Submit Smoldyn 2.67

[ssandrews]

---

id: smoldyn version: "2.67" specificationsUrl: https://raw.githubusercontent.com/ssandrews/Smoldyn/203bf3765b230fba69defdc580d3e00a71fdef26/biosimulators.json specificationsPatch: version: "2.67" image: url: ghcr.io/ssandrews/smoldyn/biosimulators_smoldyn:2.67 validateImage: true commitSimulator: true

---

[biosimulators-daemon]

Thank you @ssandrews 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 39 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:smoldyn/Lotka-Volterra
  • results_report.SimulatorGeneratesReportsOfSimulationResults
  • sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
  • sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
  • sedml.SimulatorProducesLinear2DPlots
  • sedml.SimulatorProducesLogarithmic2DPlots
  • sedml.SimulatorProducesMultiplePlots
  • sedml.SimulatorSupportsAlgorithmParameters
  • sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
  • sedml.SimulatorSupportsDataSetsWithDifferentShapes
  • sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
  • sedml.SimulatorSupportsMultipleReportsPerSedDocument
  • sedml.SimulatorSupportsMultipleTasksPerSedDocument
  • sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
  • sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges
  • sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
  • sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
  • sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
  • sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
  • sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
  • sedml.SimulatorSupportsRepeatedTasksWithVectorRanges
  • sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes
  • sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

• Failed 0 test cases

• Skipped 34 test cases:

  • published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
  • published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
  • published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator
  • published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
  • published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism
  • published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE
  • published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler
  • published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/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:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells
  • sedml.SimulatorProducesLinear3DPlots
  • sedml.SimulatorProducesLogarithmic3DPlots
  • sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
  • sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
  • sedml.SimulatorSupportsComputeModelChanges
  • sedml.SimulatorSupportsModelAttributeChanges
  • sedml.SimulatorSupportsRepeatedTasksWithChanges
  • sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
  • sedml.SimulatorSupportsSubstitutingAlgorithms

[biosimulators-daemon]

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (4.5 s)

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

Warnings:

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

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

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

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

Log:

docker_image.DeclaresSupportedEnvironmentVariables (0.3 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'
    - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
    - 'COLLECT_SED_DOCUMENT_RESULTS'
    - 'DEBUG'
    - 'H5_REPORTS_PATH'
    - 'KEEP_INDIVIDUAL_OUTPUTS'
    - 'LOG_PATH'
    - 'PLOTS_PATH'
    - 'REPORTS_PATH'
    - 'REPORT_FORMATS'
    - 'SAVE_PLOT_DATA'
    - 'VALIDATE_IMAGES'
    - 'VALIDATE_OMEX_MANIFESTS'
    - 'VALIDATE_OMEX_METADATA'
    - 'VALIDATE_RESULTS'
    - 'VALIDATE_SEDML'
    - 'VALIDATE_SEDML_MODELS'
    - 'VIZ_FORMATS'

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

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

Log:

published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (6.9 s)

Required model formats and simulation algorithms for SED tasks:

• Format: format_9001 Algorithm: KISAO_0000057

  Warnings:

  Unexpected reports were produced:
  simulation.sedml/Figure

  Log:

  Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:
  
  simulation.sedml:
  
    Tasks (1):
  
      task
  
    Reports (1):
  
      report: 3 data sets
  
    Plots (1):
  
      Figure: 2 curves
  
  Executing SED-ML file 1: simulation.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
  

[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:rba/Escherichia-coli-K12-WT (0.0 s)

  Required model formats and simulation algorithms for SED tasks:

• Format: format_9012 Algorithm: KISAO_0000669

  Reason for skip:

  Case requires model formats format_9012 and simulation algorithms KISAO_0000669

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000019

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_0000019

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000086

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_0000086

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000019

  Reason for skip:

  Case requires model formats format_2585 and simulation algorithms KISAO_0000019

  Log:

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

  Required model formats and simulation algorithms for SED tasks:

• Format: format_9010 Algorithm: KISAO_0000019

  Reason for skip:

  Case requires model formats format_9010 and simulation algorithms KISAO_0000019

  Log:

  sedml.SimulatorProducesLinear3DPlots (0.1 s)

  Test that a simulator produces linear 3D plots

  Reason for skip:

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

  Log:

  sedml.SimulatorProducesLogarithmic3DPlots (0.1 s)

  Test that a simulator produces logarithmic 3D plots

  Reason for skip:

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

  Log:

  sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.1 s)

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

  Reason for skip:

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

  Log:

  sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (0.1 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.SimulatorSupportsComputeModelChanges (0.1 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.SimulatorSupportsModelAttributeChanges (0.1 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 (0.1 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 (0.1 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.SimulatorSupportsSubstitutingAlgorithms (0.1 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 "Brownian diffusion Smoluchowski method" (http://www.biomodels.net/kisao/KISAO#KISAO_0000057) for policy SIMILAR_VARIABLES is not supported.

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