{"id":20956419,"url":"https://github.com/bluebrain/bluepysubcellular","last_synced_at":"2026-04-20T21:35:57.514Z","repository":{"id":61694395,"uuid":"546095720","full_name":"BlueBrain/BluePySubcellular","owner":"BlueBrain","description":"Python interface to BlueNaaS-Subcellular","archived":false,"fork":false,"pushed_at":"2024-02-12T08:51:43.000Z","size":93,"stargazers_count":1,"open_issues_count":0,"forks_count":2,"subscribers_count":2,"default_branch":"main","last_synced_at":"2026-03-10T18:21:22.042Z","etag":null,"topics":["database","education","experiment","subcellular"],"latest_commit_sha":null,"homepage":"https://github.com/BlueBrain/BluePySubcellular#readme","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/BlueBrain.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":"AUTHORS.txt","dei":null,"publiccode":null,"codemeta":null}},"created_at":"2022-10-05T14:12:38.000Z","updated_at":"2022-11-24T20:31:57.000Z","dependencies_parsed_at":"2025-01-19T23:34:12.480Z","dependency_job_id":"fa5cd0ed-eeaa-47ce-bc61-8202a9d66083","html_url":"https://github.com/BlueBrain/BluePySubcellular","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/BlueBrain/BluePySubcellular","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BlueBrain%2FBluePySubcellular","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BlueBrain%2FBluePySubcellular/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BlueBrain%2FBluePySubcellular/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BlueBrain%2FBluePySubcellular/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/BlueBrain","download_url":"https://codeload.github.com/BlueBrain/BluePySubcellular/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BlueBrain%2FBluePySubcellular/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":32067617,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-20T21:26:33.338Z","status":"ssl_error","status_checked_at":"2026-04-20T21:26:22.081Z","response_time":94,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["database","education","experiment","subcellular"],"created_at":"2024-11-19T01:25:52.977Z","updated_at":"2026-04-20T21:35:57.476Z","avatar_url":"https://github.com/BlueBrain.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# BluePySubcellular\n\nThis repo hosts a Python API for the Subcellular application.\nIt allows users of the Subcellular application to download their existing models and to run simulations in the cloud.\n\n# Installation\n\nTo install the API, first clone the repo:\n\n`git clone https://github.com/BlueBrain/BluePySubcellular.git`\n\nThen install the package using pip:\n\n```\ncd BluePySubcellular\npip install .\n```\n\n\n# Examples\n\nThe following section contain some examples showing how to use this API. For details on the Subcellular app please see the [documentation](https://subcellular-bsp-epfl.apps.hbp.eu/static/docs.html).\n\n## Authentication\n\nIn order to be able to create and fetch models you need you `User id`. To get it go to the Subcellular app http://subcellular-bsp-epfl.apps.hbp.eu/ and click on `User` on the top right corner.\n\n\n## Downloading models\n\nTo download your existing models simply run the following command:\n\n    import BluePySubcellular\n    BluePySubcellular.download_models(\"User id\")\n\n## Creating models\n\nTo create a model from a `bngl` file run\n\n    model_id = BluePySubcellular.create_model(path=\"example.bngl\", name=\"Example model\", user_id=\"User id\")\n\nThis command returns the `model_id` of the new model.\n\n## Adding a geometry and mesh\n\nTo add a geometry and mesh to an existing model you will need 4 files describing the geometry (`.json`, `.ele`, `.node` and `.face` files).\n\n    BluePySubcellular.create_geometry(path=\"example.json\", user_id=user_id, model_id=model_id)\n\n    path: The path to any of the 4 files mentioned above. All 4 files must have the same name (e.g. `spine.json, spine.ele, spine.node, spine.face`).\n    user_id: A valid User id.\n    model_id: A valid model id as returned e.g. from the `create_model` command.\n\n\n## Running simulations\n\nIn order to run a simulation you will need the model id as returned by the create_model command, then instantiate a simulation:\n\n    simulation = BluePySubcellular.Simulation(name, model_id, user_id, solver, dt, t_end, stimuli_path)\n    \n    name: Name of the simulation.\n    model_id: A valid model id as returned e.g. from the `create_model` command.\n    user_id: A valid User id.\n    solver: Name of the solver (one of 'tetexact', 'tetopsplit', 'nfsim', 'ode' or 'ssa'; see the [documentation](https://subcellular-bsp-epfl.apps.hbp.eu/static/docs.html) for details).\n    dt: Time step (in seconds, e.g `0.02`).\n    t_end: Total simulation time (in seconds, e.g. `10.0`)\n    stimuli_path: Optional string argument defining the path to a `.tsv` file containing the stimuli.\n\n\nTo run the simulation simply call:\n\n    simulation.run()\n\nwhich will start the simulation on the servers.\n\nTo monitor the progress of the simulation you can use:\n\n    simulation.progress\n    \nto get the progress of the simulation (in %) and \n\n    simulation.status\n    \nto get the status of the simulation which can be \n\n    started: The simulation is running.\n    error: An error occurred. Please consult the log on the Subcellular app.\n    finished: The simulation has been finished.\n\nTo wait for the results you can use a loop:\n\n\n    while simulation.status not in [\"error\", \"finished\"]:\n        time.sleep(1)\n        pass\n\nFinally you can download the simulation results using\n\n    traces = simulation.get_sim_traces()\n    \nto plot/analyze them further.      \n\n# Citation\nWhen you use this software, we kindly ask you to cite the following DOI (under \"Cite as\"):\n\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7225409.svg)](https://doi.org/10.5281/zenodo.7225409)\n\n\n# Funding \u0026 Acknowledgment\n\nThe development of this software was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government's ETH Board of the Swiss Federal Institutes of Technology and from HBP SGA3.\n\nCopyright (c) 2022-2024 Blue Brain Project/EPFL\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbluebrain%2Fbluepysubcellular","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbluebrain%2Fbluepysubcellular","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbluebrain%2Fbluepysubcellular/lists"}