biosimulators.json

{
  "id": "VCell",
  "name": "Virtual Cell",
  "version": "7.2",
  "description": "VCell (Virtual Cell) is a comprehensive platform for modeling cell biological systems that is built on a central database and disseminated as a standalone application",
  "url": "http://vcell.org/",
  "image": "docker.io/biosimulators/vcell:7.2",
  "format": {
    "namespace": "EDAM",
    "id": "format_3973" //Docker image format
  },
  "authors": [{
      "firstName": "Frank",
      "lastName": "Morgan"
    },
    {
      "firstName": "Dan",
      "lastName": "Vasilescu"
    },
    {
      "firstName": "Jim",
      "lastName": "Scaff"
    },
    {
      "firstName": "Ion",
      "lastName": "Moraru"
    },
    {
      "firstName": "Michael",
      "lastName": "Blinov"
    },
    {
      "firstName": "Michael",
      "lastName": "Wilson"
    },
    {
      "firstName": "Ann",
      "lastName": "Cowan"
    },
    {
      "firstName": "Leslie",
      "lastName": "Loew"
    },
    {
      "firstName": "Fei",
      "lastName": "Gao"
    },
    {
      "firstName": "Ye",
      "lastName": "Li"
    }
  ],
  "references": {
    "identifiers": [],
    "citations": [{
        "title": "A general computational framework for modeling cellular structure and function",
        "authors": "James C. Schaff, Charles C. Fink, Boris M. Slepchenko, John H. Carson & Leslie M. Loew",
        "journal": "Biophysical Journal",
        "volume": "73",
        "pages": "1135-1146",
        "year": 1997,
        "identifiers": [{
          "namespace": "doi",
          "id": "10.1016/S0006-3495(97)78146-3",
          "url": "https://doi.org/10.1016/S0006-3495(97)78146-3"
        }]
      },
      {
        "title": "The Virtual Cell: A software environment for computational cell biology",
        "authors": "James C. Schaff & Leslie M. Loew",
        "journal": "Trends in Biotechnology",
        "volume": "19",
        "pages": "401-406",
        "year": 2001,
        "identifiers": [{
          "namespace": "doi",
          "id": "10.1016/S0167-7799(01)01740-1",
          "url": "https://doi.org/10.1016/S0167-7799(01)01740-1"
        }]
      },
      {
        "title": "Spatial modeling of cell signaling networks",
        "authors": "Ann E. Cowan, Ion I. Moraru, James C. Scaff, Boris M. Slepchenko & Leslie M. Loew",
        "journal": "Methods in Cell Biology",
        "volume": "110",
        "pages": "195-221",
        "year": 2012,
        "identifiers": [{
          "namespace": "doi",
          "id": "10.1016/B978-0-12-388403-9.00008-4",
          "url": "https://doi.org/10.1016/B978-0-12-388403-9.00008-4"
        }]
      },
      {
        "title": "The Virtual Cell modeling and simulation software environment",
        "authors": "Ion I. Moraru, James C. Scaff, Boris M. Slepchenko, Michael L. Blinov, Frank Morgan, Anuradha Lakshminaryana, Fei Gao, Ye Li & Leslie M. Loew",
        "journal": "IET Systems Biology",
        "volume": "2",
        "pages": "352-362",
        "year": 2008,
        "identifiers": [{
          "namespace": "doi",
          "id": "10.1049/iet-syb:20080102",
          "url": "https://doi.org/10.1049/iet-syb:20080102"
        }]
      },
      {
        "title": "Compartmental and spatial rule-based modeling with Virtual Cell",
        "authors": "Michael L. Blinov, James C. Scaff, Dan Vasilescu, Ion I. Moraru, Judy E. Bloom & Leslie M. Loew",
        "journal": "Biophysical Journal",
        "volume": "113",
        "pages": "1365-1372",
        "year": 2017,
        "identifiers": [{
          "namespace": "doi",
          "id": "10.1016/j.bpj.2017.08.022",
          "url": "https://doi.org/10.1016/j.bpj.2017.08.022"
        }]
      }
    ]
  },
  "license": {
    "namespace": "SPDX",
    "id": "MIT"
  },
  "algorithms": [{
      "id": "cvode",
      "name": "C-language Variable-coefficient Ordinary Differential Equation solver",
      "kisaoId": {
        "namespace": "KISAO",
        "id": "KISAO_0000019" //cvode
      },

      "modelingFrameworks": [{
        "namespace": "SBO",
        "id": "SBO_0000293" //non-spatial continuous framework
      }],
      "modelFormats": [{
        "namespace": "EDAM",
        "id": "format_2585" //sbml
      }],
      "simulationFormats": [{
        "namespace": "EDAM",
        "id": "format_3685" //sed-ml
      }],
      "archiveFormats": [{
        "namespace": "EDAM",
        "id": "format_3686" //OMEX file
      }],
      "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": [{
        "kisaoId": {
          "namespace": "KISAO",
          "id": "KISAO_0000209" // relative tolerance 
        },
        "id": "rel_tol",
        "name": "Relative tolerance",
        "type": "float",
        "value": 1e-9
      }
      {
        "kisaoId": {
          "namespace": "KISAO",
          "id": "KISAO_0000211" // absolute tolerance 
           },
        "name": "Absolute tolerance",
        "type": "float",
        "value": 1e-9
        },  
        {
          "kisaoId": {
            "namespace": "KISAO",
            "id": "KISAO_0000467"
          },
          "name": "Maximum time step",
          "type": "float",
          "value": 1.0
        }
    ]
    },
    {
      "id": "RungeKutta2",
      "name": "Runge-Kutta (Second Order, Fixed Time Step)",
      "kisaoId": {
        "namespace": "KISAO",
        "id": "KISAO_0000064" //Runge-Kutta based method
      },
      "modelingFrameworks": [{
        "namespace": "SBO",
        "id": "SBO_0000293" //non-spatial continuous framework
      }],
      "modelFormats": [{
        "namespace": "EDAM",
        "id": "format_2585" //sbml
      }],
      "simulationFormats": [{
        "namespace": "EDAM",
        "id": "format_3685" //sed-ml
      }],
      "archiveFormats": [{
        "namespace": "EDAM",
        "id": "format_3686" //OMEX file
      }],
      "citations": [{
        "title": "A second order Runge Kutta method to solve fuzzy differential equations with fuzzy initial condition",
        "authors": "V. Parimala",
        "journal": "International Journal of Science and Research",
        "volume": 3,
        "issue": 3,
        "pages": "428-431",
        "year": 2014,
        "identifiers": [{
          "namespace": "ijsr",
          "id": "20131137",
          "url": "https://www.ijsr.net/get_abstract.php?paper_id=20131137"
        }]
      }],
      "parameters": [{
        "kisaoId": {
          "namespace": "KISAO",
          "id": "KISAO_0000209" // relative tolerance
        },
        "id": "rel_tol",
        "name": "relative tolerance",
        "type": "float",
        "value": 1e-9
      }]
    },
    {
      "id": "ForwardEuler",
      "name": "Forward Euler (First Order, Fixed Time Step)",
      "kisaoId": {
        "namespace": "KISAO",
        "id": "KISAO_0000030" //Euler forward method
      },

      "modelingFrameworks": [{
        "namespace": "SBO",
        "id": "SBO_0000293" //non-spatial continuous framework
      }],
      "modelFormats": [{
        "namespace": "EDAM",
        "id": "format_2585" //sbml
      }],
      "simulationFormats": [{
        "namespace": "EDAM",
        "id": "format_3685" //sed-ml
      }],
      "archiveFormats": [{
        "namespace": "EDAM",
        "id": "format_3686" //OMEX file
      }],
      "citations": [{
        "title": "Solving reaction-diffusion and advection problems with Richardon Extrapolation",
        "authors": "Tamás Mona, István Lagzi & Ágnes Havasi",
        "journal": "Journal of Chemistry",
        "volume": 3,
        "issue": 3,
        "pages": "2-8",
        "year": 2015,
        "identifiers": [{
          "namespace": "doi",
          "id": "10.1155/2015/350362",
          "url": "https://doi.org/10.1155/2015/350362"
        }]
      }],
      "parameters": [{
        "kisaoId": {
          "namespace": "KISAO",
          "id": "KISAO_0000209" // relative tolerance
        },
        "id": "rel_tol",
        "name": "Relative tolerance",
        "type": "float",
        "value": 1e-9
      }]
    },
    {
      "id": "RungeKutta4",
      "name": "Runge-Kutta (Fourth Order, Fixed Time Step)",
      "kisaoId": {
        "namespace": "KISAO",
        "id": "KISAO_0000032" //explicit fourth-order Runge-Kutta method
      },

      "modelingFrameworks": [{
        "namespace": "SBO",
        "id": "SBO_0000293" //non-spatial continuous framework
      }],
      "modelFormats": [{
        "namespace": "EDAM",
        "id": "format_2585" //sbml
      }],
      "simulationFormats": [{
        "namespace": "EDAM",
        "id": "format_3685" //sed-ml
      }],
      "archiveFormats": [{
        "namespace": "EDAM",
        "id": "format_3686" //OMEX file
      }],
      "citations": [{
        "title": "A fourth order Runge–Kutta RK(4,4) method with error control",
        "authors": "A. R. Yaakub & David J. Evans",
        "journal": "International Journal of Computer Mathematics",
        "volume": 71,
        "issue": 3,
        "pages": "383-411",
        "year": 2007,
        "identifiers": [{
          "namespace": "doi",
          "id": "10.1080/00207169908804817",
          "url": "https://doi.org/10.1080/00207169908804817"
        }]
      }],
      "parameters": [{
        "kisaoId": {
          "namespace": "KISAO",
          "id": "KISAO_0000209" // relative tolerance
        },
        "id": "rel_tol",
        "name": "Relative tolerance",
        "type": "float",
        "value": 1e-9
      }]
    },
    {
      "id": "RungeKuttaFehlberg",
      "name": "Runge-Kutta-Fehlberg (Fifth Order, Variable Time Step)",
      "kisaoId": {
        "namespace": "KISAO",
        "id": "KISAO_0000086" //Fehlberg method
      },

      "modelingFrameworks": [{
        "namespace": "SBO",
        "id": "SBO_0000293" //non-spatial continuous framework
      }],
      "modelFormats": [{
        "namespace": "EDAM",
        "id": "format_2585" //sbml
      }],
      "simulationFormats": [{
        "namespace": "EDAM",
        "id": "format_3685" //sed-ml
      }],
      "archiveFormats": [{
        "namespace": "EDAM",
        "id": "format_3686" //OMEX file
      }],
      "citations": [{
        "title": "Optimum Runge-Kutta Fehlberg methods for first order differential equations",
        "authors": "R. K. Jain & M. K. Jain",
        "journal": "IMA Journal of Applied Mathematics",
        "volume": 8,
        "issue": 3,
        "pages": "386-396",
        "year": 1971,
        "identifiers": [{
          "namespace": "doi",
          "id": "10.1093/imamat/8.3.386",
          "url": "https://doi.org/10.1093/imamat/8.3.386"
        }]
      }],
      "parameters": [{
        "kisaoId": {
          "namespace": "KISAO",
          "id": "KISAO_0000209" // relative tolerance
        },
        "id": "rel_tol",
        "name": "Relative tolerance",
        "type": "float",
        "value": 1e-9
      }]
    },
    {
      "id": "AdamsMoulton",
      "name": "Adams-Moulton (Fifth Order, Fixed Time Step)",
      "kisaoId": {
        "namespace": "KISAO",
        "id": "KISAO_0000280" //Adams-Moulton method
      },

      "modelingFrameworks": [{
        "namespace": "SBO",
        "id": "SBO_0000293" //non-spatial continuous framework
      }],
      "modelFormats": [{
        "namespace": "EDAM",
        "id": "format_2585" //sbml
      }],
      "simulationFormats": [{
        "namespace": "EDAM",
        "id": "format_3685" //sed-ml
      }],
      "archiveFormats": [{
        "namespace": "EDAM",
        "id": "format_3686" //OMEX file
      }],
      "citations": [{
        "title": "Solving implicit equations arising from Adams-Moulton methods",
        "authors": "Tian Min Han & Yuhuan Han",
        "journal": "BIT Numerical Mathematics",
        "volume": 42,
        "issue": 2,
        "pages": "336-350",
        "year": 2002,
        "identifiers": [{
          "namespace": "doi",
          "id": "10.1023/A:1021951025649",
          "url": "https://doi.org/10.1023/A:1021951025649"
        }]
      }],
      "parameters": [{
        "kisaoId": {
          "namespace": "KISAO",
          "id": "KISAO_0000209" // relative tolerance
        },
        "id": "rel_tol",
        "name": "Relative tolerance",
        "type": "float",
        "value": 1e-9
      }]
    },
    {
      "id": "IDA",
      "name": "IDA (Variable Order, Variable Time Step, ODE/DAE)",
      "kisaoId": {
        "namespace": "KISAO",
        "id": "KISAO_0000283" //IDA
      },

      "modelingFrameworks": [{
        "namespace": "SBO",
        "id": "SBO_0000293" //non-spatial continuous framework
      }],
      "modelFormats": [{
        "namespace": "EDAM",
        "id": "format_2585" //sbml
      }],
      "simulationFormats": [{
        "namespace": "EDAM",
        "id": "format_3685" //sed-ml
      }],
      "archiveFormats": [{
        "namespace": "EDAM",
        "id": "format_3686" //OMEX file
      }],
      "citations": [{
        "title": "Solving differential–algebraic equation systems by means of index reduction methodology",
        "authors": "Kim Sørensen, Thomas Condra & Niels Houbak",
        "journal": "Simulation Modelling Practice and Theory",
        "volume": 14,
        "issue": 3,
        "pages": "224-236",
        "year": 2006,
        "identifiers": [{
          "namespace": "doi",
          "id": "10.1016/j.simpat.2005.05.002",
          "url": "https://doi.org/10.1016/j.simpat.2005.05.002"
        }]
      }],
      "parameters": [{
        "kisaoId": {
          "namespace": "KISAO",
          "id": "KISAO_0000209" // relative tolerance
        },
        "id": "rel_tol",
        "name": "Relative tolerance",
        "type": "float",
        "value": 1e-9
      }]
    },
    {
      "id": "StochGibson",
      "name": "Gibson (Next Reaction Stochastic Method)",
      "kisaoId": {
        "namespace": "KISAO",
        "id": "KISAO_0000027" //Gibson-Bruck next reaction algorithm
      },

      "modelingFrameworks": [{
        "namespace": "SBO",
        "id": "SBO_0000295" //non-spatial discrete framework
      }],
      "modelFormats": [{
        "namespace": "EDAM",
        "id": "format_2585" //sbml
      }],
      "simulationFormats": [{
        "namespace": "EDAM",
        "id": "format_3685" //sed-ml
      }],
      "archiveFormats": [{
        "namespace": "EDAM",
        "id": "format_3686" //OMEX file
      }],
      "citations": [{
        "title": "Efficient exact stochastic simulation of chemical systems with many species and many channels",
        "authors": "Michael A. Gibson & Jehoshua Bruck",
        "journal": "Journal Physical Chemistry A",
        "volume": 104,
        "issue": 9,
        "pages": "1876-1889",
        "year": 2000,
        "identifiers": [{
          "namespace": "doi",
          "id": "10.1021/jp993732q",
          "url": "https://doi.org/10.1021/jp993732q"
        }]
      }],
    },
    {
      "id": "HybridEuler",
      "name": "Hybrid (Gibson + Euler-Maruyama Method)",
      "kisaoId": {
        "namespace": "KISAO",
        "id": "KISAO_0000352" //hybrid method
      },
      "modelingFrameworks": [{
        "namespace": "SBO",
        "id": "SBO_0000295" //non-spatial discrete framework
      }],
      "modelFormats": [{
        "namespace": "EDAM",
        "id": "format_2585" //sbml
      }],
      "simulationFormats": [{
        "namespace": "EDAM",
        "id": "format_3685" //sed-ml
      }],
      "archiveFormats": [{
        "namespace": "EDAM",
        "id": "format_3686" //OMEX file
      }],
      "citations": [{
        "title": "An Euler–Maruyama method for diffusion equations with discontinuous coefficients and a family of interface conditions",
        "authors": "Vrushali A. Bokil, Nathan L. Gibson, Son L. Nguyen, Enrique A. Thomann & Edward C. Waymire",
        "journal": "Journal of Computational and Applied Mathematics",
        "volume": 368,
        "issue": "NA",
        "pages": "112545",
        "year": 2019,
        "identifiers": [{
          "namespace": "doi",
          "id": "10.1016/j.cam.2019.112545",
          "url": "https://doi.org/10.1016/j.cam.2019.112545"
        }]
      }],
    },
    {
      "id": "HybridMilstein",
      "name": "Hybrid (Gibson + Milstein Method)",
      "kisaoId": {
        "namespace": "KISAO",
        "id": "KISAO_0000352" //hybrid method
      },

      "modelingFrameworks": [{
        "namespace": "SBO",
        "id": "SBO_0000295" //non-spatial discrete framework
      }],
      "modelFormats": [{
        "namespace": "EDAM",
        "id": "format_2585" //sbml
      }],
      "simulationFormats": [{
        "namespace": "EDAM",
        "id": "format_3685" //sed-ml
      }],
      "archiveFormats": [{
        "namespace": "EDAM",
        "id": "format_3686" //OMEX file
      }],
      "citations": [{
        "title": "A randomized Milstein method for stochastic differential equations with non-differentiable drift coefficients",
        "authors": "Raphel Kruse & Yue Wu",
        "journal": "Discrete and Continuous Dynamical Systems",
        "volume": 24,
        "issue": 8,
        "pages": "3475-3502",
        "year": 2010,
        "identifiers": [{
          "namespace": "doi",
          "id": "10.3934/dcdsb.2018253",
          "url": "https://doi.org/10.3934/dcdsb.2018253"
        }]
      }],
    },
    {
      "id": "FiniteVolumeStandalone",
      "name": "Semi-Implicit Finite Volume-Particle Hybrid, Regular Grid (Fixed Time Step)",
      "kisaoId": {
        "namespace": "KISAO",
        "id": "KISAO_0000285" //finite volume method
      },

      "modelingFrameworks": [{
        "namespace": "SBO",
        "id": "SBO_0000292" //spatial continuous framework
      }],
      "modelFormats": [{
        "namespace": "EDAM",
        "id": "format_2585" //sbml
      }],
      "simulationFormats": [{
        "namespace": "EDAM",
        "id": "format_3685" //sed-ml
      }],
      "archiveFormats": [{
        "namespace": "EDAM",
        "id": "format_3686" //OMEX file
      }],
      "citations": [{
        "title": "Finite volume methods",
        "authors": "Robert Eymard, Gallouet Thierry & Raphaèle Herbin",
        "journal": "Handbook of Numerical Analysis",
        "volume": 7,
        "issue": "",
        "pages": "731-1020",
        "year": 2000,
        "identifiers": [{
          "namespace": "doi",
          "id": "10.1016/S1570-8659(00)07005-8",
          "url": "https://doi.org/10.1016/S1570-8659(00)07005-8"
        }]
      }],
      "parameters": [{
        "kisaoId": {
          "namespace": "KISAO",
          "id": "KISAO_0000209" // relative tolerance
        },
        "id": "rel_tol",
        "name": "Relative tolerance",
        "type": "float",
        "value": 1e-9
      }]
    },
    {
      "id": "Combined IDA/CVODE",
      "name": "Combined Stiff Solver (IDA/CVODE)",
      "kisaoId": {
        "namespace": "KISAO",
        "id": "KISAO_0000019" //cvode
      },

      "modelingFrameworks": [{
        "namespace": "SBO",
        "id": "SBO_0000293" //non-spatial continous framework
      }],
      "modelFormats": [{
        "namespace": "EDAM",
        "id": "format_2585" //sbml
      }],
      "simulationFormats": [{
        "namespace": "EDAM",
        "id": "format_3685" //sed-ml
      }],
      "archiveFormats": [{
        "namespace": "EDAM",
        "id": "format_3686" //OMEX file
      }],
      "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"
          }]
        },
        {
          "title": "Solving differential–algebraic equation systems by means of index reduction methodology",
          "authors": "Kim Sørensen, Thomas Condra & Niels Houbak",
          "journal": "Simulation Modelling Practice and Theory",
          "volume": 14,
          "issue": 3,
          "pages": "224-236",
          "year": 2006,
          "identifiers": [{
            "namespace": "doi",
            "id": "10.1016/j.simpat.2005.05.002",
            "url": "https://doi.org/10.1016/j.simpat.2005.05.002"
          }]
        }
      ],
      "parameters": [{
        "kisaoId": {
          "namespace": "KISAO",
          "id": "KISAO_0000209" // relative tolerance
        },
        "id": "rel_tol",
        "name": "Relative tolerance",
        "type": "float",
        "value": 1e-9
      }]
    },
    {
      "id": "SundialsPDE",
      "name": "Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)",
      "kisaoId": {
        "namespace": "KISAO",
        "id": "KISAO_0000285" //finite volume method
      },

      "modelingFrameworks": [{
        "namespace": "SBO",
        "id": "SBO_0000292" //spatial continuous framework
      }],
      "modelFormats": [{
        "namespace": "EDAM",
        "id": "format_2585" //sbml
      }],
      "simulationFormats": [{
        "namespace": "EDAM",
        "id": "format_3685" //sed-ml
      }],
      "archiveFormats": [{
        "namespace": "EDAM",
        "id": "format_3686" //OMEX file
      }],
      "citations": [{
        "title": "Finite volume methods",
        "authors": "Robert Eymard, Gallouet Thierry & Raphaèle Herbin",
        "journal": "Handbook of Numerical Analysis",
        "volume": 7,
        "issue": "",
        "pages": "731-1020",
        "year": 2000,
        "identifiers": [{
          "namespace": "doi",
          "id": "10.1016/S1570-8659(00)07005-8",
          "url": "https://doi.org/10.1016/S1570-8659(00)07005-8"
        }]
      }],
      "parameters": [{
        "kisaoId": {
          "namespace": "KISAO",
          "id": "KISAO_0000209" // relative tolerance
        },
        "id": "rel_tol",
        "name": "Relative tolerance",
        "type": "float",
        "value": 1e-9
      }]
    },
    {
      "id": "Smoldyn",
      "name": "Smoldyn (Spatial Stochastic Simulator)",
      "kisaoId": {
        "namespace": "KISAO",
        "id": "KISAO_0000057" //Brownian diffusion Smoluchowski method
      },

      "modelingFrameworks": [{
        "namespace": "SBO",
        "id": "SBO_0000294" //spatial discrete framework
      }],
      "modelFormats": [{
        "namespace": "EDAM",
        "id": "format_2585" //sbml
      }],
      "simulationFormats": [{
        "namespace": "EDAM",
        "id": "format_3685" //sed-ml
      }],
      "archiveFormats": [{
        "namespace": "EDAM",
        "id": "format_3686" //OMEX file
      }],
      "citations": [{
        "title": "A brief account of microscopical observations made in the months of June, July and August 1827, on the particles contained in the pollen of plants; and on the general existence of active molecules in organic and inorganic bodies",
        "authors": "Robert Brown",
        "journal": "Philosophical Magazine",
        "volume": 4,
        "issue": 21,
        "pages": "161-173",
        "year": 1827,
        "identifiers": [{
          "namespace": "doi",
          "id": "10.1080/14786442808674769",
          "url": "https://doi.org/10.1080/14786442808674769"
        }]
      }],
    }
  ],
  "biosimulators": {
    "schemaVersion": "1.0.0",
    "imageVersion": "1.0.0"
  }
}