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biosimulators.json
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biosimulators.json
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{
"id": "tellurium",
"name": "tellurium",
"version": "2.2.10",
"description": "tellurium is a Python-based environment for model building, simulation, and analysis that facilitates reproducibility of models in systems and synthetic biology.",
"urls": [
{
"type": "Home page",
"url": "http://tellurium.analogmachine.org/"
},
{
"type": "Discussion forum",
"url": "https://groups.google.com/d/forum/tellurium-discuss"
},
{
"type": "Tutorial",
"url": "https://tellurium.readthedocs.io/en/latest/quickstart.html"
},
{
"type": "Installation instructions",
"url": "https://github.com/sys-bio/tellurium#installation-instructions"
},
{
"type": "Documentation",
"url": "https://tellurium.readthedocs.io/"
},
{
"type": "Source repository",
"url": "https://github.com/sys-bio/tellurium"
},
{
"type": "Guide to contributing",
"url": "https://github.com/sys-bio/tellurium/blob/develop/CONTRIBUTING.rst"
},
{
"type": "Issue tracker",
"url": "https://github.com/sys-bio/tellurium/issues"
},
{
"type": "License",
"url": "https://github.com/sys-bio/tellurium/blob/develop/LICENSE.txt"
},
{
"type": "Release notes",
"url": "http://tellurium.analogmachine.org/news/"
}
],
"image": {
"url": "ghcr.io/biosimulators/biosimulators_tellurium/tellurium:2.2.10",
"format": {
"namespace": "EDAM",
"id": "format_3973",
"version": "1.2.0",
"supportedFeatures": []
},
"operatingSystemType": "Linux"
},
"cli": {
"packageRepository": "PyPI",
"package": "biosimulators-tellurium",
"command": "biosimulators-tellurium",
"installationInstructions": "https://docs.biosimulators.org/Biosimulators_tellurium/installation.html"
},
"pythonApi": {
"package": "biosimulators-tellurium",
"module": "biosimulators_tellurium",
"installationInstructions": "https://docs.biosimulators.org/Biosimulators_tellurium/installation.html"
},
"authors": [
{
"firstName": "Jayit",
"lastName": "Biswas",
"identifiers": []
},
{
"firstName": "Kiri",
"lastName": "Choi",
"identifiers": [
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"namespace": "orcid",
"id": "0000-0002-0156-8410",
"url": "https://orcid.org/0000-0002-0156-8410"
}
]
},
{
"firstName": "Wilbert",
"lastName": "Copeland",
"identifiers": []
},
{
"firstName": "Caroline",
"lastName": "Cannistra",
"identifiers": []
},
{
"firstName": "Alex",
"lastName": "Darling",
"identifiers": []
},
{
"firstName": "Nasir",
"lastName": "Elmi",
"identifiers": []
},
{
"firstName": "Michal",
"lastName": "Galdzicki",
"identifiers": [
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"namespace": "orcid",
"id": "0000-0002-8392-8183",
"url": "https://orcid.org/0000-0002-8392-8183"
}
]
},
{
"firstName": "Stanley",
"lastName": "Gu",
"identifiers": []
},
{
"firstName": "Totte",
"lastName": "Karlsson",
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},
{
"firstName": "Matthias",
"lastName": "König",
"identifiers": [
{
"namespace": "orcid",
"id": "0000-0003-1725-179X",
"url": "https://orcid.org/0000-0003-1725-179X"
}
]
},
{
"firstName": "J",
"middleName": "Kyle",
"lastName": "Medley",
"identifiers": [
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"id": "0000-0002-9135-0844",
"url": "https://orcid.org/0000-0002-9135-0844"
}
]
},
{
"firstName": "Herbert",
"middleName": "M.",
"lastName": "Sauro",
"identifiers": [
{
"namespace": "orcid",
"id": "0000-0002-3659-6817",
"url": "https://orcid.org/0000-0002-3659-6817"
}
]
},
{
"firstName": "Andy",
"lastName": "Somogyi",
"identifiers": []
},
{
"firstName": "Lucian",
"lastName": "Smith",
"identifiers": [
{
"namespace": "orcid",
"id": "0000-0001-7002-6386",
"url": "https://orcid.org/0000-0001-7002-6386"
}
]
},
{
"firstName": "Kaylene",
"lastName": "Stocking",
"identifiers": []
}
],
"references": {
"identifiers": [
{
"namespace": "pypi",
"id": "tellurium",
"url": "https://pypi.org/project/tellurium/"
},
{
"namespace": "pypi",
"id": "biosimulators-tellurium",
"url": "https://pypi.org/project/biosimulators-tellurium/"
},
{
"namespace": "nanohub.resource",
"id": "tellurium",
"url": "https://nanohub.org/resources/tellurium"
}
],
"citations": [
{
"title": "tellurium: an extensible Python-based modeling environment for systems and synthetic biology",
"authors": "Kiri Choi, J. Kyle Medley, Matthias König, Kaylene Stocking, Lucian Smith, Stanley Gua & Herbert M. Sauro",
"journal": "BioSystems",
"volume": "171",
"pages": "74-79",
"year": 2018,
"identifiers": [
{
"namespace": "doi",
"id": "10.1016/j.biosystems.2018.07.006",
"url": "https://doi.org/10.1016/j.biosystems.2018.07.006"
}
]
}
]
},
"license": {
"namespace": "SPDX",
"id": "Apache-2.0"
},
"algorithms": [
{
"id": "cvode",
"name": "C-language Variable-coefficient Ordinary Differential Equation solver",
"kisaoId": {
"namespace": "KISAO",
"id": "KISAO_0000019"
},
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"id": "SBO_0000293"
}
],
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}
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"simulationFormats": [
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],
"simulationTypes": [
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],
"archiveFormats": [
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"version": "1",
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}
],
"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": [
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"namespace": "doi",
"id": "10.1063/1.4822377",
"url": "https://doi.org/10.1063/1.4822377"
}
]
}
],
"parameters": [
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},
"id": "relative_tolerance",
"name": "Relative tolerance",
"type": "float",
"value": "0.000001",
"recommendedRange": null,
"availableSoftwareInterfaceTypes": [
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]
},
{
"kisaoId": {
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},
"id": "absolute_tolerance",
"name": "Absolute tolerance",
"type": "float",
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]
},
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},
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"type": "float",
"value": "1e-12",
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]
},
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"kisaoId": {
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"id": "KISAO_0000220"
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"id": "maximum_bdf_order",
"name": "Maximum Backward Differentiation Formula (BDF) order",
"type": "integer",
"value": "5",
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},
"id": "initial_time_step",
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]
},
{
"kisaoId": {
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},
"id": "stiff",
"name": "Stiff",
"type": "boolean",
"value": "true",
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"availableSoftwareInterfaceTypes": [
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]
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{
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},
"id": "multiple_steps",
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"value": "false",
"recommendedRange": null,
"availableSoftwareInterfaceTypes": [
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]
}
],
"outputDimensions": [
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"id": "SIO_000418"
}
],
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"symbol": {
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"namespace": "urn:sedml:symbol"
}
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{
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{
"name": "parameter values",
"target": {
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{
"name": "reaction fluxes",
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}
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}
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],
"dependencies": [
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"name": "libRoadRunner",
"version": null,
"required": true,
"freeNonCommercialLicense": true,
"url": "http://libroadrunner.org/"
},
{
"name": "SUNDIALS",
"version": null,
"required": true,
"freeNonCommercialLicense": true,
"url": "https://computing.llnl.gov/projects/sundials"
}
]
},
{
"id": "euler",
"name": "Forward Euler method",
"kisaoId": {
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"id": "KISAO_0000030"
},
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}
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