biosimulators.json

{
  "id": "mysimulator",
  "name": "My Simulator",
  "version": "1.0.0",
  "description": "Description of My Simulator.",
  "urls": [{
    "type": "Home page",
    "url": "http://mysimulator.org/"
  }],
  "image": {
    "url": "ghcr.io/org/repo:1.0.0",
    "digest": "sha256:aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa",
    "format": {
      "namespace": "EDAM",
      "id": "format_3973",
      "version": "1.2.0",
      "supportedFeatures": []
    },
    "operatingSystemType": "Linux"
  },
  "cli": {
    "packageRepository": "PyPI",
    "package": "mysimulator",
    "command": "mysimulator",
    "installationInstructions": "https://mysimulator.org/installation.html"
  },
  "pythonApi": {
    "package": "mysimulator",
    "module": "mysimulator.biosimulators",
    "installationInstructions": "https://mysimulator.org/installation.html"
  },
  "authors": [{
    "firstName": "John",
    "lastName": "Doe",
    "identifiers": [{
      "namespace": "orcid",
      "id": "XXXX-XXXX-XXXX-XXXX",
      "url": "https://orcid.org/XXXX-XXXX-XXXX-XXXX"
    }]
  }],
  "references": {
    "identifiers": [{
      "namespace": "pypi",
      "id": "mysimulator",
      "url": "https://pypi.org/project/mysimulator/"
    }],
    "citations": [{
      "title": "My Simulator: a great simulator",
      "authors": "John Doe",
      "journal": "Journal",
      "volume": "1",
      "issue": "1",
      "pages": "1-2",
      "year": 2021,
      "identifiers": [{
        "namespace": "doi",
        "id": "10.XXXX/XXXX",
        "url": "https://doi.org/10.XXXX/XXXX"
      }]
    }]
  },
  "license": {
    "namespace": "SPDX",
    "id": "MIT"
  },
  "algorithms": [{
    "id": "cvode",
    "name": "C-language Variable-coefficient Ordinary Differential Equation solver",
    "kisaoId": {
      "namespace": "KISAO",
      "id": "KISAO_0000019"
    },
    "modelingFrameworks": [{
      "namespace": "SBO",
      "id": "SBO_0000293"
    }],
    "modelFormats": [{
      "namespace": "EDAM",
      "id": "format_2585",
      "version": "L3V2",
      "supportedFeatures": []
    }],
    "modelChangePatterns": [
        {
          "name": "Change component attributes",
          "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"],
          "target": {
            "value": "//*/@*",
            "grammar": "XPath"
          }
        },
        {
          "name": "Add components",
          "types": ["SedAddXmlModelChange"],
          "target": {
            "value": "//*",
            "grammar": "XPath"
          }
        },
        {
          "name": "Remove components",
          "types": ["SedRemoveXmlModelChange"],
          "target": {
            "value": "//*",
            "grammar": "XPath"
          }
        },
        {
          "name": "Change components",
          "types": ["SedChangeXmlModelChange"],
          "target": {
            "value": "//*",
            "grammar": "XPath"
          }
        }
      ],
    "simulationFormats": [{
      "namespace": "EDAM",
      "id": "format_3685",
      "version": "L1V3",
      "supportedFeatures": []
    }],
    "simulationTypes": ["SedUniformTimeCourseSimulation"],
    "archiveFormats": [{
      "namespace": "EDAM",
      "id": "format_3686",
      "version": "1",
      "supportedFeatures": []
    }],
    "citations": [{
      "title": "CVODE, a stiff/nonstiff ODE solver in C",
      "authors": "Scott D. Cohen, Alan C. Hindmarsh & Paul F. Dubois",
      "journal": "Computers in Physics",
      "volume": "10",
      "issue": "2",
      "pages": "138-143",
      "year": 1996,
      "identifiers": [{
        "namespace": "doi",
        "id": "10.1063/1.4822377",
        "url": "https://doi.org/10.1063/1.4822377"
      }]
    }],
    "parameters": [{
      "kisaoId": {
        "namespace": "KISAO",
        "id": "KISAO_0000209"
      },
      "id": "relative_tolerance",
      "name": "Relative tolerance",
      "type": "float",
      "value": "0.000001",
      "recommendedRange": null,
      "availableSoftwareInterfaceTypes": ["library", "command-line application", "desktop application", "BioSimulators Docker image"]
    }],
    "outputDimensions": [{
      "namespace": "SIO",
      "id": "SIO_000418"
    }],
    "outputVariablePatterns": [
      {
          "name": "time",
          "symbol": {
            "value": "time",
            "namespace": "urn:sedml:symbol"
          }
      },
      {
        "name": "species concentrations",
        "target": {"value": "/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species", "grammar": "XPath"}
      },
      {
        "name": "parameter values",
        "target": {"value": "/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter", "grammar": "XPath"}
      }
    ],
    "availableSoftwareInterfaceTypes": ["library", "command-line application", "desktop application", "BioSimulators Docker image"],
    "dependencies": [{
      "name": "SUNDIALS",
      "version": null,
      "required": true,
      "freeNonCommercialLicense": true,
      "url": "https://computing.llnl.gov/projects/sundials"
    }]
  }],
  "interfaceTypes": ["library", "command-line application", "desktop application", "BioSimulators Docker image"],
  "supportedOperatingSystemTypes": ["platform-independent"],
  "supportedProgrammingLanguages": [{
    "namespace": "Linguist",
    "id": "Python"
  }],
  "funding": [{
    "funder": {
      "namespace": "FunderRegistry",
      "id": "100000057"
    },
    "grant": "R01-GMXXXXXX",
    "url": "https://grantome.com/grant/NIH/R01-GMXXXXXX"
  }],
  "biosimulators": {
    "specificationVersion": "1.0.0",
    "imageVersion": "1.0.0",
    "validated": false,
    "validationTests": null
  }
}