biosimulators-pyneuroml.json

{
  "id": "pyneuroml",
  "name": "pyNeuroML",
  "version": "0.5.20",
  "description": "Python package for reading, writing, simulating and analysing NeuroML2/LEMS models.",
  "urls": [
    {
      "type": "Home page",
      "url": "https://github.com/NeuroML/pyNeuroML"
    }
  ],
  "image": {
    "url": "ghcr.io/biosimulators/biosimulators_pyneuroml/pyneuroml:0.5.20",
    "format": {
      "namespace": "EDAM",
      "id": "format_3973",
      "version": null,
      "supportedFeatures": []
    },
    "operatingSystemType": "Linux"
  },
  "cli": {
    "packageRepository": "PyPI",
    "package": "biosimulators-pyneuroml",
    "command": "biosimulators-pyneuroml",
    "installationInstructions": "https://docs.biosimulators.org/Biosimulators_pyNeuroML/installation.html"
  },
  "pythonApi": {
    "package": "biosimulators-pyneuroml",
    "module": "biosimulators_pyneuroml.api.pyneuroml",
    "installationInstructions": "https://docs.biosimulators.org/Biosimulators_pyNeuroML/installation.html"
  },
  "authors": [
    {
      "firstName": "Padraig",
      "lastName": "Gleeson",
      "identifiers": [
        {
          "namespace": "orcid",
          "id": "0000-0001-5963-8576",
          "url": "https://orcid.org/0000-0001-5963-8576"
        }
      ]
    },
    {
      "firstName": "Richard",
      "middleName": "C.",
      "lastName": "Gerkin",
      "identifiers": [
        {
          "namespace": "orcid",
          "id": "0000-0002-2940-3378",
          "url": "https://orcid.org/0000-0002-2940-3378"
        }
      ]
    },
    {
      "firstName": "Ankur",
      "middleName": null,
      "lastName": "Sinha",
      "identifiers": [
        {
          "namespace": "orcid",
          "id": "0000-0001-7568-7167",
          "url": "https://orcid.org/0000-0001-7568-7167"
        }
      ]
    }
  ],
  "references": {
    "identifiers": [
      {
        "namespace": "pypi",
        "id": "pyNeuroML",
        "url": "https://pypi.org/project/pyNeuroML"
      },
      {
            "namespace": "pypi",
            "id": "biosimulators-pyneuroml",
            "url": "https://pypi.org/project/biosimulators-pyneuroml/"
          }
    ],
    "citations": [
      {
        "title": "LEMS: a language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2",
        "authors": "Robert C. Cannon, Padraig Gleeson, Sharon Crook, Gautham Ganapathy, Boris Marin, Eugenio Piasini & R. Angus Silver",
        "journal": "Frontiers in Neuroinformatics",
        "volume": "8",
        "pages": "79",
        "year": 2014,
        "identifiers": [
          {
            "namespace": "doi",
            "id": "10.3389/fninf.2014.00079",
            "url": "https://doi.org/10.3389/fninf.2014.00079"
          }
        ]
      },
      {
        "title": "NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail",
        "authors": "Padraig Gleeson, Sharon Crook, Robert C. Cannon, Michael L. Hines, Guy O. Billings, Matteo Farinella, Thomas M. Morse, Andrew P. Davison, Subhasis Ray, Upinder S. Bhalla, Simon R. Barnes, Yoana D. Dimitrova & R. Angus Silver",
        "journal": "PLoS Computational Biology",
        "volume": "6",
        "pages": "e1000815",
        "year": 2010,
        "identifiers": [
          {
            "namespace": "doi",
            "id": "10.1371/journal.pcbi.1000815",
            "url": "https://doi.org/10.1371/journal.pcbi.1000815"
          }
        ]
      }
    ]
  },
  "license": {
    "namespace": "SPDX",
    "id": "LGPL-3.0"
  },
  "algorithms": [
    {
      "id": "EULER",
      "name": "Euler forward method",
      "kisaoId": {
        "namespace": "KISAO",
        "id": "KISAO_0000030"
      },
      "modelingFrameworks": [
        {
          "namespace": "SBO",
          "id": "SBO_0000293"
        }
      ],
      "modelFormats": [
        {
          "namespace": "EDAM",
          "id": "format_9004",
          "version": null,
          "supportedFeatures": []
        },
        {
          "namespace": "EDAM",
          "id": "format_3971",
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          "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": null,
          "supportedFeatures": []
        }
      ],
      "simulationTypes": ["SedUniformTimeCourseSimulation"],
      "archiveFormats": [
        {
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          "version": null,
          "supportedFeatures": []
        }
      ],
      "citations": [],
      "parameters": [],
      "outputDimensions": [
        {
          "namespace": "SIO",
          "id": "SIO_000418"
        }
      ],
      "outputVariablePatterns": [],
      "availableSoftwareInterfaceTypes": [
        "library",
        "command-line application",
        "desktop application",
        "BioSimulators Docker image"
      ],
      "dependencies": [
        {
          "name": "libNeuroML",
          "version": null,
          "required": true,
          "freeNonCommercialLicense": true,
          "url": "https://github.com/NeuralEnsemble/libNeuroML"
        },
        {
          "name": "jNeuroML",
          "version": null,
          "required": true,
          "freeNonCommercialLicense": true,
          "url": "https://github.com/NeuroML/jNeuroML"
        },
        {
          "name": "pyLEMS",
          "version": null,
          "required": true,
          "freeNonCommercialLicense": true,
          "url": "https://github.com/LEMS/pylems"
        }
      ]
    },
    {
      "id": "RK4",
      "name": "4th order Runge-kutta method",
      "kisaoId": {
        "namespace": "KISAO",
        "id": "KISAO_0000032"
      },
      "modelingFrameworks": [
        {
          "namespace": "SBO",
          "id": "SBO_0000293"
        }
      ],
      "modelFormats": [
        {
          "namespace": "EDAM",
          "id": "format_9004",
          "version": null,
          "supportedFeatures": []
        },
        {
          "namespace": "EDAM",
          "id": "format_3971",
          "version": null,
          "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": null,
          "supportedFeatures": []
        }
      ],
      "simulationTypes": ["SedUniformTimeCourseSimulation"],
      "archiveFormats": [
        {
          "namespace": "EDAM",
          "id": "format_3686",
          "version": null,
          "supportedFeatures": []
        }
      ],
      "citations": [],
      "parameters": [],
      "outputDimensions": [
        {
          "namespace": "SIO",
          "id": "SIO_000418"
        }
      ],
      "outputVariablePatterns": [],
      "availableSoftwareInterfaceTypes": [
        "library",
        "command-line application",
        "desktop application",
        "BioSimulators Docker image"
      ],
      "dependencies": [
        {
          "name": "libNeuroML",
          "version": null,
          "required": true,
          "freeNonCommercialLicense": true,
          "url": "https://github.com/NeuralEnsemble/libNeuroML"
        },
        {
          "name": "jNeuroML",
          "version": null,
          "required": true,
          "freeNonCommercialLicense": true,
          "url": "https://github.com/NeuroML/jNeuroML"
        },
        {
          "name": "pyLEMS",
          "version": null,
          "required": true,
          "freeNonCommercialLicense": true,
          "url": "https://github.com/LEMS/pylems"
        }
      ]
    }
  ],
  "interfaceTypes": [
    "library",
    "command-line application",
    "desktop application",
    "BioSimulators Docker image"
  ],
  "supportedOperatingSystemTypes": [
    "platform-independent"
  ],
  "supportedProgrammingLanguages": [
    {
      "namespace": "Linguist",
      "id": "Python"
    }
  ],
  "funding": [],
  "biosimulators": {
    "specificationVersion": "1.0.0",
    "imageVersion": "1.0.0",
    "validated": false,
    "validationTests": null
  }
}