Submit Smoldyn 2.73

[AlexPatrie]

Simulation tool

---

id: smoldyn version: "2.73" specificationsUrl: https://github.com/ssandrews/Smoldyn/blob/master/biosimulators.json specificationsPatch: version: "2.73" validateImage: true commitSimulator: true

Support for BioSimulators' conventions

• [X] The simulation tool is provided as a Docker image
• [X] The ENTRYPOINT of the image is a BioSimulators-compliant command-line interface
• [X] This command-line interface supports the COMBINE/OMEX archive format
• [X] This command-line interface supports the Simulation Experiment Description Markup Language (SED-ML) format
• [X] This command-line interface supports the Hierarchical Data Format (HDF5)
• [X] The capabilities of the tool are described using BioSimulators' format
• [X] The modeling frameworks supported by the tool are described using Systems Biology Ontology (SBO) terms
• [X] The algorithms supported by the tool are described using Kinetic Simulation Algorithm Ontology (KiSAO) ontology terms
• [X] The model formats supported by the tool are described using EMBRACE Data and Methods (EDAM) ontology terms
• [X] The licenses supported by the tool are described using Software Package Data Exchange (SPDX) identifiers
• [X] The source code for the simulation tool is publicly available
• [X] The simulation tool is available through a software repository such as CRAN or PyPI
• [X] The simulation tool is registered with bio.tools
• [X] The Docker image provides Open Containers Initiative-compliant metadata
• [X] The Docker image provides BioContainers-compliant metadata
• [X] The Docker image is registered with BioContainers

[biosimulators-daemon]

The validation/submission of your simulator failed.

- Simulator submissions should only use the keys "id", "version", "specificationsUrl", "specificationsPatch", validateImage", and "commitSimulator". The following keys are invalid:
-   - digest
-   - image
-   - url

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 @AlexPatrie 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 validation/submission of your simulator failed.

- The simulator specifications from `https://github.com/ssandrews/Smoldyn/blob/master/biosimulators.json` are invalid. The specifications of simulation tools must adhere to BioSimulators' schema. BioSimulators' schema is available in both JSON Schema and Open API Specifications formats. Documentation is available at https://api.biosimulators.org/.
- 
-   - Bad Request (400):
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-       
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-               isEmpty: false,
-               createdAt: '2019-02-22T23:06:41.000Z',
-               ownerAvatar: 'https://avatars.githubusercontent.com/u/33039297?v=4',
-               public: true,
-               private: false,
-               isOrgOwned: false
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-             symbolsExpanded: false,
-             treeExpanded: true,
-             refInfo: {
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-               canEdit: false,
-               refType: 'branch',
-               currentOid: 'ca9d2c92e1f59b795c560ed65a6b5b84e943899f'
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-             path: 'biosimulators.json',
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-                 '  "urls": [{',
-                 '      "title": null,',
-                 '      "type": "Home page",',
-                 '      "url": "http://www.smoldyn.org/"',
-                 '    },',
-                 '    {',
-                 '      "title": null,',
-                 '      "type": "Examples",',
-                 '      "url": "http://www.smoldyn.org/archive.html"',
-                 '    },',
-                 '    {',
-                 '      "title": null,',
-                 '      "type": "Installation instructions",',
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-                 '      "firstName": "Steven",',
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-       
-         Error(s):
-           - whitelistValidation: property payload should not exist
-       
-       Property 'title' is invalid.
-       
-         Value:
-           'Smoldyn/biosimulators.json at master · ssandrews/Smoldyn'
-       
-         Error(s):
-           - whitelistValidation: property title should not exist
-       
-       Property 'id' is invalid.
-       
-         Value:
-           undefined
-       
-         Error(s):
-           - isNotEmpty: id should not be empty
-           - isString: id must be a string
-       
-       Property 'name' is invalid.
-       
-         Value:
-           undefined
-       
-         Error(s):
-           - isNotEmpty: name should not be empty
-           - isString: name must be a string
-       
-       Property 'version' is invalid.
-       
-         Value:
-           undefined
-       
-         Error(s):
-           - isNotEmpty: version should not be empty
-           - isString: version must be a string
-       
-       Property 'description' is invalid.
-       
-         Value:
-           undefined
-       
-         Error(s):
-           - isNotEmpty: description should not be empty
-           - isString: description must be a string
-       
-       Property 'urls' is invalid.
-       
-         Value:
-           undefined
-       
-         Error(s):
-           - isArray: urls must be an array
-       
-       Property 'algorithms' is invalid.
-       
-         Value:
-           undefined
-       
-         Error(s):
-           - arrayUnique: Two or more algorithms have the same KiSAO id. Each algorithm must have a unique KiSAO id.
-       
-       Property 'interfaceTypes' is invalid.
-       
-         Value:
-           undefined
-       
-         Error(s):
-           - isEnum: each value in interfaceTypes must be one of the following values: library, command-line application, desktop application, mobile application, web service, web application, BioSimulators Docker image
-       
-       Property 'supportedOperatingSystemTypes' is invalid.
-       
-         Value:
-           undefined
-       
-         Error(s):
-           - isEnum: each value in supportedOperatingSystemTypes must be one of the following values: Linux, Mac OS, Windows, Unix, platform-independent

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).