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biosimulators.json
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biosimulators.json
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{
"id": "smoldyn",
"name": "Smoldyn",
"version": "2.74",
"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",
"format": {
"namespace": "EDAM",
"id": "format_3973",
"version": null,
"supportedFeatures": []
},
"operatingSystemType": "Linux"
},
"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"
}]
},
{
"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/"
},
{
"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"
}]
}
]
},
"license": {
"namespace": "SPDX",
"id": "LGPL-3.0-only"
},
"algorithms": [{
"id": "Smoldyn",
"name": "Smoldyn (Spatial Stochastic Simulator)",
"kisaoId": {
"namespace": "KISAO",
"id": "KISAO_0000057"
},
"modelingFrameworks": [{
"namespace": "SBO",
"id": "SBO_0000678"
}],
"modelFormats": [{
"namespace": "EDAM",
"id": "format_9001",
"version": null,
"supportedFeatures": []
}],
"modelChangePatterns": [
{ "name": "Change parameter value", "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"], "target": {"value": "define {name}", "grammar": "Smoldyn"}},
{ "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"}},
{ "name": "Change surface diffusion coefficient", "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"], "target": {"value": "difm {species}({state})", "grammar": "Smoldyn"}},
{ "name": "Change surface diffusion coefficient rule", "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"], "target": {"value": "difm_rule {species}({state})", "grammar": "Smoldyn"}},
{ "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"}},
{ "name": "Change drift rule", "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"], "target": {"value": "drift_rule {species}({state})", "grammar": "Smoldyn"}},
{ "name": "Change surface drift", "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"], "target": {"value": "surface_drift {species}({state}) {surface} {panel-shape}", "grammar": "Smoldyn"}},
{ "name": "Change surface drift rule", "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"], "target": {"value": "surface_drift_rule {species}({state}) {surface} {panel-shape}", "grammar": "Smoldyn"}},
{ "name": "Kill molecules of a species", "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"], "target": {"value": "killmol {species}({state})", "grammar": "Smoldyn"}},
{ "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"}}
],
"simulationFormats": [{
"namespace": "EDAM",
"id": "format_3685",
"version": "L1V3",
"supportedFeatures": []
}],
"simulationTypes": ["SedUniformTimeCourseSimulation"],
"archiveFormats": [{
"namespace": "EDAM",
"id": "format_3686",
"version": "1",
"supportedFeatures": []
}],
"citations": [],
"parameters": [{
"kisaoId": {
"namespace": "KISAO",
"id": "KISAO_0000254"
},
"id": "accuracy",
"name": "accuracy",
"type": "float",
"value": "10.0",
"recommendedRange": ["0.0", "10.0"],
"availableSoftwareInterfaceTypes": ["library", "command-line application", "BioSimulators Docker image"]
},
{
"kisaoId": {
"namespace": "KISAO",
"id": "KISAO_0000488"
},
"id": "seed",
"name": "seed",
"type": "integer",
"value": null,
"recommendedRange": null,
"availableSoftwareInterfaceTypes": ["library", "command-line application", "BioSimulators Docker image"]
}
],
"outputDimensions": [{
"namespace": "SIO",
"id": "SIO_000418"
},
{
"namespace": "SIO",
"id": "SIO_000452"
},
{
"namespace": "SIO",
"id": "SIO_000453"
},
{
"namespace": "SIO",
"id": "SIO_000454"
}
],
"outputVariablePatterns": [
{
"name": "time",
"symbol": {
"value": "time",
"namespace": "urn:sedml:symbol"
}
},
{
"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"}
},
{
"name": "molecule count of a species in a 2-D range",
"target": {"value": "molcountinbox {species} {low-x} {hi-x} {low-y} {hi-y}", "grammar": "Smoldyn"}
},
{
"name": "molecule count of a species in a 3-D range",
"target": {"value": "molcountinbox {species} {low-x} {hi-x} {low-y} {hi-y} {low-z} {hi-z}", "grammar": "Smoldyn"}
},
{
"name": "molecule count of a species in a compartment",
"target": {"value": "molcountincmpt {species} {compartment}", "grammar": "Smoldyn"}
},
{
"name": "molecule count of a state of a species in a compartment",
"target": {"value": "molcountincmpt2 {species} {compartment} {state}", "grammar": "Smoldyn"}
},
{
"name": "molecule count of a species on a surface",
"target": {"value": "molcountonsurf {species} {surface}", "grammar": "Smoldyn"}
},
{
"name": "distribution of molecule counts of a species along a line",
"target": {"value": "molcountspace {species}({state}) {axis} {low} {hi} {bins}", "grammar": "Smoldyn"}
},
{
"name": "1-D distribution of molecule counts of a state of a species along a line of a plane",
"target": {"value": "molcountspace {species}({state}) {axis} {low} {hi} {bins} {low} {hi}", "grammar": "Smoldyn"}
},
{
"name": "1-D distribution of molecule counts of a state of a species along a line of a cube",
"target": {"value": "molcountspace {species}({state}) {axis} {low} {hi} {bins} {low} {hi} {low} {hi}", "grammar": "Smoldyn"}
},
{
"name": "2-D distribution of molecule counts of a state of a species in a plane",
"target": {"value": "molcountspace2d {species}({state}) z {low-x} {hi-x} {bins-x} {low-y} {hi-y} {bins-y}", "grammar": "Smoldyn"}
},
{
"name": "2-D distribution of molecule counts of a state of a species in a cube",
"target": {"value": "molcountspace2d {species}({state}) {axis} {low-1} {hi-1} {bins-1} {low-2} {hi-2} {bins-2} {low-3} {hi-3}", "grammar": "Smoldyn"}
},
{
"name": "1-D distribution of molecule counts of a state of a species along radii of a 1-D circle",
"target": {"value": "molcountspaceradial {species}({state}) {center-x} {radius} {bins}", "grammar": "Smoldyn"}
},
{
"name": "1-D distribution of molecule counts of a state of a species along radii of a circle",
"target": {"value": "molcountspaceradial {species}({state}) {center-x} {center-y} {radius} {bins}", "grammar": "Smoldyn"}
},
{
"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"}
},
{
"name": "1-D distribution of molecule counts of a state of a species along radii of an angular segment of a shere",
"target": {"value": "molcountspacepolarangle {species}({state}) {center-x} {center-y} {center-z} {pole-x} {pole-y} {pole-z} {radius-min} {radius-max} {bins}", "grammar": "Smoldyn"}
},
{
"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"}
},
{
"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"}
}
],
"availableSoftwareInterfaceTypes": ["command-line application", "library", "BioSimulators Docker image"],
"dependencies": []
}],
"interfaceTypes": [
"command-line application",
"library",
"BioSimulators Docker image"
],
"supportedOperatingSystemTypes": [
"Mac OS",
"Linux",
"Windows"
],
"supportedProgrammingLanguages": [{
"namespace": "Linguist",
"id": "C"
},
{
"namespace": "Linguist",
"id": "C++"
},
{
"namespace": "Linguist",
"id": "Python"
}
],
"funding": [],
"biosimulators": {
"imageVersion": "1.0.0",
"specificationVersion": "1.0.0",
"validationTests": null,
"validated": false
}
}