Submit tellurium 2.2.8

[biosimulators-daemon]

---

id: tellurium
version: 2.2.8
specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_tellurium/f29d257be165f5eb12afc360545fce0fca096338/biosimulators.json
specificationsPatch:
version: 2.2.8
image:
url: ghcr.io/biosimulators/biosimulators_tellurium/tellurium:2.2.8
digest: "sha256:8142fc0f07418f77a27785f1797f4c74e72ca6554b613360d3c62236e728d931"
validateImage: true
commitSimulator: true

---

[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 74 test cases

• Passed 48 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-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/Elowitz-Nature-2000-Repressilator
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA
  • results_report.SimulatorGeneratesReportsOfSimulationResults
  • sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
  • sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
  • sedml.SimulatorProducesLinear2DPlots
  • sedml.SimulatorProducesLogarithmic2DPlots
  • sedml.SimulatorProducesMultiplePlots
  • sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
  • sedml.SimulatorSupportsAlgorithmParameters
  • sedml.SimulatorSupportsComputeModelChanges
  • sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
  • sedml.SimulatorSupportsDataSetsWithDifferentShapes
  • sedml.SimulatorSupportsModelAttributeChanges
  • sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
  • sedml.SimulatorSupportsMultipleReportsPerSedDocument
  • sedml.SimulatorSupportsMultipleTasksPerSedDocument
  • sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
  • sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges
  • sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
  • sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
  • sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
  • sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
  • sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
  • sedml.SimulatorSupportsRepeatedTasksWithVectorRanges
  • sedml.SimulatorSupportsSubstitutingAlgorithms
  • sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes
  • sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

• Failed 0 test cases

• Skipped 26 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/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-discrete-NRM
  • 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:vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength
  • published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells
  • sedml.SimulatorProducesLinear3DPlots
  • sedml.SimulatorProducesLogarithmic3DPlots
  • sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
  • sedml.SimulatorSupportsRepeatedTasksWithChanges
  • sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables

[biosimulators-daemon]

Warnings

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'
  - 'OMEX_METADATA_INPUT_FORMAT'
  - 'OMEX_METADATA_OUTPUT_FORMAT'
  - 'OMEX_METADATA_SCHEMA'
  - 'PLOTS_PATH'
  - 'REPORTS_PATH'
  - 'REPORT_FORMATS'
  - 'SAVE_PLOT_DATA'
  - 'VALIDATE_IMAGES'
  - 'VALIDATE_IMPORTED_MODEL_FILES'
  - '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: None

docker_image.HasBioContainersLabels (0.2 s)

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

Warnings:

Docker images are encouraged to have the following BioContainers labels:
  extra.identifiers.biotools

Log: None

[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: None

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: None

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: None

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: None

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: None

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: None

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: None

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: None

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: None

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: None

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: None

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: None

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: None

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

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000019, KISAO_0000027

Log: None

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: None

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: None

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: None

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: None

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: None

published_project.SimulatorCanExecutePublishedProject:vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength (0.0 s)

Required model formats and simulation algorithms for SED tasks:

• Format: format_9000
  Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_9000 and simulation algorithms KISAO_0000019

Log: None

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: None

sedml.SimulatorProducesLinear3DPlots (0.3 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: None

sedml.SimulatorProducesLogarithmic3DPlots (0.3 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: None

sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.3 s)

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

Reason for skip:

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

Log: None

sedml.SimulatorSupportsRepeatedTasksWithChanges (10.4 s)

Test that a simulator supports repeated tasks with multiple subtasks

Reason for skip:

The image 'ghcr.io/biosimulators/biosimulators_tellurium/tellurium:2.2.8' could not execute the archive:

  Unknown error

Log:

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:





�[33mCOMBINE/OMEX archive has warnings.


  - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives.�[0m





/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:





�[33mThe SED document is potentially incorrect.


  - Model `BIOMD0000000912` has warnings.


    - The model file `Caravagna2010.xml` has warnings.


      - 6 warnings of type SBML unit consistency (99505). The following is the first warning at line 570, column 8:


        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. 


           The units of the <kineticLaw> <math> expression 'compartment * Function_for_induction_of_tumor(r2, T, b, V)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.


      - 14 warnings of type Modeling practice (80701). The following is the first warning at line 525, column 6:


        - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.


           The <parameter> with the id 'r2' does not have a 'units' attribute.


  - Output `__repeated_task_report` has warnings.


    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.�[0m





/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:





�[33mThe COMBINE/OMEX archive has warnings.


  - The SED-ML file at location `./BIOMD0000000912_sim.sedml` has warnings.


    - Model `BIOMD0000000912` has warnings.


      - The model file `Caravagna2010.xml` has warnings.


        - 6 warnings of type SBML unit consistency (99505). The following is the first warning at line 570, column 8:


          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. 


             The units of the <kineticLaw> <math> expression 'compartment * Function_for_induction_of_tumor(r2, T, b, V)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.


        - 14 warnings of type Modeling practice (80701). The following is the first warning at line 525, column 6:


          - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.


             The <parameter> with the id 'r2' does not have a 'units' attribute.


    - Output `__repeated_task_report` has warnings.


      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.�[0m





/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:





�[33mThe SED document is potentially incorrect.


  - Output `__repeated_task_report` has warnings.


    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.�[0m





Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:


  BIOMD0000000912_sim.sedml:


    Tasks (2):


      BIOMD0000000912_task


      __repeated_task_0


    Reports (2):


      __repeated_task_report: 4 data sets


      task_report: 4 data sets





Executing SED-ML file 1: BIOMD0000000912_sim.sedml ...





Bundling outputs ...


Cleaning up ...





============= SUMMARY =============


Executed 1 SED documents:


  SED documents (1):


    Succeeded: 0


    Skipped: 0


    Failed: 1


  Tasks (2):


    Succeeded: 1


    Skipped: 0


    Failed: 1


  Outputs (2):


    Succeeded: 1


    Skipped: 1


    Failed: 0





�[31mThe COMBINE/OMEX did not execute successfully:



  The SED document did not execute successfully:

  

    No stored variable with target '/sbml:sbml[1]/@level' and symbol '' in model BIOMD0000000912�[0m

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:





�[33mCOMBINE/OMEX archive has warnings.


  - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives.�[0m





/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:





�[33mThe SED document is potentially incorrect.


  - Model `BIOMD0000000912` has warnings.


    - The model file `Caravagna2010.xml` has warnings.


      - 6 warnings of type SBML unit consistency (99505). The following is the first warning at line 570, column 8:


        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. 


           The units of the <kineticLaw> <math> expression 'compartment * Function_for_induction_of_tumor(r2, T, b, V)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.


      - 14 warnings of type Modeling practice (80701). The following is the first warning at line 525, column 6:


        - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.


           The <parameter> with the id 'r2' does not have a 'units' attribute.


  - Output `__repeated_task_report` has warnings.


    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.�[0m





/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:





�[33mThe COMBINE/OMEX archive has warnings.


  - The SED-ML file at location `./BIOMD0000000912_sim.sedml` has warnings.


    - Model `BIOMD0000000912` has warnings.


      - The model file `Caravagna2010.xml` has warnings.


        - 6 warnings of type SBML unit consistency (99505). The following is the first warning at line 570, column 8:


          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. 


             The units of the <kineticLaw> <math> expression 'compartment * Function_for_induction_of_tumor(r2, T, b, V)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.


        - 14 warnings of type Modeling practice (80701). The following is the first warning at line 525, column 6:


          - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.


             The <parameter> with the id 'r2' does not have a 'units' attribute.


    - Output `__repeated_task_report` has warnings.


      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.�[0m





/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:





�[33mThe SED document is potentially incorrect.


  - Output `__repeated_task_report` has warnings.


    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.�[0m





Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:


  BIOMD0000000912_sim.sedml:


    Tasks (2):


      BIOMD0000000912_task


      __repeated_task_0


    Reports (2):


      __repeated_task_report: 4 data sets


      task_report: 4 data sets





Executing SED-ML file 1: BIOMD0000000912_sim.sedml ...





Bundling outputs ...


Cleaning up ...





============= SUMMARY =============


Executed 1 SED documents:


  SED documents (1):


    Succeeded: 0


    Skipped: 0


    Failed: 1


  Tasks (2):


    Succeeded: 1


    Skipped: 0


    Failed: 1


  Outputs (2):


    Succeeded: 1


    Skipped: 1


    Failed: 0





�[31mThe COMBINE/OMEX did not execute successfully:



  The SED document did not execute successfully:

  

    No stored variable with target '/sbml:sbml[1]/@level' and symbol '' in model BIOMD0000000912�[0m

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (10.6 s)

Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables

Reason for skip:

The image 'ghcr.io/biosimulators/biosimulators_tellurium/tellurium:2.2.8' could not execute the archive:

  Unknown error

Log:

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:





�[33mCOMBINE/OMEX archive has warnings.


  - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives.�[0m





/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:





�[33mThe SED document is potentially incorrect.


  - Model `BIOMD0000000912` has warnings.


    - The model file `Caravagna2010.xml` has warnings.


      - 6 warnings of type SBML unit consistency (99505). The following is the first warning at line 570, column 8:


        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. 


           The units of the <kineticLaw> <math> expression 'compartment * Function_for_induction_of_tumor(r2, T, b, V)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.


      - 14 warnings of type Modeling practice (80701). The following is the first warning at line 525, column 6:


        - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.


           The <parameter> with the id 'r2' does not have a 'units' attribute.


  - Output `__repeated_task_report` has warnings.


    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.�[0m





/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:





�[33mThe COMBINE/OMEX archive has warnings.


  - The SED-ML file at location `./BIOMD0000000912_sim.sedml` has warnings.


    - Model `BIOMD0000000912` has warnings.


      - The model file `Caravagna2010.xml` has warnings.


        - 6 warnings of type SBML unit consistency (99505). The following is the first warning at line 570, column 8:


          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. 


             The units of the <kineticLaw> <math> expression 'compartment * Function_for_induction_of_tumor(r2, T, b, V)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.


        - 14 warnings of type Modeling practice (80701). The following is the first warning at line 525, column 6:


          - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.


             The <parameter> with the id 'r2' does not have a 'units' attribute.


    - Output `__repeated_task_report` has warnings.


      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.�[0m





/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:





�[33mThe SED document is potentially incorrect.


  - Output `__repeated_task_report` has warnings.


    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.�[0m





Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:


  BIOMD0000000912_sim.sedml:


    Tasks (2):


      BIOMD0000000912_task


      __repeated_task_0


    Reports (2):


      __repeated_task_report: 4 data sets


      task_report: 4 data sets





Executing SED-ML file 1: BIOMD0000000912_sim.sedml ...





Bundling outputs ...


Cleaning up ...





============= SUMMARY =============


Executed 1 SED documents:


  SED documents (1):


    Succeeded: 0


    Skipped: 0


    Failed: 1


  Tasks (2):


    Succeeded: 1


    Skipped: 0


    Failed: 1


  Outputs (2):


    Succeeded: 1


    Skipped: 1


    Failed: 0





�[31mThe COMBINE/OMEX did not execute successfully:



  The SED document did not execute successfully:

  

    No stored variable with target '/sbml:sbml[1]/@level' and symbol '' in model BIOMD0000000912�[0m

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:





�[33mCOMBINE/OMEX archive has warnings.


  - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives.�[0m





/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:





�[33mThe SED document is potentially incorrect.


  - Model `BIOMD0000000912` has warnings.


    - The model file `Caravagna2010.xml` has warnings.


      - 6 warnings of type SBML unit consistency (99505). The following is the first warning at line 570, column 8:


        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. 


           The units of the <kineticLaw> <math> expression 'compartment * Function_for_induction_of_tumor(r2, T, b, V)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.


      - 14 warnings of type Modeling practice (80701). The following is the first warning at line 525, column 6:


        - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.


           The <parameter> with the id 'r2' does not have a 'units' attribute.


  - Output `__repeated_task_report` has warnings.


    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.�[0m





/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:





�[33mThe COMBINE/OMEX archive has warnings.


  - The SED-ML file at location `./BIOMD0000000912_sim.sedml` has warnings.


    - Model `BIOMD0000000912` has warnings.


      - The model file `Caravagna2010.xml` has warnings.


        - 6 warnings of type SBML unit consistency (99505). The following is the first warning at line 570, column 8:


          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. 


             The units of the <kineticLaw> <math> expression 'compartment * Function_for_induction_of_tumor(r2, T, b, V)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.


        - 14 warnings of type Modeling practice (80701). The following is the first warning at line 525, column 6:


          - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.


             The <parameter> with the id 'r2' does not have a 'units' attribute.


    - Output `__repeated_task_report` has warnings.


      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.�[0m





/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:





�[33mThe SED document is potentially incorrect.


  - Output `__repeated_task_report` has warnings.


    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute.�[0m





Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:


  BIOMD0000000912_sim.sedml:


    Tasks (2):


      BIOMD0000000912_task


      __repeated_task_0


    Reports (2):


      __repeated_task_report: 4 data sets


      task_report: 4 data sets





Executing SED-ML file 1: BIOMD0000000912_sim.sedml ...





Bundling outputs ...


Cleaning up ...





============= SUMMARY =============


Executed 1 SED documents:


  SED documents (1):


    Succeeded: 0


    Skipped: 0


    Failed: 1


  Tasks (2):


    Succeeded: 1


    Skipped: 0


    Failed: 1


  Outputs (2):


    Succeeded: 1


    Skipped: 1


    Failed: 0





�[31mThe COMBINE/OMEX did not execute successfully:



  The SED document did not execute successfully:

  

    No stored variable with target '/sbml:sbml[1]/@level' and symbol '' in model BIOMD0000000912�[0m

[biosimulators-daemon]

The image for your simulator is valid!

[biosimulators-daemon]

The validation/submission of your simulator failed.

- 504 Server Error: Gateway Time-out for url: https://api.biosimulations.org/images/refresh

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).