biosimulators-netpyne.json

{
  "id": "netpyne",
  "name": "NetPyNe",
  "version": "1.0.0.2",
  "description": "Python package to facilitate the development, simulation, parallelization, analysis, and optimization of biological neuronal networks using the NEURON simulator.",
  "urls": [
    {
      "type": "Home page",
      "url": "http://www.netpyne.org/"
    }
  ],
  "image": {
    "url": "ghcr.io/biosimulators/biosimulators_pyneuroml/netpyne:1.0.0.2",
    "format": {
      "namespace": "EDAM",
      "id": "format_3973",
      "version": null,
      "supportedFeatures": []
    },
    "operatingSystemType": "Linux"
  },
  "cli": {
    "packageRepository": "PyPI",
    "package": "biosimulators-pyneuroml",
    "command": "biosimulators-netpyne",
    "installationInstructions": "https://docs.biosimulators.org/Biosimulators_pyNeuroML/installation.html"
  },
  "pythonApi": {
    "package": "biosimulators-pyneuroml",
    "module": "biosimulators_pyneuroml.api.netpyne",
    "installationInstructions": "https://docs.biosimulators.org/Biosimulators_pyNeuroML/installation.html"
  },
  "authors": [
    {
      "firstName": "Salvador",
      "lastName": "Dura-Bernal",
      "identifiers": []
    },
    {
      "firstName": "Benjamin",
      "middleName": "A",
      "lastName": "Suter",
      "identifiers": []
    },
    {
      "firstName": "Padraig",
      "lastName": "Gleeson",
      "identifiers": []
    },
    {
      "firstName": "Matteo",
      "lastName": "Cantarelli",
      "identifiers": []
    },
    {
      "firstName": "Adrian",
      "lastName": "Quintana",
      "identifiers": []
    },
    {
      "firstName": "Facundo",
      "lastName": "Rodriguez",
      "identifiers": []
    },
    {
      "firstName": "David",
      "middleName": "J",
      "lastName": "Kedziora",
      "identifiers": []
    },
    {
      "firstName": "George",
      "middleName": "L",
      "lastName": "Chadderdon",
      "identifiers": []
    },
    {
      "firstName": "Cliff",
      "middleName": "C",
      "lastName": "Kerr",
      "identifiers": []
    },
    {
      "firstName": "Samuel",
      "middleName": "A",
      "lastName": "Neymotin",
      "identifiers": []
    },
    {
      "firstName": "Robert",
      "middleName": "A",
      "lastName": "McDougal",
      "identifiers": []
    },
    {
      "firstName": "Michael",
      "lastName": "Hines",
      "identifiers": []
    },
    {
      "firstName": "Gordon",
      "middleName": "MG",
      "lastName": "Shepherd",
      "identifiers": []
    },
    {
      "firstName": "William",
      "middleName": "W",
      "lastName": "Lytton",
      "identifiers": []
    }
  ],
  "references": {
    "identifiers": [
      {
        "namespace": "pypi",
        "id": "netpyne",
        "url": "https://pypi.org/project/netpyne"
      },
      {
            "namespace": "pypi",
            "id": "biosimulators-pyneuroml",
            "url": "https://pypi.org/project/biosimulators-pyneuroml/"
          }
    ],
    "citations": [
      {
        "title": "NetPyNE, a tool for data-driven multiscale modeling of brain circuits",
        "authors": "Salvador Dura-Bernal, Benjamin A Suter, Padraig Gleeson, Matteo Cantarelli, Adrian Quintana, Facundo Rodriguez, David J Kedziora, George L Chadderdon, Cliff C Kerr, Samuel A Neymotin, Robert A McDougal, Michael Hines, Gordon MG Shepherd & William W Lytton",
        "journal": "eLife",
        "volume": "8",
        "pages": "e44494",
        "year": 2019,
        "identifiers": [
          {
            "namespace": "doi",
            "id": "10.7554/eLife.44494.001",
            "url": "https://doi.org/10.7554/eLife.44494.001"
          }
        ]
      }
    ]
  },
  "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_9004",
          "version": null,
          "supportedFeatures": []
        },
        {
          "namespace": "EDAM",
          "id": "format_3971",
          "version": null,
          "supportedFeatures": []
        },
        {
          "namespace": "EDAM",
          "id": "format_9005",
          "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": [
        {
          "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": [],
      "outputDimensions": [
        {
          "namespace": "SIO",
          "id": "SIO_000418"
        }
      ],
      "outputVariablePatterns": [],
      "availableSoftwareInterfaceTypes": [
        "library",
        "web application",
        "BioSimulators Docker image"
      ],
      "dependencies": [
        {
          "name": "SUNDIALS",
          "version": null,
          "required": true,
          "freeNonCommercialLicense": true,
          "url": "https://computing.llnl.gov/projects/sundials"
        },
        {
          "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"
        },
        {
          "name": "pyNeuroML",
          "version": null,
          "required": true,
          "freeNonCommercialLicense": true,
          "url": "https://github.com/NeuroML/pyNeuroML"
        }
      ]
    }
  ],
  "interfaceTypes": [
    "library",
    "web 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
  }
}