From 4852d31c3bac2c9d12fdf139f417d9a9db3bd220 Mon Sep 17 00:00:00 2001 From: "spaceBearAmadeus (Alex)" Date: Wed, 28 Aug 2024 11:05:08 -0400 Subject: [PATCH] updated to add biosimulators --- biosimulators.json | 374 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 374 insertions(+) create mode 100644 biosimulators.json diff --git a/biosimulators.json b/biosimulators.json new file mode 100644 index 0000000..2b649bd --- /dev/null +++ b/biosimulators.json @@ -0,0 +1,374 @@ +{ + "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 + } + } \ No newline at end of file