupportsRepeatedTasksWithVectorRanges (0.0 s)

  Test that a simulator supports repeated tasks over vector ranges

  Reason for skip:

  No module named 'libsbml'

  Log:

  sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (0.0 s)

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

  Reason for skip:

  No module named 'libsbml'

  Log:

[biosimulators-daemon]

- After correcting your simulator, please edit the first block of this issue to re-initiate this validation.
- 
- The complete log of your validation/submission job, including further information about the failure, is available [here](https://github.com/biosimulators/Biosimulators/actions/runs/761207948). The results of the validation of your image will also be available shortly as a JSON file. A link to this file will be available from the "Artifacts" section at the bottom of [this page](https://github.com/biosimulators/Biosimulators/actions/runs/761207948).

[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 here. The results of the validation of your tool will also be saved as a JSON file.A link to this file will be available from the "Artifacts" section at the bottom of this page.

[biosimulators-daemon]

The specifications of your simulator is valid!

[biosimulators-daemon]

Summary of tests

• Executed 60 test cases

• Passed 44 test cases:

  • cli.CliDescribesSupportedEnvironmentVariablesInline
  • cli.CliDisplaysHelpInline
  • cli.CliDisplaysVersionInformationInline
  • combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
  • combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
  • combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
  • combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
  • docker_image.DeclaresSupportedEnvironmentVariables
  • docker_image.DefaultUserIsRoot
  • docker_image.HasBioContainersLabels
  • docker_image.HasOciLabels
  • log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
  • log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
  • log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
  • log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA
  • results_report.SimulatorGeneratesReportsOfSimulationResults
  • sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
  • sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
  • sedml.SimulatorProducesLinear2DPlots
  • sedml.SimulatorProducesLogarithmic2DPlots
  • sedml.SimulatorProducesMultiplePlots
  • sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
  • sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
  • sedml.SimulatorSupportsAlgorithmParameters
  • sedml.SimulatorSupportsComputeModelChanges
  • sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
  • sedml.SimulatorSupportsDataSetsWithDifferentShapes
  • sedml.SimulatorSupportsModelAttributeChanges
  • sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
  • sedml.SimulatorSupportsMultipleReportsPerSedDocument
  • sedml.SimulatorSupportsMultipleTasksPerSedDocument
  • sedml.SimulatorSupportsRepeatedTasksWithChanges
  • sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
  • sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
  • sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges
  • sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
  • sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
  • sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
  • sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
  • sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
  • sedml.SimulatorSupportsRepeatedTasksWithVectorRanges
  • sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

• Failed 0 test cases

• Skipped 16 test cases:

  • published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
  • published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM
  • published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism
  • published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling
  • sedml.SimulatorProducesLinear3DPlots
  • sedml.SimulatorProducesLogarithmic3DPlots
  • sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes

[biosimulators-daemon]

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (6.2 s)

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

Warnings:

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

  The command-line interface does not describe the following standard environment variables recognized by BioSimulators:
    - 'ALGORITHM_SUBSTITUTION_POLICY'

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

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

Log:

docker_image.DeclaresSupportedEnvironmentVariables (0.9 s)

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

Warnings:

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

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

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

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

Log:

docker_image.HasBioContainersLabels (0.6 s)

Test that a Docker image has BioContainers labels with metadata about the image

Warnings:

  The Docker image should have the following BioContainers labels:
    extra.identifiers.biotools

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (4.5 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:

  Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:
  
  BIOMD0000000002_sim.sedml:
  
    Tasks (1):
  
      BIOMD0000000002_task
  
    Reports (1):
  
      report: 14 data sets
  
    Plots (1):
  
      Figure_4b: 5 curves
  
  Executing SED-ML file 0: BIOMD0000000002_sim.sedml ...
  
  Bundling outputs ...
  
  Cleaning up ...
  
  ============= SUMMARY =============
  
  Executed 1 SED documents:
  
  SED documents (1):
  
    Succeeded: 1
  
    Skipped: 0
  
    Failed: 0
  
  Tasks (1):
  
    Succeeded: 1
  
    Skipped: 0
  
    Failed: 0
  
  Outputs (2):
  
    Succeeded: 2
  
    Skipped: 0
  
    Failed: 0
  

  published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (5.8 s)

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000029

  Warnings:

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

  Log:

  Archive contains 1 SED-ML documents with 2 models, 2 simulations, 2 tasks, 2 reports, and 2 plots:
  
  simulation.sedml:
  
    Tasks (2):
  
      tsk_1_0
  
      tsk_1_1
  
    Reports (2):
  
      report_Fig_1_c: 10 data sets
  
      report_low_delta_R_stoch: 10 data sets
  
    Plots (2):
  
      plot2d_Fig_1_c: 9 curves
  
      plot2d_low_delta_R_stoch: 9 curves
  
  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 (2):
  
    Succeeded: 2
  
    Skipped: 0
  
    Failed: 0
  
  Outputs (4):
  
    Succeeded: 4
  
    Skipped: 0
  
    Failed: 0
  

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000019

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_0000019

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000019

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_0000019

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_000019

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_000019

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000496

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_0000496

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000560

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_0000560

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000560

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_0000560

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000019

• Format: format_2585 Algorithm: KISAO_0000027

• Format: format_2585 Algorithm: KISAO_0000030

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_0000019, KISAO_0000027, KISAO_0000030

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000019

• Format: format_2585 Algorithm: KISAO_0000030

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_0000019, KISAO_0000030

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000027

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_0000027

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000437

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_0000437

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000449

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_0000449

  Log:

  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 (0.0 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.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (3.6 s)

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

  Reason for skip:

  The image 'ghcr.io/biosimulators/biosimulators_gillespy2/gillespy2:1.5.7' could not execute the archive:
  
  Unknown error

  Log:

  Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:
  
  BIOMD0000000002_sim.sedml:
  
    Tasks (1):
  
      BIOMD0000000002_task
  
    Reports (1):
  
      report: 14 data sets
  
  Executing SED-ML file 0: BIOMD0000000002_sim.sedml ...
  
  Bundling outputs ...
  
  Cleaning up ...
  
  ============= SUMMARY =============
  
  Executed 1 SED documents:
  
  SED documents (1):
  
    Succeeded: 0
  
    Skipped: 0
  
    Failed: 1
  
  Tasks (1):
  
    Succeeded: 0
  
    Skipped: 0
  
    Failed: 1
  
  Outputs (1):
  
    Succeeded: 0
  
    Skipped: 1
  
    Failed: 0
  
  The COMBINE/OMEX did not execute successfully:
  
  The SED document did not execute successfully:
  
    Initial simulation time 0.5 is not supported. Initial time must be 0.
  

[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 gillespy2 to the BioSimulators registry will be automatically validated. These submissions will not require manual review by the BioSimulators Team.