FPbase: The Fluorescent Protein Database

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

3. Create/activate environment with pipenv/virtualenv/conda (python 3 required)
4. Install python requirements for local development

    $ pip install -r requirements/local.txt

5. Install Node.js & npm (homebrew: brew install node)
6. Install frontend requirements and gulpjs

    $ npm install
    $ npm install gulp-cli -g

7. Install a local postgreSQL database (for mac: postgres.app)
8. Create database, and apply migrations

    $ createdb fpbase
    $ python manage.py migrate

9. If desired, load sample data (this may eventually break if the database schema changes enough).

    $ python manage.py loaddata fixtures/testdata.json.gz

10. 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!