biosimulators.json

{
  "id": "xpp",
  "name": "XPP",
  "version": "8.0",
  "description": "Tool for solving differential, difference, delay, functional, and stochastic equations and boundary value problems.",
  "urls": [{
      "type": "Home page",
      "url": "http://www.math.pitt.edu/~bard/xpp/xpp.html"
    },
    {
      "type": "Source repository",
      "url": "https://github.com/Ermentrout/xppaut"
    },
    {
      "type": "License",
      "url": "https://github.com/Ermentrout/xppaut/blob/master/LICENSE"
    }
  ],
  "image": {
    "url": "ghcr.io/biosimulators/biosimulators_xpp/xpp:8.0",
    "format": {
      "namespace": "EDAM",
      "id": "format_3973",
      "version": null,
      "supportedFeatures": []
    },
    "operatingSystemType": "Linux"
  },
  "cli": {
    "packageRepository": "PyPI",
    "package": "biosimulators-xpp",
    "command": "biosimulators-xpp",
    "installationInstructions": "https://docs.biosimulators.org/Biosimulators_XPP/installation.html"
  },
  "pythonApi": {
    "package": "biosimulators-xpp",
    "module": "biosimulators_xpp",
      "installationInstructions": "https://docs.biosimulators.org/Biosimulators_XPP/installation.html"
  },
  "authors": [{
    "firstName": "G. Bard",
    "lastName": "Ermentrout",
    "identifiers": [{
      "namespace": "orcid",
      "id": "0000-0002-5854-0654",
      "url": "https://orcid.org/0000-0002-5854-0654"
    }]
  }],
  "references": {
    "identifiers": [{
            "namespace": "pypi",
            "id": "biosimulators-xpp",
            "url": "https://pypi.org/project/biosimulators-xpp/"
          }],
    "citations": [{
        "title": "XPPAUT",
        "authors": "Bard Ermentrout",
        "journal": "Computational Systems Neurobiology",
        "year": 2012,
        "pages": "519-531",
        "identifiers": [{
          "namespace": "doi",
          "id": "10.1007/978-94-007-3858-4_17",
          "url": "https://doi.org/10.1007/978-94-007-3858-4_17"
        }]
      },
      {
        "title": "Simulating, analyzing, and animating dynamical systems: a guide to XPPAUT for researchers and students",
        "authors": "Bard Ermentrout",
        "journal": "Society for Industrial and Applied Mathematics",
        "year": 2002,
        "identifiers": [{
          "namespace": "doi",
          "id": "10.1137/1.9780898718195",
          "url": "https://doi.org/10.1137/1.9780898718195"
        }]
      }
    ]
  },
  "license": {
    "namespace": "SPDX",
    "id": "GPL-2.0-only"
  },
  "algorithms": [{
      "id": "discrete",
      "name": "Gillepie's method",
      "kisaoId": {
        "namespace": "KISAO",
        "id": "KISAO_0000029"
      },
      "modelingFrameworks": [{
        "namespace": "SBO",
        "id": "SBO_0000295"
      }],
      "modelFormats": [{
        "namespace": "EDAM",
        "id": "format_9010",
        "version": null,
        "supportedFeatures": []
      }],      
      "modelChangePatterns": [
        {
          "name": "Change parameter values or variable initial conditions",
          "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"],
          "target": {
            "value": "{ parameter or variable name }",
            "grammar": "XPP"
          }
        }     
      ],
      "simulationFormats": [{
        "namespace": "EDAM",
        "id": "format_3685",
        "version": "L1V3",
        "supportedFeatures": []
      }],
      "simulationTypes": ["SedUniformTimeCourseSimulation"],
      "archiveFormats": [{
        "namespace": "EDAM",
        "id": "format_3686",
        "version": null,
        "supportedFeatures": []
      }],
      "parameters": [{
        "kisaoId": {
          "namespace": "KISAO",
          "id": "KISAO_0000488"
        },
        "id": "seed",
        "name": "Random number generator seed",
        "type": "integer",
        "value": null,
        "recommendedRange": null,
        "availableSoftwareInterfaceTypes": [
          "desktop application",
          "library",
          "command-line application",
          "BioSimulators Docker image"
        ]
      }],
      "outputDimensions": [{
        "namespace": "SIO",
        "id": "SIO_000418"
      }],
      "outputVariablePatterns": [
        {
          "name": "variable of integration (time)",
          "symbol": {
                    "value": "time",
                    "namespace": "urn:sedml:symbol"
                  }
        },
        {
          "name": "variables",
          "target": {"value": "variable name (case insensitive)", "grammar": "XPP"}
        },
        {
          "name": "auxiliary variables",
          "target": {"value": "auxiliary variable name (case insensitive)", "grammar": "XPP"}
        }
      ],
      "availableSoftwareInterfaceTypes": [
        "desktop application",
        "library",
        "command-line application",
        "BioSimulators Docker image"
      ],
      "dependencies": null,
      "citations": [{
        "title": "Exact stochastic simulation of coupled chemical reactions",
        "authors": "Daniel T. Gillespie",
        "journal": "Journal of Physical Chemistry",
        "volume": "81",
        "issue": "25",
        "pages": "2340-2361",
        "year": 1977,
        "identifiers": [{
          "namespace": "doi",
          "id": "10.1021/j100540a008",
          "url": "https://doi.org/10.1021/j100540a008"
        }]
      }]
    },
    {
      "id": "euler",
      "name": "Forward Euler one step method",
      "kisaoId": {
        "namespace": "KISAO",
        "id": "KISAO_0000030"
      },
      "modelingFrameworks": [{
        "namespace": "SBO",
        "id": "SBO_0000293"
      }],
      "modelFormats": [{
        "namespace": "EDAM",
        "id": "format_9010",
        "version": null,
        "supportedFeatures": []
      }],
      "modelChangePatterns": [
        {
          "name": "Change parameter values or variable initial conditions",
          "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"],
          "target": {
            "value": "{ parameter or variable name }",
            "grammar": "XPP"
          }
        }    
      ],
      "simulationFormats": [{
        "namespace": "EDAM",
        "id": "format_3685",
        "version": "L1V3",
        "supportedFeatures": []
      }],
      "simulationTypes": ["SedUniformTimeCourseSimulation"],
      "archiveFormats": [{
        "namespace": "EDAM",
        "id": "format_3686",
        "version": null,
        "supportedFeatures": []
      }],
      "parameters": [],
      "outputDimensions": [{
        "namespace": "SIO",
        "id": "SIO_000418"
      }],
      "outputVariablePatterns": [
        {
          "name": "variable of integration (time)",
          "symbol": {
                    "value": "time",
                    "namespace": "urn:sedml:symbol"
                  }
        },
        {
          "name": "variables",
          "target": {"value": "variable name (case insensitive)", "grammar": "XPP"}
        },
        {
          "name": "auxiliary variables",
          "target": {"value": "auxiliary variable name (case insensitive)", "grammar": "XPP"}
        }
      ],
      "availableSoftwareInterfaceTypes": [
        "desktop application",
        "library",
        "command-line application",
        "BioSimulators Docker image"
      ],
      "dependencies": null,
      "citations": []
    },
    {
      "id": "backeul",
      "name": "Backward Euler method",
      "kisaoId": {
        "namespace": "KISAO",
        "id": "KISAO_0000031"
      },
      "modelingFrameworks": [{
        "namespace": "SBO",
        "id": "SBO_0000293"
      }],
      "modelFormats": [{
        "namespace": "EDAM",
        "id": "format_9010",
        "version": null,
        "supportedFeatures": []
      }],
      "modelChangePatterns": [
        {
          "name": "Change parameter values or variable initial conditions",
          "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"],
          "target": {
            "value": "{ parameter or variable name }",
            "grammar": "XPP"
          }
        }     
      ],
      "simulationFormats": [{
        "namespace": "EDAM",
        "id": "format_3685",
        "version": "L1V3",
        "supportedFeatures": []
      }],
      "simulationTypes": ["SedUniformTimeCourseSimulation"],
      "archiveFormats": [{
        "namespace": "EDAM",
        "id": "format_3686",
        "version": null,
        "supportedFeatures": []
      }],
      "parameters": [{
          "kisaoId": {
            "namespace": "KISAO",
            "id": "KISAO_0000597"
          },
          "id": null,
          "name": "tolerance",
          "type": "float",
          "value": "1e-7",
          "recommendedRange": null,
          "availableSoftwareInterfaceTypes": [
            "desktop application"
          ]
        },
        {
          "kisaoId": {
            "namespace": "KISAO",
            "id": "KISAO_0000486"
          },
          "id": null,
          "name": "Maximum number of iterates for each step",
          "type": "integer",
          "value": "10",
          "recommendedRange": null,
          "availableSoftwareInterfaceTypes": [
            "desktop application"
          ]
        }
      ],
      "outputDimensions": [{
        "namespace": "SIO",
        "id": "SIO_000418"
      }],
      "outputVariablePatterns": [
        {
          "name": "variable of integration (time)",
          "symbol": {
                    "value": "time",
                    "namespace": "urn:sedml:symbol"
                  }
        },
        {
          "name": "variables",
          "target": {"value": "variable name (case insensitive)", "grammar": "XPP"}
        },
        {
          "name": "auxiliary variables",
          "target": {"value": "auxiliary variable name (case insensitive)", "grammar": "XPP"}
        }
      ],
      "availableSoftwareInterfaceTypes": [
        "desktop application",
        "library",
        "command-line application",
        "BioSimulators Docker image"
      ],
      "dependencies": null,
      "citations": []
    },
    {
      "id": "adams",
      "name": "Adams-Bashforth fourth order predictor-corrector method",
      "kisaoId": {
        "namespace": "KISAO",
        "id": "KISAO_0000279"
      },
      "modelingFrameworks": [{
        "namespace": "SBO",
        "id": "SBO_0000293"
      }],
      "modelFormats": [{
        "namespace": "EDAM",
        "id": "format_9010",
        "version": null,
        "supportedFeatures": []
      }],
      "modelChangePatterns": [
        {
          "name": "Change parameter values or variable initial conditions",
          "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"],
          "target": {
            "value": "{ parameter or variable name }",
            "grammar": "XPP"
          }
        }     
      ],
      "simulationFormats": [{
        "namespace": "EDAM",
        "id": "format_3685",
        "version": "L1V3",
        "supportedFeatures": []
      }],
      "simulationTypes": ["SedUniformTimeCourseSimulation"],
      "archiveFormats": [{
        "namespace": "EDAM",
        "id": "format_3686",
        "version": null,
        "supportedFeatures": []
      }],
      "parameters": [],
      "outputDimensions": [{
        "namespace": "SIO",
        "id": "SIO_000418"
      }],
      "outputVariablePatterns": [
        {
          "name": "variable of integration (time)",
          "symbol": {
                    "value": "time",
                    "namespace": "urn:sedml:symbol"
                  }
        },
        {
          "name": "variables",
          "target": {"value": "variable name (case insensitive)", "grammar": "XPP"}
        },
        {
          "name": "auxiliary variables",
          "target": {"value": "auxiliary variable name (case insensitive)", "grammar": "XPP"}
        }
      ],
      "availableSoftwareInterfaceTypes": [
        "desktop application",
        "library",
        "command-line application",
        "BioSimulators Docker image"
      ],
      "dependencies": null,
      "citations": []
    },
    {
      "id": "gear",
      "name": "Gear method",
      "kisaoId": {
        "namespace": "KISAO",
        "id": "KISAO_0000288"
      },
      "modelingFrameworks": [{
        "namespace": "SBO",
        "id": "SBO_0000293"
      }],
      "modelFormats": [{
        "namespace": "EDAM",
        "id": "format_9010",
        "version": null,
        "supportedFeatures": []
      }],
      "modelChangePatterns": [
        {
          "name": "Change parameter values or variable initial conditions",
          "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"],
          "target": {
            "value": "{ parameter or variable name }",
            "grammar": "XPP"
          }
        }     
      ],
      "simulationFormats": [{
        "namespace": "EDAM",
        "id": "format_3685",
        "version": "L1V3",
        "supportedFeatures": []
      }],
      "simulationTypes": ["SedUniformTimeCourseSimulation"],
      "archiveFormats": [{
        "namespace": "EDAM",
        "id": "format_3686",
        "version": null,
        "supportedFeatures": []
      }],
      "parameters": [{
          "kisaoId": {
            "namespace": "KISAO",
            "id": "KISAO_0000485"
          },
          "id": "dtmin",
          "name": "minimum allowable timestep",
          "type": "float",
          "value": "1e-12",
          "recommendedRange": null,
          "availableSoftwareInterfaceTypes": [
            "desktop application",
            "library",
            "command-line application",
            "BioSimulators Docker image"
          ]
        },
        {
          "kisaoId": {
            "namespace": "KISAO",
            "id": "KISAO_0000467"
          },
          "id": "dtmax",
          "name": "maximum allowable timestep",
          "type": "float",
          "value": "1",
          "recommendedRange": null,
          "availableSoftwareInterfaceTypes": [
            "desktop application",
            "library",
            "command-line application",
            "BioSimulators Docker image"
          ]
        },
        {
          "kisaoId": {
            "namespace": "KISAO",
            "id": "KISAO_0000597"
          },
          "id": "toler",
          "name": "tolerance",
          "type": "float",
          "value": "0.001",
          "recommendedRange": null,
          "availableSoftwareInterfaceTypes": [
            "desktop application",
            "library",
            "command-line application",
            "BioSimulators Docker image"
          ]
        }
      ],
      "outputDimensions": [{
        "namespace": "SIO",
        "id": "SIO_000418"
      }],
      "outputVariablePatterns": [
        {
          "name": "variable of integration (time)",
          "symbol": {
                    "value": "time",
                    "namespace": "urn:sedml:symbol"
                  }
        },
        {
          "name": "variables",
          "target": {"value": "variable name (case insensitive)", "grammar": "XPP"}
        },
        {
          "name": "auxiliary variables",
          "target": {"value": "auxiliary variable name (case insensitive)", "grammar": "XPP"}
        }
      ],
      "availableSoftwareInterfaceTypes": [
        "desktop application",
        "library",
        "command-line application",
        "BioSimulators Docker image"
      ],
      "dependencies": null,
      "citations": []
    },
    {
      "id": "5dp",
      "name": "Dormand-Prince method",
      "kisaoId": {
        "namespace": "KISAO",
        "id": "KISAO_0000087"
      },
      "modelingFrameworks": [{
        "namespace": "SBO",
        "id": "SBO_0000293"
      }],
      "modelFormats": [{
        "namespace": "EDAM",
        "id": "format_9010",
        "version": null,
        "supportedFeatures": []
      }],
      "modelChangePatterns": [
        {
          "name": "Change parameter values or variable initial conditions",
          "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"],
          "target": {
            "value": "{ parameter or variable name }",
            "grammar": "XPP"
          }
        }     
      ],
      "simulationFormats": [{
        "namespace": "EDAM",
        "id": "format_3685",
        "version": "L1V3",
        "supportedFeatures": []
      }],
      "simulationTypes": ["SedUniformTimeCourseSimulation"],
      "archiveFormats": [{
        "namespace": "EDAM",
        "id": "format_3686",
        "version": null,
        "supportedFeatures": []
      }],
      "parameters": [{
          "kisaoId": {
            "namespace": "KISAO",
            "id": "KISAO_0000209"
          },
          "id": "toler",
          "name": "relative tolerance",
          "type": "float",
          "value": "0.001",
          "recommendedRange": null,
          "availableSoftwareInterfaceTypes": [
            "desktop application",
            "library",
            "command-line application",
            "BioSimulators Docker image"
          ]
        },
        {
          "kisaoId": {
            "namespace": "KISAO",
            "id": "KISAO_0000211"
          },
          "id": "atoler",
          "name": "absolute tolerance",
          "type": "float",
          "value": "0.001",
          "recommendedRange": null,
          "availableSoftwareInterfaceTypes": [
            "desktop application",
            "library",
            "command-line application",
            "BioSimulators Docker image"
          ]
        }
      ],
      "outputDimensions": [{
        "namespace": "SIO",
        "id": "SIO_000418"
      }],
      "outputVariablePatterns": [
        {
          "name": "variable of integration (time)",
          "symbol": {
                    "value": "time",
                    "namespace": "urn:sedml:symbol"
                  }
        },
        {
          "name": "variables",
          "target": {"value": "variable name (case insensitive)", "grammar": "XPP"}
        },
        {
          "name": "auxiliary variables",
          "target": {"value": "auxiliary variable name (case insensitive)", "grammar": "XPP"}
        }
      ],
      "availableSoftwareInterfaceTypes": [
        "desktop application",
        "library",
        "command-line application",
        "BioSimulators Docker image"
      ],
      "dependencies": null,
      "citations": []
    },
    {
      "id": "83dp",
      "name": "Dormand-Prince 8(5,3) method",
      "kisaoId": {
        "namespace": "KISAO",
        "id": "KISAO_0000436"
      },
      "modelingFrameworks": [{
        "namespace": "SBO",
        "id": "SBO_0000293"
      }],
      "modelFormats": [{
        "namespace": "EDAM",
        "id": "format_9010",
        "version": null,
        "supportedFeatures": []
      }],
      "modelChangePatterns": [
        {
          "name": "Change parameter values or variable initial conditions",
          "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"],
          "target": {
            "value": "{ parameter or variable name }",
            "grammar": "XPP"
          }
        }     
      ],
      "simulationFormats": [{
        "namespace": "EDAM",
        "id": "format_3685",
        "version": "L1V3",
        "supportedFeatures": []
      }],
      "simulationTypes": ["SedUniformTimeCourseSimulation"],
      "archiveFormats": [{
        "namespace": "EDAM",
        "id": "format_3686",
        "version": null,
        "supportedFeatures": []
      }],
      "parameters": [{
          "kisaoId": {
            "namespace": "KISAO",
            "id": "KISAO_0000209"
          },
          "id": "toler",
          "name": "relative tolerance",
          "type": "float",
          "value": "0.001",
          "recommendedRange": null,
          "availableSoftwareInterfaceTypes": [
            "desktop application",
            "library",
            "command-line application",
            "BioSimulators Docker image"
          ]
        },
        {
          "kisaoId": {
            "namespace": "KISAO",
            "id": "KISAO_0000211"
          },
          "id": "atoler",
          "name": "absolute tolerance",
          "type": "float",
          "value": "0.001",
          "recommendedRange": null,
          "availableSoftwareInterfaceTypes": [
            "desktop application",
            "library",
            "command-line application",
            "BioSimulators Docker image"
          ]
        }
      ],
      "outputDimensions": [{
        "namespace": "SIO",
        "id": "SIO_000418"
      }],
      "outputVariablePatterns": [
        {
          "name": "variable of integration (time)",
          "symbol": {
                    "value": "time",
                    "namespace": "urn:sedml:symbol"
                  }
        },
        {
          "name": "variables",
          "target": {"value": "variable name (case insensitive)", "grammar": "XPP"}
        },
        {
          "name": "auxiliary variables",
          "target": {"value": "auxiliary variable name (case insensitive)", "grammar": "XPP"}
        }
      ],
      "availableSoftwareInterfaceTypes": [
        "desktop application",
        "library",
        "command-line application",
        "BioSimulators Docker image"
      ],
      "dependencies": null,
      "citations": []
    },
    {
      "id": "2rb",
      "name": "Two step Rosenbrock method",
      "kisaoId": {
        "namespace": "KISAO",
        "id": "KISAO_0000033"
      },
      "modelingFrameworks": [{
        "namespace": "SBO",
        "id": "SBO_0000293"
      }],
      "modelFormats": [{
        "namespace": "EDAM",
        "id": "format_9010",
        "version": null,
        "supportedFeatures": []
      }],
      "modelChangePatterns": [
        {
          "name": "Change parameter values or variable initial conditions",
          "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"],
          "target": {
            "value": "{ parameter or variable name }",
            "grammar": "XPP"
          }
        }     
      ],
      "simulationFormats": [{
        "namespace": "EDAM",
        "id": "format_3685",
        "version": "L1V3",
        "supportedFeatures": []
      }],
      "simulationTypes": ["SedUniformTimeCourseSimulation"],
      "archiveFormats": [{
        "namespace": "EDAM",
        "id": "format_3686",
        "version": null,
        "supportedFeatures": []
      }],
      "parameters": [{
          "kisaoId": {
            "namespace": "KISAO",
            "id": "KISAO_0000209"
          },
          "id": "toler",
          "name": "relative tolerance",
          "type": "float",
          "value": "0.001",
          "recommendedRange": null,
          "availableSoftwareInterfaceTypes": [
            "desktop application",
            "library",
            "command-line application",
            "BioSimulators Docker image"
          ]
        },
        {
          "kisaoId": {
            "namespace": "KISAO",
            "id": "KISAO_0000211"
          },
          "id": "atoler",
          "name": "absolute tolerance",
          "type": "float",
          "value": "0.001",
          "recommendedRange": null,
          "availableSoftwareInterfaceTypes": [
            "desktop application",
            "library",
            "command-line application",
            "BioSimulators Docker image"
          ]
        },
        {
          "kisaoId": {
            "namespace": "KISAO",
            "id": "KISAO_0000480"
          },
          "id": "bandlo",
          "name": "lower half-bandwidth",
          "type": "integer",
          "value": "0",
          "recommendedRange": null,
          "availableSoftwareInterfaceTypes": [
            "desktop application",
            "library",
            "command-line application",
            "BioSimulators Docker image"
          ]
        },
        {
          "kisaoId": {
            "namespace": "KISAO",
            "id": "KISAO_0000479"
          },
          "id": "bandup",
          "name": "upper half-bandwidth",
          "type": "integer",
          "value": "0",
          "recommendedRange": null,
          "availableSoftwareInterfaceTypes": [
            "desktop application",
            "library",
            "command-line application",
            "BioSimulators Docker image"
          ]
        }
      ],
      "outputDimensions": [{
        "namespace": "SIO",
        "id": "SIO_000418"
      }],
      "outputVariablePatterns": [
        {
          "name": "variable of integration (time)",
          "symbol": {
                    "value": "time",
                    "namespace": "urn:sedml:symbol"
                  }
        },
        {
          "name": "variables",
          "target": {"value": "variable name (case insensitive)", "grammar": "XPP"}
        },
        {
          "name": "auxiliary variables",
          "target": {"value": "auxiliary variable name (case insensitive)", "grammar": "XPP"}
        }
      ],
      "availableSoftwareInterfaceTypes": [
        "desktop application",
        "library",
        "command-line application",
        "BioSimulators Docker image"
      ],
      "dependencies": null,
      "citations": []
    },
    {
      "id": "cvode",
      "name": "CVODE",
      "kisaoId": {
        "namespace": "KISAO",
        "id": "KISAO_0000019"
      },
      "modelingFrameworks": [{
        "namespace": "SBO",
        "id": "SBO_0000293"
      }],
      "modelFormats": [{
        "namespace": "EDAM",
        "id": "format_9010",
        "version": null,
        "supportedFeatures": []
      }],
      "modelChangePatterns": [
        {
          "name": "Change parameter values or variable initial conditions",
          "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"],
          "target": {
            "value": "{ parameter or variable name }",
            "grammar": "XPP"
          }
        }     
      ],
      "simulationFormats": [{
        "namespace": "EDAM",
        "id": "format_3685",
        "version": "L1V3",
        "supportedFeatures": []
      }],
      "simulationTypes": ["SedUniformTimeCourseSimulation"],
      "archiveFormats": [{
        "namespace": "EDAM",
        "id": "format_3686",
        "version": null,
        "supportedFeatures": []
      }],
      "parameters": [{
          "kisaoId": {
            "namespace": "KISAO",
            "id": "KISAO_0000209"
          },
          "id": "toler",
          "name": "relative tolerance",
          "type": "float",
          "value": "0.001",
          "recommendedRange": null,
          "availableSoftwareInterfaceTypes": [
            "desktop application",
            "library",
            "command-line application",
            "BioSimulators Docker image"
          ]
        },
        {
          "kisaoId": {
            "namespace": "KISAO",
            "id": "KISAO_0000211"
          },
          "id": "atoler",
          "name": "absolute tolerance",
          "type": "float",
          "value": "0.001",
          "recommendedRange": null,
          "availableSoftwareInterfaceTypes": [
            "desktop application",
            "library",
            "command-line application",
            "BioSimulators Docker image"
          ]
        },
        {
          "kisaoId": {
            "namespace": "KISAO",
            "id": "KISAO_0000480"
          },
          "id": "bandlo",
          "name": "lower half-bandwidth",
          "type": "integer",
          "value": "0",
          "recommendedRange": null,
          "availableSoftwareInterfaceTypes": [
            "desktop application",
            "library",
            "command-line application",
            "BioSimulators Docker image"
          ]
        },
        {
          "kisaoId": {
            "namespace": "KISAO",
            "id": "KISAO_0000479"
          },
          "id": "bandup",
          "name": "upper half-bandwidth",
          "type": "integer",
          "value": "0",
          "recommendedRange": null,
          "availableSoftwareInterfaceTypes": [
            "desktop application",
            "library",
            "command-line application",
            "BioSimulators Docker image"
          ]
        }
      ],
      "outputDimensions": [{
        "namespace": "SIO",
        "id": "SIO_000418"
      }],
      "outputVariablePatterns": [
        {
          "name": "variable of integration (time)",
          "symbol": {
                    "value": "time",
                    "namespace": "urn:sedml:symbol"
                  }
        },
        {
          "name": "variables",
          "target": {"value": "variable name (case insensitive)", "grammar": "XPP"}
        },
        {
          "name": "auxiliary variables",
          "target": {"value": "auxiliary variable name (case insensitive)", "grammar": "XPP"}
        }
      ],
      "availableSoftwareInterfaceTypes": [
        "desktop application",
        "library",
        "command-line application",
        "BioSimulators Docker image"
      ],
      "dependencies": [{
        "name": "SUNDIALS",
        "version": null,
        "required": true,
        "freeNonCommercialLicense": true,
        "url": "https://computing.llnl.gov/projects/sundials"
      }],
      "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"
        }]
      }]
    },
    {
      "id": "rungekutta",
      "name": "4th order Runge-Kutta method",
      "kisaoId": {
        "namespace": "KISAO",
        "id": "KISAO_0000032"
      },
      "modelingFrameworks": [{
        "namespace": "SBO",
        "id": "SBO_0000293"
      }],
      "modelFormats": [{
        "namespace": "EDAM",
        "id": "format_9010",
        "version": null,
        "supportedFeatures": []
      }],
      "modelChangePatterns": [
        {
          "name": "Change parameter values or variable initial conditions",
          "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"],
          "target": {
            "value": "{ parameter or variable name }",
            "grammar": "XPP"
          }
        }     
      ],
      "simulationFormats": [{
        "namespace": "EDAM",
        "id": "format_3685",
        "version": "L1V3",
        "supportedFeatures": []
      }],
      "simulationTypes": ["SedUniformTimeCourseSimulation"],
      "archiveFormats": [{
        "namespace": "EDAM",
        "id": "format_3686",
        "version": null,
        "supportedFeatures": []
      }],
      "parameters": [],
      "outputDimensions": [{
        "namespace": "SIO",
        "id": "SIO_000418"
      }],
      "outputVariablePatterns": [
        {
          "name": "variable of integration (time)",
          "symbol": {
                    "value": "time",
                    "namespace": "urn:sedml:symbol"
                  }
        },
        {
          "name": "variables",
          "target": {"value": "variable name (case insensitive)", "grammar": "XPP"}
        },
        {
          "name": "auxiliary variables",
          "target": {"value": "auxiliary variable name (case insensitive)", "grammar": "XPP"}
        }
      ],
      "availableSoftwareInterfaceTypes": [
        "desktop application",
        "library",
        "command-line application",
        "BioSimulators Docker image"
      ],
      "dependencies": null,
      "citations": []
    },
    {
      "id": "qualrk",
      "name": "Quality 4th order Runge-Kutta method",
      "kisaoId": {
        "namespace": "KISAO",
        "id": "KISAO_0000672"
      },
      "modelingFrameworks": [{
        "namespace": "SBO",
        "id": "SBO_0000293"
      }],
      "modelFormats": [{
        "namespace": "EDAM",
        "id": "format_9010",
        "version": null,
        "supportedFeatures": []
      }],
      "modelChangePatterns": [
        {
          "name": "Change parameter values or variable initial conditions",
          "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"],
          "target": {
            "value": "{ parameter or variable name }",
            "grammar": "XPP"
          }
        }     
      ],
      "simulationFormats": [{
        "namespace": "EDAM",
        "id": "format_3685",
        "version": "L1V3",
        "supportedFeatures": []
      }],
      "simulationTypes": ["SedUniformTimeCourseSimulation"],
      "archiveFormats": [{
        "namespace": "EDAM",
        "id": "format_3686",
        "version": null,
        "supportedFeatures": []
      }],
      "parameters": [{
          "kisaoId": {
            "namespace": "KISAO",
            "id": "KISAO_0000597"
          },
          "id": "toler",
          "name": "tolerance",
          "type": "float",
          "value": "0.001",
          "recommendedRange": null,
          "availableSoftwareInterfaceTypes": [
            "desktop application",
            "library",
            "command-line application",
            "BioSimulators Docker image"
          ]
        },
        {
          "kisaoId": {
            "namespace": "KISAO",
            "id": "KISAO_0000485"
          },
          "id": "dtmin",
          "name": "minimum allowable timestep",
          "type": "float",
          "value": "1e-12",
          "recommendedRange": null,
          "availableSoftwareInterfaceTypes": [
            "desktop application",
            "library",
            "command-line application",
            "BioSimulators Docker image"
          ]
        },
        {
          "kisaoId": {
            "namespace": "KISAO",
            "id": "KISAO_0000467"
          },
          "id": "dtmax",
          "name": "maximum allowable timestep",
          "type": "float",
          "value": "1",
          "recommendedRange": null,
          "availableSoftwareInterfaceTypes": [
            "desktop application",
            "library",
            "command-line application",
            "BioSimulators Docker image"
          ]
        },
        {
          "kisaoId": {
            "namespace": "KISAO",
            "id": "KISAO_0000665"
          },
          "id": "newt_iter",
          "name": "Maximum number of iterates per root finding step",
          "type": "integer",
          "value": "1000",
          "recommendedRange": null,
          "availableSoftwareInterfaceTypes": [
            "desktop application",
            "library",
            "command-line application",
            "BioSimulators Docker image"
          ]
        },
        {
          "kisaoId": {
            "namespace": "KISAO",
            "id": "KISAO_0000565"
          },
          "id": "newt_tol",
          "name": "Newton tolerance",
          "type": "float",
          "value": "1e-3",
          "recommendedRange": null,
          "availableSoftwareInterfaceTypes": [
            "desktop application",
            "library",
            "command-line application",
            "BioSimulators Docker image"
          ]
        },
        {
          "kisaoId": {
            "namespace": "KISAO",
            "id": "KISAO_0000666"
          },
          "id": "jac_eps",
          "name": "Jacobian epsilon",
          "type": "float",
          "value": "1e-5",
          "recommendedRange": null,
          "availableSoftwareInterfaceTypes": [
            "desktop application",
            "library",
            "command-line application",
            "BioSimulators Docker image"
          ]
        }
      ],
      "outputDimensions": [{
        "namespace": "SIO",
        "id": "SIO_000418"
      }],
      "outputVariablePatterns": [
        {
          "name": "variable of integration (time)",
          "symbol": {
                    "value": "time",
                    "namespace": "urn:sedml:symbol"
                  }
        },
        {
          "name": "variables",
          "target": {"value": "variable name (case insensitive)", "grammar": "XPP"}
        },
        {
          "name": "auxiliary variables",
          "target": {"value": "auxiliary variable name (case insensitive)", "grammar": "XPP"}
        }
      ],
      "availableSoftwareInterfaceTypes": [
        "desktop application",
        "library",
        "command-line application",
        "BioSimulators Docker image"
      ],
      "dependencies": null,
      "citations": [{
        "title": "Numerical Recipes in C",
        "authors": "William H. Press, Saul A. Teukolsky, William T. Vetterling & Brian P. Flannery",
        "pages": "719",
        "year": 1992,
        "identifiers": [{
          "namespace": "doi",
          "id": "10.5555/148286",
          "url": "https://dl.acm.org/doi/10.5555/148286"
        }]
      }]
    },
    {
      "id": "modeuler",
      "name": "Two step modified Euler method",
      "kisaoId": {
        "namespace": "KISAO",
        "id": "KISAO_0000301"
      },
      "modelingFrameworks": [{
        "namespace": "SBO",
        "id": "SBO_0000293"
      }],
      "modelFormats": [{
        "namespace": "EDAM",
        "id": "format_9010",
        "version": null,
        "supportedFeatures": []
      }],
      "modelChangePatterns": [
        {
          "name": "Change parameter values or variable initial conditions",
          "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"],
          "target": {
            "value": "{ parameter or variable name }",
            "grammar": "XPP"
          }
        }     
      ],
      "simulationFormats": [{
        "namespace": "EDAM",
        "id": "format_3685",
        "version": "L1V3",
        "supportedFeatures": []
      }],
      "simulationTypes": ["SedUniformTimeCourseSimulation"],
      "archiveFormats": [{
        "namespace": "EDAM",
        "id": "format_3686",
        "version": null,
        "supportedFeatures": []
      }],
      "parameters": [],
      "outputDimensions": [{
        "namespace": "SIO",
        "id": "SIO_000418"
      }],
      "outputVariablePatterns": [
        {
          "name": "variable of integration (time)",
          "symbol": {
                    "value": "time",
                    "namespace": "urn:sedml:symbol"
                  }
        },
        {
          "name": "variables",
          "target": {"value": "variable name (case insensitive)", "grammar": "XPP"}
        },
        {
          "name": "auxiliary variables",
          "target": {"value": "auxiliary variable name (case insensitive)", "grammar": "XPP"}
        }
      ],
      "availableSoftwareInterfaceTypes": [
        "desktop application",
        "library",
        "command-line application",
        "BioSimulators Docker image"
      ],
      "dependencies": null,
      "citations": []
    },
    {
      "id": "ymp",
      "name": "Symplectic method",
      "kisaoId": {
        "namespace": "KISAO",
        "id": "KISAO_0000367"
      },
      "modelingFrameworks": [{
        "namespace": "SBO",
        "id": "SBO_0000293"
      }],
      "modelFormats": [{
        "namespace": "EDAM",
        "id": "format_9010",
        "version": null,
        "supportedFeatures": []
      }],
      "modelChangePatterns": [
        {
          "name": "Change parameter values or variable initial conditions",
          "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"],
          "target": {
            "value": "{ parameter or variable name }",
            "grammar": "XPP"
          }
        }     
      ],
      "simulationFormats": [{
        "namespace": "EDAM",
        "id": "format_3685",
        "version": "L1V3",
        "supportedFeatures": []
      }],
      "simulationTypes": ["SedUniformTimeCourseSimulation"],
      "archiveFormats": [{
        "namespace": "EDAM",
        "id": "format_3686",
        "version": null,
        "supportedFeatures": []
      }],
      "parameters": [],
      "outputDimensions": [{
        "namespace": "SIO",
        "id": "SIO_000418"
      }],
      "outputVariablePatterns": [
        {
          "name": "variable of integration (time)",
          "symbol": {
                    "value": "time",
                    "namespace": "urn:sedml:symbol"
                  }
        },
        {
          "name": "variables",
          "target": {"value": "variable name (case insensitive)", "grammar": "XPP"}
        },
        {
          "name": "auxiliary variables",
          "target": {"value": "auxiliary variable name (case insensitive)", "grammar": "XPP"}
        }
      ],
      "availableSoftwareInterfaceTypes": [
        "desktop application",
        "library",
        "command-line application",
        "BioSimulators Docker image"
      ],
      "dependencies": null,
      "citations": []
    },
    {
      "id": "volterra",
      "name": "Second order backward method for Volterra equations",
      "kisaoId": {
        "namespace": "KISAO",
        "id": "KISAO_0000664"
      },
      "modelingFrameworks": [{
        "namespace": "SBO",
        "id": "SBO_0000293"
      }],
      "modelFormats": [{
        "namespace": "EDAM",
        "id": "format_9010",
        "version": null,
        "supportedFeatures": []
      }],
      "modelChangePatterns": [
        {
          "name": "Change parameter values or variable initial conditions",
          "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"],
          "target": {
            "value": "{ parameter or variable name }",
            "grammar": "XPP"
          }
        }     
      ],
      "simulationFormats": [{
        "namespace": "EDAM",
        "id": "format_3685",
        "version": "L1V3",
        "supportedFeatures": []
      }],
      "simulationTypes": ["SedUniformTimeCourseSimulation"],
      "archiveFormats": [{
        "namespace": "EDAM",
        "id": "format_3686",
        "version": null,
        "supportedFeatures": []
      }],
      "parameters": [{
          "kisaoId": {
            "namespace": "KISAO",
            "id": "KISAO_0000597"
          },
          "id": null,
          "name": "tolerance",
          "type": "float",
          "value": "1e-7",
          "recommendedRange": null,
          "availableSoftwareInterfaceTypes": [
            "desktop application"
          ]
        },
        {
          "kisaoId": {
            "namespace": "KISAO",
            "id": "KISAO_0000486"
          },
          "id": null,
          "name": "Maximum number of iterates for each step",
          "type": "integer",
          "value": "10",
          "recommendedRange": null,
          "availableSoftwareInterfaceTypes": [
            "desktop application"
          ]
        },
        {
          "kisaoId": {
            "namespace": "KISAO",
            "id": "KISAO_0000667"
          },
          "id": "vmaxpts",
          "name": "maximum number of points",
          "type": "integer",
          "value": "4000",
          "recommendedRange": null,
          "availableSoftwareInterfaceTypes": [
            "desktop application",
            "library",
            "command-line application",
            "BioSimulators Docker image"
          ]
        }
      ],
      "outputDimensions": [{
        "namespace": "SIO",
        "id": "SIO_000418"
      }],
      "outputVariablePatterns": [
        {
          "name": "variable of integration (time)",
          "symbol": {
                    "value": "time",
                    "namespace": "urn:sedml:symbol"
                  }
        },
        {
          "name": "variables",
          "target": {"value": "variable name (case insensitive)", "grammar": "XPP"}
        },
        {
          "name": "auxiliary variables",
          "target": {"value": "auxiliary variable name (case insensitive)", "grammar": "XPP"}
        }
      ],
      "availableSoftwareInterfaceTypes": [
        "desktop application",
        "library",
        "command-line application",
        "BioSimulators Docker image"
      ],
      "dependencies": null,
      "citations": [{
          "title": "Numerical methods for Volterra integral equations of the first kind",
          "authors": "Peter Linz",
          "journal": "Computer Journal",
          "volume": "12",
          "issue": "4",
          "pages": "393-397",
          "year": 1969,
          "identifiers": [{
            "namespace": "doi",
            "id": "10.1093/comjnl/12.4.393",
            "url": "http://doi.org/10.1093/comjnl/12.4.393"
          }]
        },
        {
          "title": "Analytical and Numerical Methods for Volterra Equations",
          "authors": "Peter Linz",
          "year": 1985,
          "identifiers": [{
            "namespace": "doi",
            "id": "10.1137/1.9781611970852",
            "url": "https://doi.org/10.1137/1.9781611970852"
          }]
        }
      ]
    },
    {
      "id": "stiff",
      "name": "Gear-like method for stiff ODE systems",
      "kisaoId": {
        "namespace": "KISAO",
        "id": "KISAO_0000668"
      },
      "modelingFrameworks": [{
        "namespace": "SBO",
        "id": "SBO_0000293"
      }],
      "modelFormats": [{
        "namespace": "EDAM",
        "id": "format_9010",
        "version": null,
        "supportedFeatures": []
      }],
      "modelChangePatterns": [
        {
          "name": "Change parameter values or variable initial conditions",
          "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"],
          "target": {
            "value": "{ parameter or variable name }",
            "grammar": "XPP"
          }
        }     
      ],
      "simulationFormats": [{
        "namespace": "EDAM",
        "id": "format_3685",
        "version": "L1V3",
        "supportedFeatures": []
      }],
      "simulationTypes": ["SedUniformTimeCourseSimulation"],
      "archiveFormats": [{
        "namespace": "EDAM",
        "id": "format_3686",
        "version": null,
        "supportedFeatures": []
      }],
      "parameters": [{
          "kisaoId": {
            "namespace": "KISAO",
            "id": "KISAO_0000485"
          },
          "id": "dtmin",
          "name": "minimum allowable timestep",
          "type": "float",
          "value": "1e-12",
          "recommendedRange": null,
          "availableSoftwareInterfaceTypes": [
            "desktop application",
            "library",
            "command-line application",
            "BioSimulators Docker image"
          ]
        },
        {
          "kisaoId": {
            "namespace": "KISAO",
            "id": "KISAO_0000467"
          },
          "id": "dtmax",
          "name": "maximum allowable timestep",
          "type": "float",
          "value": "1",
          "recommendedRange": null,
          "availableSoftwareInterfaceTypes": [
            "desktop application",
            "library",
            "command-line application",
            "BioSimulators Docker image"
          ]
        },
        {
          "kisaoId": {
            "namespace": "KISAO",
            "id": "KISAO_0000597"
          },
          "id": "toler",
          "name": "tolerance",
          "type": "float",
          "value": "0.001",
          "recommendedRange": null,
          "availableSoftwareInterfaceTypes": [
            "desktop application",
            "library",
            "command-line application",
            "BioSimulators Docker image"
          ]
        }
      ],
      "outputDimensions": [{
        "namespace": "SIO",
        "id": "SIO_000418"
      }],
      "outputVariablePatterns": [
        {
          "name": "variable of integration (time)",
          "symbol": {
                    "value": "time",
                    "namespace": "urn:sedml:symbol"
                  }
        },
        {
          "name": "variables",
          "target": {"value": "variable name (case insensitive)", "grammar": "XPP"}
        },
        {
          "name": "auxiliary variables",
          "target": {"value": "auxiliary variable name (case insensitive)", "grammar": "XPP"}
        }
      ],
      "availableSoftwareInterfaceTypes": [
        "desktop application",
        "library",
        "command-line application",
        "BioSimulators Docker image"
      ],
      "dependencies": null,
      "citations": [{
          "title": "Numerical Recipes in C",
          "authors": "William H. Press, Saul A. Teukolsky, William T. Vetterling & Brian P. Flannery",
          "pages": "739-741",
          "year": 1992,
          "identifiers": [{
            "namespace": "doi",
            "id": "10.5555/148286",
            "url": "https://dl.acm.org/doi/10.5555/148286"
          }]
        },
        {
          "title": "Mathematical Software III",
          "authors": "LF Shampine & HA and Watts",
          "journal": "Applied Mathematics and Computation",
          "volume": "5",
          "year": 1977,
          "identifiers": []
        }
      ]
    }
  ],
  "interfaceTypes": [
    "desktop application",
    "library",
    "command-line application",
    "BioSimulators Docker image"
  ],
  "supportedOperatingSystemTypes": [
    "Linux",
    "Mac OS",
    "Windows"
  ],
  "supportedProgrammingLanguages": [{
      "namespace": "Linguist",
      "id": "C"
    },
    {
      "namespace": "Linguist",
      "id": "MATLAB"
    },
    {
      "namespace": "Linguist",
      "id": "Python"
    }
  ],
  "funding": [],
  "biosimulators": {
    "specificationVersion": "1.0.0",
    "imageVersion": "1.0.0",
    "validated": false,
    "validationTests": null
  }
}