{"id":20956479,"url":"https://github.com/bluebrain/bluenaas-subcellular","last_synced_at":"2025-07-03T17:35:33.143Z","repository":{"id":63359685,"uuid":"537068186","full_name":"BlueBrain/BlueNaaS-Subcellular","owner":"BlueBrain","description":"A web environment for the simulation of brain molecular networks.","archived":false,"fork":false,"pushed_at":"2024-05-29T18:55:19.000Z","size":5705,"stargazers_count":4,"open_issues_count":0,"forks_count":2,"subscribers_count":8,"default_branch":"main","last_synced_at":"2025-03-13T06:11:56.989Z","etag":null,"topics":["database","experiment","gui","subcellular","visualization"],"latest_commit_sha":null,"homepage":"https://github.com/bluebrain/bluenaas-subcellular#readme","language":"Vue","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.txt","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":"2022-09-15T14:36:03.000Z","updated_at":"2024-05-29T18:55:22.000Z","dependencies_parsed_at":"2024-01-22T13:31:21.135Z","dependency_job_id":"b193e0c3-3280-4da4-bb22-393dc36f1747","html_url":"https://github.com/BlueBrain/BlueNaaS-Subcellular","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/BlueBrain/BlueNaaS-Subcellular","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BlueBrain%2FBlueNaaS-Subcellular","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BlueBrain%2FBlueNaaS-Subcellular/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BlueBrain%2FBlueNaaS-Subcellular/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BlueBrain%2FBlueNaaS-Subcellular/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/BlueBrain","download_url":"https://codeload.github.com/BlueBrain/BlueNaaS-Subcellular/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BlueBrain%2FBlueNaaS-Subcellular/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":263370158,"owners_count":23456423,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","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","experiment","gui","subcellular","visualization"],"created_at":"2024-11-19T01:26:11.254Z","updated_at":"2025-07-03T17:35:33.125Z","avatar_url":"https://github.com/BlueBrain.png","language":"Vue","funding_links":[],"categories":[],"sub_categories":[],"readme":"# BlueNaaS-Subcellular\n\n\u003cimg alt=\"eFEL Banner\" src=\"https://github.com/BlueBrain/BlueNaaS-Subcellular/blob/main/BPP-BlueNaaS-Subcellular-Github.jpg\" width=\"800\"/\u003e\n\nBlueNaaS-Subcllular was developed as a software environment for\nsimulation of brain molecular networks.\nIt was designed to reach several objectives related to major restrictions of currently available\nsoftware tools, such as the lack of integration with existing biological data relevant for modeling\nand low compatibility of different types of models.\n\n## System design\n\nSee [System design document](SYSTEM-DESIGN.md)\n\n## Dev env run\n\nThere are targets in makefile to start development environment for all parts of the app.\nBackend dev setup needs docker image to be present in the system when starting, which can\nbe build with `make docker_build_latest` from `./backend` directory.\n\nBackend dev environment requires docker engine to be installed and consists of:\n\n- mongoDB instance\n- backend server\n- sim worker replica with minimum one instance\n\nCheck the `./backend/docker-compose.yml` for more information.\n\nTo start:\n\n```bash\nmake run_dev_backend\n```\n\nDev frontend env is powered by Webpack and can be started with:\n\n```bash\nmake run_dev_frontend\n```\n\nTo start both dev envs in a single session use:\n\n```bash\nmake run_dev\n```\n\n## Usage\n\nSee [Guidebook](https://subcellular-bsp-epfl.apps.hbp.eu/static/docs.html)\n\n## Deployment\n\nMakefile has a `create_oo_deployment` target that will deploy current version of the app to an\nOpenShift instance. This target will create OpenShift deployment configs, services and external\nroutes needed by the app to function.\nSee `makefile` for configuration and options; requires OpenShift CLI.\n\n## Citation\n\nWhen you use this software, we kindly ask you to cite the following DOI (under \"Cite as\"):\n[![DOI](https://zenodo.org/badge/537068186.svg)](https://zenodo.org/badge/latestdoi/537068186)\n\n\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.\n\nThis  project/research  received  funding  from  the  European  Union’s  Horizon  2020  Framework  Programme  for  Research  and  Innovation  under  the  Framework  Partnership  Agreement  No.  650003  (HBP FPA).\n\nCopyright (c) 2022-2024 Blue Brain Project/EPFL\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbluebrain%2Fbluenaas-subcellular","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbluebrain%2Fbluenaas-subcellular","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbluebrain%2Fbluenaas-subcellular/lists"}