README.md

FPbase: The Fluorescent Protein Database

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