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Logo

FPbase: The Fluorescent Protein Database

License: GPL v3 cookie Build Status DOI

https://www.fpbase.org

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

Installation for local development

  1. Clone repo and cd into directory
    $ git clone https://github.com/tlambert03/FPbase.git
    $ cd FPbase
  1. Create/activate environment with pipenv/virtualenv/conda (python 3 required)
  2. Install python requirements for local development
    $ pip install -r requirements/local.txt
  1. Install Node.js & npm (homebrew: brew install node)
  2. Install frontend requirements and gulpjs
    $ npm install
    $ npm install gulp-cli -g
  1. Install a local postgreSQL database (for mac: postgres.app)
  2. Create database, and apply migrations
    $ createdb fpbase
    $ python manage.py migrate
  1. If desired, load sample data (this may eventually break if the database schema changes enough).
    $ python manage.py loaddata fixtures/testdata.json.gz
  1. Compile assets and start server:
    $ gulp

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!