Submit BioNetGen 2.5.2 - Githubissues

id: bionetgen version: 2.5.2 specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_BioNetGen/2a0a103bb2c89a64cca7b9d1b0e70bfa485b195e/biosimulators.json specificationsPatch: version: 2.5.2 image: url: ghcr.io/biosimulators/biosimulators_bionetgen/bionetgen:2.5.2 validateImage: true commitSimulator: true

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

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

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

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

The specifications of your simulator is valid!

Summary of tests

Executed 60 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
- log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
- log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
- log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
- log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
- published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
- published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
- results_report.SimulatorGeneratesReportsOfSimulationResults
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
- sedml.SimulatorProducesLinear2DPlots
- sedml.SimulatorProducesLogarithmic2DPlots
- sedml.SimulatorProducesMultiplePlots
- sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
- 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.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes
Failed 0 test cases
Skipped 21 test cases:
- 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/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
- 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
- sedml.SimulatorProducesLinear3DPlots
- sedml.SimulatorProducesLogarithmic3DPlots
- sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
- sedml.SimulatorSupportsComputeModelChanges
- sedml.SimulatorSupportsModelAttributeChanges
- sedml.SimulatorSupportsRepeatedTasksWithChanges
- sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes

Warnings

`cli.CliDescribesSupportedEnvironmentVariablesInline` (7.3 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` (2.2 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:

`published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ` (12.5 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_3972 Algorithm: KISAO_0000263

Warnings:

Unexpected reports were produced:
Dolan2015.sedml/Figure

Plots were not produced:
simulation.sedml/Figure

Extra plots were produced:
Dolan2015.sedml/Figure

Log:

/usr/local/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe SED document is potentially incorrect.

- Model `model` may be invalid.

  - The model file `Dolan2015.bngl` may be invalid.

    - No validation is available for models encoded in `urn:sedml:language:bngl`[0m

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

/usr/local/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe COMBINE/OMEX archive may be invalid.

- The SED-ML file at location `./Dolan2015.sedml` may be invalid.

  - Model `model` may be invalid.

    - The model file `Dolan2015.bngl` may be invalid.

      - No validation is available for models encoded in `urn:sedml:language:bngl`[0m

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

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

Dolan2015.sedml:

  Tasks (1):

    simulation_1

  Reports (1):

    report: 3 data sets

  Plots (1):

    Figure: 2 curves

Executing SED-ML file 0: Dolan2015.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:bngl/test-bngl` (3.7 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_3972 Algorithm: KISAO_0000019

Warnings:

Unexpected reports were produced:
test.sedml/Figure

Plots were not produced:
simulation.sedml/Figure

Extra plots were produced:
test.sedml/Figure

Log:

/usr/local/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe SED document is potentially incorrect.

- Model `test_model` may be invalid.

  - The model file `test.bngl` may be invalid.

    - No validation is available for models encoded in `urn:sedml:language:bngl`[0m

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

/usr/local/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe COMBINE/OMEX archive may be invalid.

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

  - Model `test_model` may be invalid.

    - The model file `test.bngl` may be invalid.

      - No validation is available for models encoded in `urn:sedml:language:bngl`[0m

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

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

test.sedml:

  Tasks (1):

    task_simulation_1

  Reports (1):

    report: 9 data sets

  Plots (1):

    Figure: 8 curves

Executing SED-ML file 0: test.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

Skips

`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/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/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-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:

`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.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.SimulatorSupportsAddReplaceRemoveModelElementChanges` (0.0 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.SimulatorSupportsComputeModelChanges` (0.0 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.SimulatorSupportsModelAttributeChanges` (0.0 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` (0.0 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` (0.0 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.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes` (4.9 s)

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

Reason for skip:

The image 'ghcr.io/biosimulators/biosimulators_bionetgen/bionetgen:2.5.2' could not execute the archive:

Unknown error

Log:

/usr/local/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe SED document is potentially incorrect.

- Model `model` may be invalid.

  - The model file `Dolan2015.bngl` may be invalid.

    - No validation is available for models encoded in `urn:sedml:language:bngl`[0m

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

/usr/local/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe COMBINE/OMEX archive may be invalid.

- The SED-ML file at location `./Dolan2015.sedml` may be invalid.

  - Model `model` may be invalid.

    - The model file `Dolan2015.bngl` may be invalid.

      - No validation is available for models encoded in `urn:sedml:language:bngl`[0m

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

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

Dolan2015.sedml:

  Tasks (1):

    simulation_1

  Reports (1):

    report: 3 data sets

Executing SED-ML file 0: Dolan2015.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

[31mThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

  The initial time of a network free simulation (KISAO_0000263) must be 0.[0m

The image for your simulator is valid!

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

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

biosimulators / Biosimulators

Submit BioNetGen 2.5.2 #186

Summary of tests

Warnings

`cli.CliDescribesSupportedEnvironmentVariablesInline` (7.3 s)

`docker_image.DeclaresSupportedEnvironmentVariables` (2.2 s)

`published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ` (12.5 s)

`published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl` (3.7 s)

Skips

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

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

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation` (0.0 s)

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

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

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

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

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

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

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

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

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

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

`sedml.SimulatorProducesLinear3DPlots` (0.0 s)

`sedml.SimulatorProducesLogarithmic3DPlots` (0.0 s)

`sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges` (0.0 s)

`sedml.SimulatorSupportsComputeModelChanges` (0.0 s)

`sedml.SimulatorSupportsModelAttributeChanges` (0.0 s)

`sedml.SimulatorSupportsRepeatedTasksWithChanges` (0.0 s)

`sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables` (0.0 s)

`sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes` (4.9 s)

biosimulators / Biosimulators

Submit BioNetGen 2.5.2 #186

Summary of tests

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (7.3 s)

docker_image.DeclaresSupportedEnvironmentVariables (2.2 s)

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (12.5 s)

published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (3.7 s)

Skips

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

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

published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)

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

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

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

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

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

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

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

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

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

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

sedml.SimulatorProducesLinear3DPlots (0.0 s)

sedml.SimulatorProducesLogarithmic3DPlots (0.0 s)

sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (0.0 s)

sedml.SimulatorSupportsComputeModelChanges (0.0 s)

sedml.SimulatorSupportsModelAttributeChanges (0.0 s)

sedml.SimulatorSupportsRepeatedTasksWithChanges (0.0 s)

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (0.0 s)

sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (4.9 s)

`cli.CliDescribesSupportedEnvironmentVariablesInline` (7.3 s)

`docker_image.DeclaresSupportedEnvironmentVariables` (2.2 s)

`published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ` (12.5 s)

`published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl` (3.7 s)

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

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

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation` (0.0 s)

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

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

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

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

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

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

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

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

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

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

`sedml.SimulatorProducesLinear3DPlots` (0.0 s)

`sedml.SimulatorProducesLogarithmic3DPlots` (0.0 s)

`sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges` (0.0 s)

`sedml.SimulatorSupportsComputeModelChanges` (0.0 s)

`sedml.SimulatorSupportsModelAttributeChanges` (0.0 s)

`sedml.SimulatorSupportsRepeatedTasksWithChanges` (0.0 s)

`sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables` (0.0 s)

`sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes` (4.9 s)