biosimulators.json

{
  "id": "ibiosim",
  "name": "iBioSim",
  "version": "3.1.0",
  "description": "iBioSim is a computer-aided design (CAD) tool aimed for the modeling, analysis, and design of genetic circuits. While iBioSim primarily targets models of genetic circuits, models representing metabolic networks, cell-signaling pathways, and other biological and chemical systems can also be analyzed.",
  "url": "https://github.com/MyersResearchGroup/iBioSim",
  "image": "docker.io/paytonco/ibiosim:latest",
  "format": {
    "namespace": "EDAM",
    "id": "format_3973"
  },
  "authors": [{
      "firstName": "Chris",
      "middleName": "J.",
      "lastName": "Myers"
    },
    {
      "firstName": "Leandro",
      "middleName": null,
      "lastName": "Watanabe"
    },
    {
      "firstName": "Tramy",
      "middleName": null,
      "lastName": "Nguyen"
    },
    {
      "firstName": "Pedro",
      "middleName": null,
      "lastName": "Fontanarosa"
    },
    {
      "firstName": "Michael",
      "middleName": null,
      "lastName": "Zhang"
    },
    {
      "firstName": "Zach",
      "middleName": null,
      "lastName": "Zundel"
    },
    {
      "firstName": "Mihai",
      "middleName": null,
      "lastName": "Glont"
    },
    {
      "firstName": "Nathan",
      "middleName": null,
      "lastName": "Barker"
    },
    {
      "firstName": "Scott",
      "middleName": null,
      "lastName": "Glass"
    },
    {
      "firstName": "Kevin",
      "middleName": null,
      "lastName": "Jones"
    },
    {
      "firstName": "Hiroyuki",
      "middleName": null,
      "lastName": "Kuwahara"
    },
    {
      "firstName": "Curtis",
      "middleName": null,
      "lastName": "Madsen"
    },
    {
      "firstName": "Nam",
      "middleName": null,
      "lastName": "Nguyen"
    },
    {
      "firstName": "Tyler",
      "middleName": null,
      "lastName": "Patterson"
    },
    {
      "firstName": "Nicholas",
      "middleName": null,
      "lastName": "Roehner"
    },
    {
      "firstName": "Jason",
      "middleName": null,
      "lastName": "Stevens"
    },
    {
      "firstName": "Payton",
      "middleName": "J.",
      "lastName": "Thomas"
    },
    {
      "firstName": "Zhen",
      "middleName": null,
      "lastName": "Zhang"
    }
  ],
  "references": {
    "identifiers": [],
    "citations": [{
        "title": "Design and test of genetic circuits using iBioSim",
        "authors": "Curtis Madsen, Chris J. Myers, Tyler Patterson, Nicholas Roehner, Jason T. Stevens & Chris Winstead",
        "journal": "IEEE Design Test of Computers",
        "volume": 29,
        "pages": "32-39",
        "year": 2012,
        "identifiers": [{
          "namespace": "doi",
          "id": "10.1109/MDT.2012.2187875",
          "url": "https://doi.org/10.1109/MDT.2012.2187875"
        }]
      },
      {
        "title": "Dynamic modeling of cellular populations within iBioSim",
        "authors": "Jason T. Stevens & Chris J. Myers",
        "journal": "ACS Synthetic Biology",
        "volume": 2,
        "pages": "223-229",
        "year": 2013,
        "identifiers": [{
          "namespace": "doi",
          "id": "10.1021/sb300082b",
          "url": "https://doi.org/10.1021/sb300082b"
        }]
      },
      {
        "title": "iBioSim: a tool for the analysis and design of genetic circuits",
        "authors": "Chris J. Myers, Nathan Barker, Kevin Jones, Hiroyuki Kuwahara, Curtis Madsen & Nam-Phuong D. Nguyen",
        "journal": "Bioinformatics",
        "volume": 25,
        "pages": "2848-2849",
        "year": 2009,
        "identifiers": [{
          "namespace": "doi",
          "id": "10.1093/bioinformatics/btp457",
          "url": "https://doi.org/10.1093/bioinformatics/btp457"
        }]
      },
      {
        "title": "iBioSim 3: a tool for model-based genetic circuit design",
        "authors": "Leandro Watanabe, Tramy Nguyen, Michael Zhang, Zach Zundel, Zhen Zhang, Curtis Madsen, Nicholas Roehner & Chris J. Myers",
        "journal": "ACS Synthetic Biology",
        "volume": 8,
        "pages": "1560-1563",
        "year": 2019,
        "identifiers": [{
          "namespace": "doi",
          "id": "10.1021/acssynbio.8b00078",
          "url": "https://doi.org/10.1021/acssynbio.8b00078"
        }]
      }
    ]
  },
  "license": {
    "namespace": "SPDX",
    "id": "Apache-2.0"
  },
  "algorithms": [{
    "id": "hode",
    "name": "Runge-Kutta-Fehlberg (Hierarchical)",
    "kisaoId": {
      "namespace": "KISAO",
      "id": "KISAO_0000086"
    },
    "modelingFrameworks": [{
      "namespace": "SBO",
      "id": "SBO_0000293"
    }],
    "modelFormats": [{
      "namespace": "EDAM",
      "id": "format_2585"
    }],
    "simulationFormats": [{
      "namespace": "EDAM",
      "id": "format_3685"
    }],
    "archiveFormats": [{
      "namespace": "EDAM",
      "id": "format_3686"
    }],
    "citations": [{
      "title": "Low-order classical Runge-Kutta formulas with stepsize control and their application to some heat transfer problems",
      "authors": "Erwin Fehlberg",
      "journal": "NASA Technical Report",
      "pages": "1-49",
      "year": 1969,
      "identifiers": [{
        "namespace": "NTRS",
        "id": "NASA-TR-R-315",
        "url": "https://ntrs.nasa.gov/citations/19690021375"
      }]
    }],
    "parameters": [{
      "kisaoId": {
        "namespace": "KISAO",
        "id": "KISAO_0000209"
      },
      "id": "rel_tol",
      "name": "Relative tolerance",
      "type": "float",
      "value": 0.000001
    }]
  }],
  "biosimulators": {
    "schemaVersion": "1.0.0",
    "imageVersion": "1.0.0"
  },
  "created": "2020-01-01T12:00:00Z",
  "updated": "2020-01-01T12:00:00Z"
}