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updated to add biosimulators
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‎biosimulators.json‎

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{
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"id": "smoldyn",
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"name": "Smoldyn",
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"version": "2.74",
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"description": "Computer program for cell-scale biochemical simulations.",
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"urls": [{
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"title": null,
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"type": "Home page",
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"url": "http://www.smoldyn.org/"
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},
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{
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"title": null,
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"type": "Examples",
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"url": "http://www.smoldyn.org/archive.html"
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},
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{
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"title": null,
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"type": "Installation instructions",
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"url": "https://smoldyn.readthedocs.io/en/latest/user/install.html"
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},
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{
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"title": null,
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"type": "Documentation",
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"url": "https://smoldyn.readthedocs.io/"
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},
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{
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"title": null,
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"type": "Source repository",
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"url": "https://github.com/ssandrews/Smoldyn"
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},
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{
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"title": null,
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"type": "License",
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"url": "https://github.com/ssandrews/Smoldyn/blob/master/LICENSE"
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},
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{
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"title": null,
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"type": "Issue tracker",
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"url": "https://github.com/ssandrews/Smoldyn/issues"
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}
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],
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"image": {
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"url": "ghcr.io/ssandrews/smoldyn/biosimulators_smoldyn:latest",
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"format": {
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"namespace": "EDAM",
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"id": "format_3973",
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"version": null,
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"supportedFeatures": []
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},
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"operatingSystemType": "Linux"
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},
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"cli": {
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"packageRepository": "PyPI",
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"package": "smoldyn",
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"command": "python -m smoldyn.biosimulators",
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"installationInstructions": null
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},
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"pythonApi": {
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"package": "smoldyn",
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"module": "smoldyn.biosimulators",
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"installationInstructions": null
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},
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"authors": [{
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"middleName": "S.",
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"firstName": "Steven",
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"lastName": "Andrews",
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"identifiers": [{
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"namespace": "orcid",
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"id": "0000-0002-4576-8107",
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"url": "https://orcid.org/0000-0002-4576-8107"
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}]
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},
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{
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"middleName": null,
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"firstName": "Dilawar",
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"lastName": "Singh",
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"identifiers": [{
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"namespace": "orcid",
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"id": "0000-0002-4645-3211",
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"url": "https://orcid.org/0000-0002-4645-3211"
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}]
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}
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],
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"references": {
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"identifiers": [{
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"namespace": "pypi",
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"id": "smoldyn",
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"url": "https://pypi.org/project/smoldyn/"
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},
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{
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"namespace": "bio.tools",
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"id": "smoldyn",
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"url": "https://bio.tools/smoldyn"
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}
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],
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"citations": [{
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"volume": "33",
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"issue": "5",
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"pages": "710-717",
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"journal": "Bioinformatics",
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"title": "Smoldyn: particle-based simulation with rule-based modeling, improved molecular interaction and a library interface",
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"authors": "Steve S. Andrews",
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"year": 2017,
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"identifiers": [{
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"namespace": "doi",
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"id": "10.1093/bioinformatics/btw700",
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"url": "https://doi.org/10.1093/bioinformatics/btw700"
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}]
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},
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{
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"volume": "31",
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"issue": "14",
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"pages": "2406-2408",
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"journal": "Bioinformatics",
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"title": "Multiscale reaction-diffusion simulations with Smoldyn",
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"authors": "Martin Robinson, Steven S. Andrews & Radek Erban",
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"year": 2015,
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"identifiers": [{
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"namespace": "doi",
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"id": "10.1093/bioinformatics/btv149",
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"url": "https://doi.org/10.1093/bioinformatics/btv149"
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}]
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},
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{
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"pages": "519-542",
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"volume": "804",
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"journal": "Methods in Molecular Biology",
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"title": "Spatial and stochastic cellular modeling with the Smoldyn simulator",
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"authors": "Steven S. Andrews",
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"year": 2012,
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"identifiers": [{
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"namespace": "doi",
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"id": "10.1007/978-1-61779-361-5_26",
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"url": "https://doi.org/10.1007/978-1-61779-361-5_26"
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}]
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},
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{
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"volume": "6",
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"issue": "3",
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"pages": "e1000705",
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"journal": "PLoS Compututational Biology",
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"title": "Detailed simulations of cell biology with Smoldyn 2.1",
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"authors": "Steven S. Andrews, Nathan J. Addy, Roger Brent & Adam P. Arkin",
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"year": 2010,
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"identifiers": [{
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"namespace": "doi",
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"id": "10.1371/journal.pcbi.1000705",
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"url": "https://doi.org/10.1371/journal.pcbi.1000705"
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}]
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}
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]
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},
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"license": {
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"namespace": "SPDX",
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"id": "LGPL-3.0-only"
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},
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"algorithms": [{
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"id": "Smoldyn",
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"name": "Smoldyn (Spatial Stochastic Simulator)",
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"kisaoId": {
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"namespace": "KISAO",
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"id": "KISAO_0000057"
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},
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"modelingFrameworks": [{
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"namespace": "SBO",
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"id": "SBO_0000678"
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}],
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"modelFormats": [{
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"namespace": "EDAM",
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"id": "format_9001",
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"version": null,
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"supportedFeatures": []
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}],
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"modelChangePatterns": [
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{ "name": "Change parameter value", "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"], "target": {"value": "define {name}", "grammar": "Smoldyn"}},
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{ "name": "Change diffusion coefficient", "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"], "target": {"value": "difc {species}", "grammar": "Smoldyn"}},
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{ "name": "Change diffusion coefficient", "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"], "target": {"value": "difc {species}({state})", "grammar": "Smoldyn"}},
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{ "name": "Change diffusion coefficient rule", "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"], "target": {"value": "difc_rule {species}({state})", "grammar": "Smoldyn"}},
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{ "name": "Change surface diffusion coefficient", "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"], "target": {"value": "difm {species}", "grammar": "Smoldyn"}},
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{ "name": "Change surface diffusion coefficient", "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"], "target": {"value": "difm {species}({state})", "grammar": "Smoldyn"}},
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{ "name": "Change surface diffusion coefficient rule", "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"], "target": {"value": "difm_rule {species}({state})", "grammar": "Smoldyn"}},
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{ "name": "Change drift", "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"], "target": {"value": "drift {species}", "grammar": "Smoldyn"}},
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{ "name": "Change drift", "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"], "target": {"value": "drift {species}({state})", "grammar": "Smoldyn"}},
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{ "name": "Change drift rule", "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"], "target": {"value": "drift_rule {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": "Change surface drift rule", "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"], "target": {"value": "surface_drift_rule {species}({state}) {surface} {panel-shape}", "grammar": "Smoldyn"}},
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{ "name": "Kill molecules of a species", "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"], "target": {"value": "killmol {species}({state})", "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"}},
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{ "name": "Kill molecules of a species in a compartment", "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"], "target": {"value": "killmolincmpt {species}({state}) {surface}", "grammar": "Smoldyn"}},
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{ "name": "Kill molecules of a species on a surface", "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"], "target": {"value": "killmolinsphere {species}({state}) {surface}", "grammar": "Smoldyn"}},
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{ "name": "Kill molecules of a species outside the system boundaries", "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"], "target": {"value": "killmoloutsidesystem {species}({state})", "grammar": "Smoldyn"}},
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{ "name": "Change the molecules of a species", "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"], "target": {"value": "fixmolcount {species}", "grammar": "Smoldyn"}},
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{ "name": "Change the molecules of a species in a compartment", "types": ["SedAttributeModelChange", "SedComputeAttributeChangeModelChange", "SedSetValueAttributeModelChange"], "target": {"value": "fixmolcountincmpt {species}({state}) {compartment}", "grammar": "Smoldyn"}},
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{ "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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],
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"simulationFormats": [{
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"namespace": "EDAM",
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"id": "format_3685",
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"version": "L1V3",
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"supportedFeatures": []
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}],
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"simulationTypes": ["SedUniformTimeCourseSimulation"],
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"archiveFormats": [{
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"namespace": "EDAM",
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"id": "format_3686",
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"version": "1",
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"supportedFeatures": []
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}],
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"citations": [],
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"parameters": [{
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"kisaoId": {
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"namespace": "KISAO",
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"id": "KISAO_0000254"
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},
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"id": "accuracy",
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"name": "accuracy",
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"type": "float",
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"value": "10.0",
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"recommendedRange": ["0.0", "10.0"],
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"availableSoftwareInterfaceTypes": ["library", "command-line application", "BioSimulators Docker image"]
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},
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{
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"kisaoId": {
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"namespace": "KISAO",
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"id": "KISAO_0000488"
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},
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"id": "seed",
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"name": "seed",
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"type": "integer",
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"value": null,
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"recommendedRange": null,
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"availableSoftwareInterfaceTypes": ["library", "command-line application", "BioSimulators Docker image"]
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}
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],
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"outputDimensions": [{
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"namespace": "SIO",
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"id": "SIO_000418"
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},
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{
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"namespace": "SIO",
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"id": "SIO_000452"
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},
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{
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"namespace": "SIO",
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"id": "SIO_000453"
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},
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{
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"namespace": "SIO",
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"id": "SIO_000454"
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}
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],
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"outputVariablePatterns": [
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{
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"name": "time",
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"symbol": {
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"value": "time",
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"namespace": "urn:sedml:symbol"
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}
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},
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{
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"name": "molecule count of a species",
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"target": {"value": "molcount {species}", "grammar": "Smoldyn"}
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},
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{
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"name": "molecule count of a state of a species",
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"target": {"value": "molcountspecies {species}({state})", "grammar": "Smoldyn"}
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},
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{
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"name": "molecule count of a species in a 1-D range",
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"target": {"value": "molcountinbox {species} {low-x} {hi-x}", "grammar": "Smoldyn"}
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},
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{
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"name": "molecule count of a species in a 2-D range",
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"target": {"value": "molcountinbox {species} {low-x} {hi-x} {low-y} {hi-y}", "grammar": "Smoldyn"}
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},
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{
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"name": "molecule count of a species in a 3-D range",
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"target": {"value": "molcountinbox {species} {low-x} {hi-x} {low-y} {hi-y} {low-z} {hi-z}", "grammar": "Smoldyn"}
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},
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{
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"name": "molecule count of a species in a compartment",
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"target": {"value": "molcountincmpt {species} {compartment}", "grammar": "Smoldyn"}
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},
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{
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"name": "molecule count of a state of a species in a compartment",
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"target": {"value": "molcountincmpt2 {species} {compartment} {state}", "grammar": "Smoldyn"}
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},
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{
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"name": "molecule count of a species on a surface",
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"target": {"value": "molcountonsurf {species} {surface}", "grammar": "Smoldyn"}
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},
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{
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"name": "distribution of molecule counts of a species along a line",
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"target": {"value": "molcountspace {species}({state}) {axis} {low} {hi} {bins}", "grammar": "Smoldyn"}
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},
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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 plane",
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"target": {"value": "molcountspace {species}({state}) {axis} {low} {hi} {bins} {low} {hi}", "grammar": "Smoldyn"}
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},
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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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"target": {"value": "molcountspace {species}({state}) {axis} {low} {hi} {bins} {low} {hi} {low} {hi}", "grammar": "Smoldyn"}
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},
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{
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"name": "2-D distribution of molecule counts of a state of a species in a plane",
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"target": {"value": "molcountspace2d {species}({state}) z {low-x} {hi-x} {bins-x} {low-y} {hi-y} {bins-y}", "grammar": "Smoldyn"}
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},
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{
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"name": "2-D distribution of molecule counts of a state of a species in a cube",
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"target": {"value": "molcountspace2d {species}({state}) {axis} {low-1} {hi-1} {bins-1} {low-2} {hi-2} {bins-2} {low-3} {hi-3}", "grammar": "Smoldyn"}
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},
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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 1-D circle",
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"target": {"value": "molcountspaceradial {species}({state}) {center-x} {radius} {bins}", "grammar": "Smoldyn"}
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},
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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 circle",
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"target": {"value": "molcountspaceradial {species}({state}) {center-x} {center-y} {radius} {bins}", "grammar": "Smoldyn"}
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},
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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",
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"target": {"value": "molcountspaceradial {species}({state}) {center-x} {center-y} {center-z} {radius} {bins}", "grammar": "Smoldyn"}
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},
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{
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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 circle",
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"target": {"value": "molcountspacepolarangle {species}({state}) {center-x} {center-y} {pole-x} {pole-y} {radius-min} {radius-max} {bins}", "grammar": "Smoldyn"}
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},
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{
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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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"target": {"value": "molcountspacepolarangle {species}({state}) {center-x} {center-y} {center-z} {pole-x} {pole-y} {pole-z} {radius-min} {radius-max} {bins}", "grammar": "Smoldyn"}
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},
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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 circle around molecules of second state of a second species",
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"target": {"value": "radialdistribution {species-1}({state-1}) {species-2}({state-2}) {radius} {bins}", "grammar": "Smoldyn"}
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},
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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 around molecules of second state of a second species",
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"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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}
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],
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"availableSoftwareInterfaceTypes": ["command-line application", "library", "BioSimulators Docker image"],
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"dependencies": []
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}],
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"interfaceTypes": [
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"command-line application",
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"library",
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"BioSimulators Docker image"
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],
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"supportedOperatingSystemTypes": [
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"Mac OS",
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"Linux",
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"Windows"
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],
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"supportedProgrammingLanguages": [{
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"namespace": "Linguist",
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"id": "C"
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},
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{
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"namespace": "Linguist",
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"id": "C++"
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},
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{
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"namespace": "Linguist",
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"id": "Python"
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}
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],
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"funding": [],
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"biosimulators": {
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"imageVersion": "1.0.0",
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"specificationVersion": "1.0.0",
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"validationTests": null,
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"validated": false
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}
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}

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