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FPbase: The Fluorescent Protein Database

License: GPL v3 CI Cov DOI

Source code for https://www.fpbase.org

Documentation and info on using the site: https://help.fpbase.org.

See also: Using FPbase: The Fluorescent Protein Database (2023) Methods Mol Biol . 2023;2564:1-45. doi: 10.1007/978-1-0716-2667-2_1

Installation for local development

  1. Clone repo and cd into directory

    git clone https://github.com/tlambert03/FPbase.git
    cd FPbase
  2. Create/activate environment using python 3.11 with pipenv/virtualenv/conda

  3. Install python requirements for local development

    pip install -r backend/requirements/local.txt
    # note: on mac silicon, you might have difficulty compiling psycopg2
    # in which case you should pip install psycopg2-binary instead
  4. Make sure that you have postgres installed.

    On macOS, with homebrew:

    brew install postgresql@15
    brew services start postgresql@15
  5. Install Node.js & pnpm (homebrew: brew install node)

    npm i -g pnpm
  6. Install frontend requirements

    pnpm install
  7. Install a local postgreSQL database (for mac: postgres.app)

  8. Create database, and apply migrations

    createdb fpbase
    python backend/manage.py migrate
  9. start dev servers:

    npm run start
    python backend/manage.py runserver

How to cite FPbase

If you have used FPbase in a publication, or are referencing an FPbase protein collection or microscope in your methods, please cite the following paper:

Lambert, TJ (2019) FPbase: a community-editable fluorescent protein database. Nature Methods. doi: 10.1038/s41592-019-0352-8

Contributing

If you would like to contribute to the website directly (for instance, to add a feature or fix an error), please branch off of develop and submit a pull request.

If you have data that you would like to contribute to the database, please do not do that here. All data can be submitted directly on the website:

Submit a fluorescent protein

Submit spectral information

Thank you to these providers for supporting open source projects