{
  "id": "smoldyn",
  "name": "Smoldyn",
  "version": "2.67",
  "description": "Computer program for cell-scale biochemical simulations.",
  "urls": [{
      "title": null,
      "type": "Home page",
      "url": "http://www.smoldyn.org/"
    },
    {
      "title": null,
      "type": "Examples",
      "url": "http://www.smoldyn.org/archive.html"
    },
    {
      "title": null,
      "type": "Installation instructions",
      "url": "https://smoldyn.readthedocs.io/en/latest/user/install.html"
    },
    {
      "title": null,
      "type": "Documentation",
      "url": "https://smoldyn.readthedocs.io/"
    },
    {
      "title": null,
      "type": "Source repository",
      "url": "https://github.com/ssandrews/Smoldyn"
    },
    {
      "title": null,
      "type": "License",
      "url": "https://github.com/ssandrews/Smoldyn/blob/master/LICENSE"
    },
    {
      "title": null,
      "type": "Issue tracker",
      "url": "https://github.com/ssandrews/Smoldyn/issues"
    }
  ],
  "image": {
    "url": "ghcr.io/ssandrews/smoldyn/biosimulators_smoldyn:latest",
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    "operatingSystemType": "Linux"
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  "cli": {
    "packageRepository": "PyPI",
    "package": "smoldyn",
    "command": "python -m smoldyn.biosimulators",
    "installationInstructions": null
  },
  "pythonApi": {
    "package": "smoldyn",
    "module": "smoldyn.biosimulators",
    "installationInstructions": null
  },
  "authors": [{
      "middleName": "S.",
      "firstName": "Steven",
      "lastName": "Andrews",
      "identifiers": [{
        "namespace": "orcid",
        "id": "0000-0002-4576-8107",
        "url": "https://orcid.org/0000-0002-4576-8107"
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    },
    {
      "middleName": null,
      "firstName": "Dilawar",
      "lastName": "Singh",
      "identifiers": [{
        "namespace": "orcid",
        "id": "0000-0002-4645-3211",
        "url": "https://orcid.org/0000-0002-4645-3211"
      }]
    }
  ],
  "references": {
    "identifiers": [{
        "namespace": "pypi",
        "id": "smoldyn",
        "url": "https://pypi.org/project/smoldyn/"
      },
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        "namespace": "bio.tools",
        "id": "smoldyn",
        "url": "https://bio.tools/smoldyn"
      }
    ],
    "citations": [{
        "volume": "33",
        "issue": "5",
        "pages": "710-717",
        "journal": "Bioinformatics",
        "title": "Smoldyn: particle-based simulation with rule-based modeling, improved molecular interaction and a library interface",
        "authors": "Steve S. Andrews",
        "year": 2017,
        "identifiers": [{
          "namespace": "doi",
          "id": "10.1093/bioinformatics/btw700",
          "url": "https://doi.org/10.1093/bioinformatics/btw700"
        }]
      },
      {
        "volume": "31",
        "issue": "14",
        "pages": "2406-2408",
        "journal": "Bioinformatics",
        "title": "Multiscale reaction-diffusion simulations with Smoldyn",
        "authors": "Martin Robinson, Steven S. Andrews & Radek Erban",
        "year": 2015,
        "identifiers": [{
          "namespace": "doi",
          "id": "10.1093/bioinformatics/btv149",
          "url": "https://doi.org/10.1093/bioinformatics/btv149"
        }]
      },
      {
        "pages": "519-542",
        "volume": "804",
        "journal": "Methods in Molecular Biology",
        "title": "Spatial and stochastic cellular modeling with the Smoldyn simulator",
        "authors": "Steven S. Andrews",
        "year": 2012,
        "identifiers": [{
          "namespace": "doi",
          "id": "10.1007/978-1-61779-361-5_26",
          "url": "https://doi.org/10.1007/978-1-61779-361-5_26"
        }]
      },
      {
        "volume": "6",
        "issue": "3",
        "pages": "e1000705",
        "journal": "PLoS Compututational Biology",
        "title": "Detailed simulations of cell biology with Smoldyn 2.1",
        "authors": "Steven S. Andrews, Nathan J. Addy, Roger Brent & Adam P. Arkin",
        "year": 2010,
        "identifiers": [{
          "namespace": "doi",
          "id": "10.1371/journal.pcbi.1000705",
          "url": "https://doi.org/10.1371/journal.pcbi.1000705"
        }]
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    ]
  },
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    "namespace": "SPDX",
    "id": "LGPL-3.0-only"
  },
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      "id": "KISAO_0000057"
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        { "name": "Change diffusion coefficient", "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"], "target": {"value": "difc {species}", "grammar": "Smoldyn"}},
        { "name": "Change diffusion coefficient", "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"], "target": {"value": "difc {species}({state})", "grammar": "Smoldyn"}},
        { "name": "Change diffusion coefficient rule", "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"], "target": {"value": "difc_rule {species}({state})", "grammar": "Smoldyn"}},
        { "name": "Change surface diffusion coefficient", "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"], "target": {"value": "difm {species}", "grammar": "Smoldyn"}},
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        { "name": "Change drift", "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"], "target": {"value": "drift {species}", "grammar": "Smoldyn"}},
        { "name": "Change drift", "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"], "target": {"value": "drift {species}({state})", "grammar": "Smoldyn"}},
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        { "name": "Change surface drift", "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"], "target": {"value": "surface_drift {species}({state}) {surface} {panel-shape}", "grammar": "Smoldyn"}},
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        { "name": "Probabilistically kill some molecules of a species", "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"], "target": {"value": "killmolprob {species}({state}) {prob}", "grammar": "Smoldyn"}},
        { "name": "Kill molecules of a species in a compartment", "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"], "target": {"value": "killmolincmpt {species}({state}) {surface}", "grammar": "Smoldyn"}},
        { "name": "Kill molecules of a species on a surface", "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"], "target": {"value": "killmolinsphere {species}({state}) {surface}", "grammar": "Smoldyn"}},
        { "name": "Kill molecules of a species outside the system boundaries", "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"], "target": {"value": "killmoloutsidesystem {species}({state})", "grammar": "Smoldyn"}},
        { "name": "Change the molecules of a species", "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"], "target": {"value": "fixmolcount {species}", "grammar": "Smoldyn"}},
        { "name": "Change the molecules of a species in a compartment", "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"], "target": {"value": "fixmolcountincmpt {species}({state}) {compartment}", "grammar": "Smoldyn"}},
        { "name": "Change the molecules of a species on a surface", "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"], "target": {"value": "fixmolcountonsurf {species}({state}) {surface}]", "grammar": "Smoldyn"}}
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      "version": "1",
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    "citations": [],
    "parameters": [{
        "kisaoId": {
          "namespace": "KISAO",
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        "id": "accuracy",
        "name": "accuracy",
        "type": "float",
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        "availableSoftwareInterfaceTypes": ["library", "command-line application", "BioSimulators Docker image"]
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        "namespace": "SIO",
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    "outputVariablePatterns": [
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        "name": "time",
        "symbol": {
                    "value": "time",
                    "namespace": "urn:sedml:symbol"
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      },
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        "name": "molecule count of a species",
        "target": {"value": "molcount {species}", "grammar": "Smoldyn"}
      },
      {
        "name": "molecule count of a state of a species",
        "target": {"value": "molcountspecies {species}({state})", "grammar": "Smoldyn"}
      },
      {
        "name": "molecule count of a species in a 1-D range",
        "target": {"value": "molcountinbox {species} {low-x} {hi-x}", "grammar": "Smoldyn"}
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        "name": "molecule count of a state of a species in a compartment",
        "target": {"value": "molcountincmpt2 {species} {compartment} {state}", "grammar": "Smoldyn"}
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        "name": "molecule count of a species on a surface",
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        "name": "distribution of molecule counts of a species along a line",
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      },
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        "name": "1-D distribution of molecule counts of a state of a species along a line of a cube",
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        "name": "2-D distribution of molecule counts of a state of a species in a cube",
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      },
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        "name": "1-D distribution of molecule counts of a state of a species along radii of a sphere",
        "target": {"value": "molcountspaceradial {species}({state}) {center-x} {center-y} {center-z} {radius} {bins}", "grammar": "Smoldyn"}
      },
      {
        "name": "1-D distribution of molecule counts of a state of a species along radii of an angular segment of a circle",
        "target": {"value": "molcountspacepolarangle {species}({state}) {center-x} {center-y} {pole-x} {pole-y} {radius-min} {radius-max} {bins}", "grammar": "Smoldyn"}
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        "name": "1-D distribution of molecule counts of a state of a species along radii of an angular segment of a shere",
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        "name": "1-D distribution of molecule counts of a state of a species along radii of a circle around molecules of second state of a second species",
        "target": {"value": "radialdistribution {species-1}({state-1}) {species-2}({state-2}) {radius} {bins}", "grammar": "Smoldyn"}
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        "name": "1-D distribution of molecule counts of a state of a species along radii of a sphere around molecules of second state of a second species",
        "target": {"value": "radialdistribution2 {species-1}({state-1}) {species-2}({state-2}) {low-x} {hi-x} {low-y} {hi-y} {low-z} {hi-z} {radius} {bins}", "grammar": "Smoldyn"}
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  "supportedOperatingSystemTypes": [
    "Mac OS",
    "Linux",
    "Windows"
  ],
  "supportedProgrammingLanguages": [{
      "namespace": "Linguist",
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    },
    {
      "namespace": "Linguist",
      "id": "C++"
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    {
      "namespace": "Linguist",
      "id": "Python"
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  "funding": [],
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    "specificationVersion": "1.0.0",
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}