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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 | ||
} | ||
} |