Submit BoolNet 2.1.5

[biosimulators-daemon]

---

id: boolnet version: 2.1.5 specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_BoolNet/ec9628b25c3c531d7c8979fc8f34452b1cbf7ef2/biosimulators.json specificationsPatch: version: 2.1.5 image: url: ghcr.io/biosimulators/biosimulators_boolnet/boolnet:2.1.5 validateImage: true commitSimulator: true

---

Changelog:

• HPC connection restored

[biosimulators-daemon]

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

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

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

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

[biosimulators-daemon]

The specifications of your simulator is valid!

[biosimulators-daemon]

Summary of tests

• Executed 73 test cases

• Passed 45 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:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling
  • published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle
  • 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.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
  • sedml.SimulatorSupportsMultipleReportsPerSedDocument
  • sedml.SimulatorSupportsMultipleTasksPerSedDocument
  • sedml.SimulatorSupportsRepeatedTasksWithChanges
  • sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
  • sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
  • sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges
  • sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
  • sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
  • sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
  • sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
  • sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
  • sedml.SimulatorSupportsRepeatedTasksWithVectorRanges
  • sedml.SimulatorSupportsSubstitutingAlgorithms
  • sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

• Failed 0 test cases

• Skipped 28 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:smoldyn/Lotka-Volterra
  • published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells
  • sedml.SimulatorProducesLinear3DPlots
  • sedml.SimulatorProducesLogarithmic3DPlots
  • sedml.SimulatorSupportsModelAttributeChanges
  • sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes

[biosimulators-daemon]

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (4.0 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:

docker_image.HasBioContainersLabels (0.2 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-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (5.0 s)

Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000449

  Warnings:

  Unexpected reports were produced:
  simulation.sedml/Figure_4a

  Log:

  /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect.
  
  - Model `model` may be invalid.
  
    - The model file `BIOMD0000000562_url.xml` may be invalid.
  
      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 
  
         The units of the <compartment> 'main' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.
  
      - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.
  
        Reference: L3V1 Section 4.5
  
         The <compartment> 'main' has no discernable units.
  
        
  
  warnings.warn(termcolor.colored(message, Colors.warning.value), category)
  
  /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid.
  
  - The SED-ML file at location `./simulation.sedml` may be invalid.
  
    - Model `model` may be invalid.
  
      - The model file `BIOMD0000000562_url.xml` may be invalid.
  
        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 
  
           The units of the <compartment> 'main' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.
  
        - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.
  
          Reference: L3V1 Section 4.5
  
           The <compartment> 'main' has no discernable units.
  
          
  
  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:
  
  simulation.sedml:
  
    Tasks (1):
  
      task
  
    Reports (1):
  
      report: 5 data sets
  
    Plots (1):
  
      Figure_4a: 4 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 (1):
  
    Succeeded: 1
  
    Skipped: 0
  
    Failed: 0
  
  Outputs (2):
  
    Succeeded: 2
  
    Skipped: 0
  
    Failed: 0
  
  R[write to console]: Warning messages:
  
  R[write to console]: 1: 
  
  R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :
  
  R[write to console]: 
  
  R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages
  
  R[write to console]: 2: 
  
  R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :
  
  R[write to console]: 
  
  R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages
  

[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: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 (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.SimulatorSupportsModelAttributeChanges (0.1 s)

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

  Reason for skip:

  The SED document is invalid.
  - Model `model` is invalid.
    - The changes of the model are invalid.
      - Change 3 is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/@qual:required` are not defined. Only the following namespaces are defined for the target: `sbml`.

  Log:

  sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (4.3 s)

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

  Reason for skip:

  The image 'ghcr.io/biosimulators/biosimulators_boolnet/boolnet:2.1.5' could not execute the archive:
  
  Unknown error

  Log:

  /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect.
  
  - Model `model` may be invalid.
  
    - The model file `BIOMD0000000562_url.xml` may be invalid.
  
      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 
  
         The units of the <compartment> 'main' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.
  
      - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.
  
        Reference: L3V1 Section 4.5
  
         The <compartment> 'main' has no discernable units.
  
        
  
  warnings.warn(termcolor.colored(message, Colors.warning.value), category)
  
  /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid.
  
  - The SED-ML file at location `./simulation.sedml` may be invalid.
  
    - Model `model` may be invalid.
  
      - The model file `BIOMD0000000562_url.xml` may be invalid.
  
        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 
  
           The units of the <compartment> 'main' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.
  
        - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.
  
          Reference: L3V1 Section 4.5
  
           The <compartment> 'main' has no discernable units.
  
          
  
  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:
  
  simulation.sedml:
  
    Tasks (1):
  
      task
  
    Reports (1):
  
      report: 5 data sets
  
  Executing SED-ML file 0: simulation.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:
  
    Simulation `simulation` is invalid.
  
      - Initial time must be 0.
  
  R[write to console]: Warning message:
  
  R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :
  
  R[write to console]: 
  
  R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages
  

[biosimulators-daemon]

The image for your simulator is valid!

[biosimulators-daemon]

The validation/submission of your simulator failed.

- A Singularity image could not be generated for the Docker image
- 
-   - Internal Server Error (500):

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

If you chose to validate your Docker image, the results of the validation of your image will be available shortly as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

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

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

[biosimulators-daemon]

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

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

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

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

[biosimulators-daemon]

The specifications of your simulator is valid!

[biosimulators-daemon]

Summary of tests

• Executed 73 test cases

• Passed 45 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:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling
  • published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle
  • 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.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
  • sedml.SimulatorSupportsMultipleReportsPerSedDocument
  • sedml.SimulatorSupportsMultipleTasksPerSedDocument
  • sedml.SimulatorSupportsRepeatedTasksWithChanges
  • sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
  • sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
  • sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges
  • sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
  • sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
  • sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
  • sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
  • sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
  • sedml.SimulatorSupportsRepeatedTasksWithVectorRanges
  • sedml.SimulatorSupportsSubstitutingAlgorithms
  • sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

• Failed 0 test cases

• Skipped 28 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:smoldyn/Lotka-Volterra
  • published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells
  • sedml.SimulatorProducesLinear3DPlots
  • sedml.SimulatorProducesLogarithmic3DPlots
  • sedml.SimulatorSupportsModelAttributeChanges
  • sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes

[biosimulators-daemon]

Warnings

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 (0.3 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:

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-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (4.6 s)

Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000449

  Warnings:

  Unexpected reports were produced:
  simulation.sedml/Figure_4a

  Log:

  /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect.
  
  - Model `model` may be invalid.
  
    - The model file `BIOMD0000000562_url.xml` may be invalid.
  
      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 
  
         The units of the <compartment> 'main' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.
  
      - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.
  
        Reference: L3V1 Section 4.5
  
         The <compartment> 'main' has no discernable units.
  
        
  
  warnings.warn(termcolor.colored(message, Colors.warning.value), category)
  
  /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid.
  
  - The SED-ML file at location `./simulation.sedml` may be invalid.
  
    - Model `model` may be invalid.
  
      - The model file `BIOMD0000000562_url.xml` may be invalid.
  
        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 
  
           The units of the <compartment> 'main' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.
  
        - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.
  
          Reference: L3V1 Section 4.5
  
           The <compartment> 'main' has no discernable units.
  
          
  
  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:
  
  simulation.sedml:
  
    Tasks (1):
  
      task
  
    Reports (1):
  
      report: 5 data sets
  
    Plots (1):
  
      Figure_4a: 4 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 (1):
  
    Succeeded: 1
  
    Skipped: 0
  
    Failed: 0
  
  Outputs (2):
  
    Succeeded: 2
  
    Skipped: 0
  
    Failed: 0
  
  R[write to console]: Warning messages:
  
  R[write to console]: 1: 
  
  R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :
  
  R[write to console]: 
  
  R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages
  
  R[write to console]: 2: 
  
  R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :
  
  R[write to console]: 
  
  R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages
  

[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: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 (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.SimulatorSupportsModelAttributeChanges (0.1 s)

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

  Reason for skip:

  The SED document is invalid.
  - Model `model` is invalid.
    - The changes of the model are invalid.
      - Change 3 is invalid.
        - One or more namespaces required for target `/sbml:sbml[1]/@qual:required` are not defined. Only the following namespaces are defined for the target: `sbml`.

  Log:

  sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (3.9 s)

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

  Reason for skip:

  The image 'ghcr.io/biosimulators/biosimulators_boolnet/boolnet:2.1.5' could not execute the archive:
  
  Unknown error

  Log:

  /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect.
  
  - Model `model` may be invalid.
  
    - The model file `BIOMD0000000562_url.xml` may be invalid.
  
      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 
  
         The units of the <compartment> 'main' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.
  
      - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.
  
        Reference: L3V1 Section 4.5
  
         The <compartment> 'main' has no discernable units.
  
        
  
  warnings.warn(termcolor.colored(message, Colors.warning.value), category)
  
  /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid.
  
  - The SED-ML file at location `./simulation.sedml` may be invalid.
  
    - Model `model` may be invalid.
  
      - The model file `BIOMD0000000562_url.xml` may be invalid.
  
        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. 
  
           The units of the <compartment> 'main' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.
  
        - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.
  
          Reference: L3V1 Section 4.5
  
           The <compartment> 'main' has no discernable units.
  
          
  
  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:
  
  simulation.sedml:
  
    Tasks (1):
  
      task
  
    Reports (1):
  
      report: 5 data sets
  
  Executing SED-ML file 0: simulation.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:
  
    Simulation `simulation` is invalid.
  
      - Initial time must be 0.
  
  R[write to console]: Warning message:
  
  R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :
  
  R[write to console]: 
  
  R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages
  

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