Closed biosimulators-daemon closed 3 years ago
Thank you @biosimulators-daemon for your submission to the BioSimulators simulator validation/submission system!
The BioSimulators validator bot is validating the specifications of your simulator, validating your Docker image, and committing your simulator to the BioSimulators registry.
We will discuss any concerns with your submission in this issue.
A complete log of your simulator submission job will be available for 90 days here. The results of the validation of your tool will also be saved as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.
The specifications of your simulator is valid!
Executed 73 test cases
Passed 40 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: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 33 test cases:
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:smoldyn/Lotka-Volterra
published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells
sedml.SimulatorProducesLinear3DPlots
sedml.SimulatorProducesLogarithmic3DPlots
sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
sedml.SimulatorSupportsComputeModelChanges
sedml.SimulatorSupportsModelAttributeChanges
sedml.SimulatorSupportsRepeatedTasksWithChanges
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
sedml.SimulatorSupportsSubstitutingAlgorithms
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes
cli.CliDescribesSupportedEnvironmentVariablesInline
(3.6 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
(0.7 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:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
(30.8 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:
Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:
Dolan2015.sedml:
Tasks (1):
task_1
Reports (1):
report: 3 data sets
Plots (1):
Figure: 2 curves
Executing SED-ML file 1: 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
(5.1 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:
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 1: 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
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:smoldyn/Lotka-Volterra
(0.0 s)Required model formats and simulation algorithms for SED tasks:
Format: format_9001
Algorithm: KISAO_0000057
Reason for skip:
Case requires model formats format_9001 and simulation algorithms KISAO_0000057
Log:
published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells
(0.0 s)Required model formats and simulation algorithms for SED tasks:
Format: format_9010
Algorithm: KISAO_0000019
Reason for skip:
Case requires model formats format_9010 and simulation algorithms KISAO_0000019
Log:
sedml.SimulatorProducesLinear3DPlots
(8.9 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
(8.7 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
(8.6 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
(8.4 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
(8.6 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
(8.7 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
(8.7 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
(8.8 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 "NFSim agent-based simulation method" (http://www.biomodels.net/kisao/KISAO#KISAO_0000263) for policy SIMILAR_VARIABLES is not supported.
Log:
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes
(38.5 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:2.6.0' 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:
Dolan2015.sedml:
Tasks (1):
task_1
Reports (1):
report: 3 data sets
Executing SED-ML file 1: 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.
id: bionetgen version: 2.6.0 specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_BioNetGen/e9fba6df81f2c4889a58202da9330dd35f9515d8/biosimulators.json specificationsPatch: version: 2.6.0 image: url: ghcr.io/biosimulators/biosimulators_bionetgen/bionetgen:2.6.0 validateImage: true commitSimulator: true