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biosimulators / Biosimulators

Registry of containerized biosimulation tools that support a standard command-line interface
https://biosimulators.org
MIT License
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Submit COPASI 4.30.240 #203

Closed biosimulators-daemon closed 3 years ago

biosimulators-daemon commented 3 years ago

id: copasi version: 4.30.240 specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_COPASI/df57975ba3c19b2b27c3f5b49457ce5d60b55ecc/biosimulators.json specificationsPatch: version: 4.30.240 image: url: ghcr.io/biosimulators/biosimulators_copasi/copasi:4.30.240 validateImage: true commitSimulator: true

Changelog

biosimulators-daemon commented 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 here. The results of the validation of your tool will also be saved as a JSON file.A link to this file will be available from the "Artifacts" section at the bottom of this page.

biosimulators-daemon commented 3 years ago

The specifications of your simulator is valid!

biosimulators-daemon commented 3 years ago

Summary of tests

biosimulators-daemon commented 3 years ago

Failures

sedml.SimulatorSupportsMultipleReportsPerSedDocument (4.5 s)

Test that a simulator supports multiple reports per SED document

Exception:

  The image 'ghcr.io/biosimulators/biosimulators_copasi/copasi:4.30.240' 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 `BIOMD0000000678` may be invalid.

      - The model file `BIOMD0000000678_url.xml` may be invalid.

        - 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 <initialAssignment> <math> expression 'stim_duration' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - 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 <initialAssignment> <math> expression 'stim_frequency' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - 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 <assignmentRule> <math> expression '1 - NFAT_phosphorylated - NFAT_dephosphorylated' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - 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 <assignmentRule> <math> expression '100 * NFAT_phosphorylated' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - 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 <assignmentRule> <math> expression '100 * NFAT_transported' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - 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 <assignmentRule> <math> expression '100 * NFAT_dephosphorylated' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - 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 <assignmentRule> <math> expression 'piecewise(1, lt(time - floor(time / ModelValue_13) * ModelValue_13, ModelValue_17), 0)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - 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 'Jurkat_cell * function_for_modified_reaction_1(NFAT_phosphorylated, k1, stimulus)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - 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 'Jurkat_cell * k2 * NFAT_dephosphorylated' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - 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 'Jurkat_cell * k3 * NFAT_dephosphorylated' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - 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 'Jurkat_cell * k4 * NFAT_transported' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

        - 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 'k1' does not have a 'units' attribute.

        - 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 'k2' does not have a 'units' attribute.

        - 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 'k3' does not have a 'units' attribute.

        - 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 'k4' does not have a 'units' attribute.

        - 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 'stim_frequency' does not have a 'units' attribute.

        - 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 'dNFAT' does not have a 'units' attribute.

        - 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 'pNFAT' does not have a 'units' attribute.

        - 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 'tNFAT' does not have a 'units' attribute.

        - 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 'stim_duration' does not have a 'units' attribute.

        - 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 'ModelValue_17' does not have a 'units' attribute.

        - 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 'ModelValue_13' does not have a 'units' attribute.

          

    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 `./BIOMD0000000678_sim.sedml` may be invalid.

      - Model `BIOMD0000000678` may be invalid.

        - The model file `BIOMD0000000678_url.xml` may be invalid.

          - 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 <initialAssignment> <math> expression 'stim_duration' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

          - 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 <initialAssignment> <math> expression 'stim_frequency' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

          - 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 <assignmentRule> <math> expression '1 - NFAT_phosphorylated - NFAT_dephosphorylated' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

          - 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 <assignmentRule> <math> expression '100 * NFAT_phosphorylated' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

          - 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 <assignmentRule> <math> expression '100 * NFAT_transported' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

          - 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 <assignmentRule> <math> expression '100 * NFAT_dephosphorylated' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

          - 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 <assignmentRule> <math> expression 'piecewise(1, lt(time - floor(time / ModelValue_13) * ModelValue_13, ModelValue_17), 0)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

          - 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 'Jurkat_cell * function_for_modified_reaction_1(NFAT_phosphorylated, k1, stimulus)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

          - 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 'Jurkat_cell * k2 * NFAT_dephosphorylated' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

          - 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 'Jurkat_cell * k3 * NFAT_dephosphorylated' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

          - 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 'Jurkat_cell * k4 * NFAT_transported' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.

          - 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 'k1' does not have a 'units' attribute.

          - 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 'k2' does not have a 'units' attribute.

          - 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 'k3' does not have a 'units' attribute.

          - 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 'k4' does not have a 'units' attribute.

          - 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 'stim_frequency' does not have a 'units' attribute.

          - 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 'dNFAT' does not have a 'units' attribute.

          - 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 'pNFAT' does not have a 'units' attribute.

          - 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 'tNFAT' does not have a 'units' attribute.

          - 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 'stim_duration' does not have a 'units' attribute.

          - 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 'ModelValue_17' does not have a 'units' attribute.

          - 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 'ModelValue_13' does not have a 'units' attribute.

            

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

  The COMBINE/OMEX archive is invalid.

    - The SED-ML file at location `./BIOMD0000000678_sim.sedml` is invalid.

      - Each identified SED object must have a unique id. Multiple objects have the following ids:

        - __single_var_output_el__1
biosimulators-daemon commented 3 years ago

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (4.7 s)

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

Warnings:

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

  The command-line interface does not describe the following standard environment variables recognized by BioSimulators:
    - 'ALGORITHM_SUBSTITUTION_POLICY'

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

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

Log:

docker_image.HasBioContainersLabels (0.4 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-core/Tomida-EMBO-J-2003-NFAT-translocation (3.5 s)

Required model formats and simulation algorithms for SED tasks:

biosimulators-daemon commented 3 years ago

Skips

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)

Required model formats and simulation algorithms for SED tasks:

biosimulators-daemon commented 3 years ago 
- After correcting your simulator, please edit the first block of this issue to re-initiate this validation.
- 
- The complete log of your validation/submission job, including further information about the failure, is available [here](https://github.com/biosimulators/Biosimulators/actions/runs/808416568). The results of the validation of your image will also be available shortly as a JSON file. A link to this file will be available from the "Artifacts" section at the bottom of [this page](https://github.com/biosimulators/Biosimulators/actions/runs/808416568).
biosimulators-daemon commented 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 here. The results of the validation of your tool will also be saved as a JSON file.A link to this file will be available from the "Artifacts" section at the bottom of this page.

biosimulators-daemon commented 3 years ago

The specifications of your simulator is valid!

biosimulators-daemon commented 3 years ago

Summary of tests

biosimulators-daemon commented 3 years ago

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (6.8 s)

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

Warnings:

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

  The command-line interface does not describe the following standard environment variables recognized by BioSimulators:
    - 'ALGORITHM_SUBSTITUTION_POLICY'

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

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

Log:

docker_image.HasBioContainersLabels (2.2 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-core/Tomida-EMBO-J-2003-NFAT-translocation (4.1 s)

Required model formats and simulation algorithms for SED tasks:

biosimulators-daemon commented 3 years ago

Skips

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)

Required model formats and simulation algorithms for SED tasks:

biosimulators-daemon commented 3 years ago

The image for your simulator is valid!

biosimulators-daemon commented 3 years ago

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

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