{"id":15576807,"url":"https://github.com/tlambert03/fpbase","last_synced_at":"2025-04-09T14:08:36.895Z","repository":{"id":53732325,"uuid":"111461793","full_name":"tlambert03/FPbase","owner":"tlambert03","description":"The Fluorescent Protein Database","archived":false,"fork":false,"pushed_at":"2025-04-01T16:56:36.000Z","size":68795,"stargazers_count":66,"open_issues_count":21,"forks_count":5,"subscribers_count":3,"default_branch":"main","last_synced_at":"2025-04-02T08:48:37.065Z","etag":null,"topics":["database","fluorescence","microscopy"],"latest_commit_sha":null,"homepage":"https://www.fpbase.org","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/tlambert03.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"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":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2017-11-20T20:55:19.000Z","updated_at":"2025-03-19T12:11:21.000Z","dependencies_parsed_at":"2025-03-10T21:31:58.276Z","dependency_job_id":null,"html_url":"https://github.com/tlambert03/FPbase","commit_stats":{"total_commits":1745,"total_committers":9,"mean_commits":"193.88888888888889","dds":"0.11117478510028656","last_synced_commit":"28eb1fe9e4a3bc4e5f8334f5fec41f70f7982cba"},"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tlambert03%2FFPbase","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tlambert03%2FFPbase/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tlambert03%2FFPbase/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tlambert03%2FFPbase/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/tlambert03","download_url":"https://codeload.github.com/tlambert03/FPbase/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248054206,"owners_count":21039952,"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","fluorescence","microscopy"],"created_at":"2024-10-02T18:58:32.956Z","updated_at":"2025-04-09T14:08:36.847Z","avatar_url":"https://github.com/tlambert03.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![Logo](_resources/logo_green_wide@1x.gif)](https://www.fpbase.org)\n\n# FPbase: The Fluorescent Protein Database\n\n[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-brightgreen.svg)](https://www.gnu.org/licenses/gpl-3.0)\n[![CI](https://github.com/tlambert03/FPbase/actions/workflows/ci.yml/badge.svg)](https://github.com/tlambert03/FPbase/actions/workflows/ci.yml)\n[![Cov](https://codecov.io/gh/tlambert03/FPbase/branch/main/graph/badge.svg)](https://codecov.io/gh/tlambert03/FPbase)\n[![DOI](https://zenodo.org/badge/DOI/10.1038/s41592-019-0352-8.svg)](https://doi.org/10.1038/s41592-019-0352-8)\n\nSource code for \u003chttps://www.fpbase.org\u003e\n\nDocumentation and info on using the site: \u003chttps://help.fpbase.org\u003e.\n\nSee also: [Using FPbase: The Fluorescent Protein\nDatabase](https://pubmed.ncbi.nlm.nih.gov/36107335/) (2023) *Methods Mol Biol* .\n2023;2564:1-45. doi: 10.1007/978-1-0716-2667-2_1\n\n## Installation for local development\n\n1. Clone repo and cd into directory\n\n    ```bash\n    git clone https://github.com/tlambert03/FPbase.git\n    cd FPbase\n    ```\n\n1. Create/activate environment **using python 3.11** with pipenv/virtualenv/conda\n1. Install python requirements for local development\n\n    ```bash\n    pip install -r backend/requirements/local.txt\n    # note: on mac silicon, you might have difficulty compiling psycopg2\n    # in which case you should pip install psycopg2-binary instead\n    ```\n\n1. Make sure that you have `postgres` installed.\n\n   On macOS, with homebrew:\n\n   ```sh\n   brew install postgresql@15\n   brew services start postgresql@15\n   ```\n\n1. Install [Node.js](https://nodejs.org/en/) \u0026 [pnpm](https://pnpm.js.org/en/) (homebrew: `brew install node`)\n\n    ```bash\n    npm i -g pnpm\n    ```\n\n1. Install frontend requirements\n\n    ```bash\n    pnpm install\n    ```\n\n1. Install a local postgreSQL database (for mac: [postgres.app](https://postgresapp.com/))\n1. Create database, and apply migrations\n\n    ```bash\n    createdb fpbase\n    python backend/manage.py migrate\n    ```\n\n1. start dev servers:\n\n    ```bash\n    npm run start\n    python backend/manage.py runserver\n    ```\n\n### How to cite FPbase\n\nIf you have used FPbase in a publication, or are referencing an FPbase protein\ncollection or microscope in your methods, please cite the following paper:\n\nLambert, TJ (2019) FPbase: a community-editable fluorescent protein database.\n*Nature Methods*. doi:\n[10.1038/s41592-019-0352-8](https://doi.org/10.1038/s41592-019-0352-8)\n\n### Contributing\n\nIf you would like to contribute to the website directly (for instance, to add a\nfeature or fix an error), please branch off of develop and submit a pull\nrequest.\n\nIf you have data that you would like to contribute to the database, please do\n*not* do that here.  All data can be submitted directly on the website:\n\n[Submit a fluorescent protein](https://www.fpbase.org/submit/)\n\n[Submit spectral information](https://www.fpbase.org/spectra/submit/)\n\n### Thank you to these providers for supporting open source projects\n\n\u003cbr/\u003e\n\n[\u003cimg src=\"backend/proteins/static/images/logo-algolia-nebula-blue-full.svg\"\nwidth=\"170\"\u003e](https://www.algolia.com/)\n\n[\u003cimg src=\"_resources/sentry-logo-black.svg\"\nwidth=\"200\"\u003e](https://sentry.io/)\n\n[\u003cimg src=\"_resources/gitbook_avatar-rectangle.png\"\nwidth=\"200\"\u003e](https://www.gitbook.com/)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftlambert03%2Ffpbase","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftlambert03%2Ffpbase","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftlambert03%2Ffpbase/lists"}