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https://github.com/tlambert03/fpbase
The Fluorescent Protein Database
https://github.com/tlambert03/fpbase
database fluorescence microscopy
Last synced: 5 days ago
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The Fluorescent Protein Database
- Host: GitHub
- URL: https://github.com/tlambert03/fpbase
- Owner: tlambert03
- License: gpl-3.0
- Created: 2017-11-20T20:55:19.000Z (over 7 years ago)
- Default Branch: main
- Last Pushed: 2025-02-03T23:47:19.000Z (18 days ago)
- Last Synced: 2025-02-07T05:05:07.806Z (14 days ago)
- Topics: database, fluorescence, microscopy
- Language: Python
- Homepage: https://www.fpbase.org
- Size: 65.3 MB
- Stars: 65
- Watchers: 4
- Forks: 5
- Open Issues: 21
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
[](https://www.fpbase.org)
# FPbase: The Fluorescent Protein Database
[](https://www.gnu.org/licenses/gpl-3.0)
[](https://github.com/tlambert03/FPbase/actions/workflows/ci.yml)
[](https://codecov.io/gh/tlambert03/FPbase)
[](https://doi.org/10.1038/s41592-019-0352-8)
Source code for
Documentation and info on using the site: .
See also: [Using FPbase: The Fluorescent Protein
Database](https://pubmed.ncbi.nlm.nih.gov/36107335/) (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
```bash
git clone https://github.com/tlambert03/FPbase.git
cd FPbase
```
1. Create/activate environment **using python 3.11** with pipenv/virtualenv/conda
1. Install python requirements for local development
```bash
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
```
1. Make sure that you have `postgres` installed.
On macOS, with homebrew:
```sh
brew install postgresql@15
brew services start postgresql@15
```
1. Install [Node.js](https://nodejs.org/en/) & [pnpm](https://pnpm.js.org/en/) (homebrew: `brew install node`)
```bash
npm i -g pnpm
```
1. Install frontend requirements
```bash
pnpm install
```
1. Install a local postgreSQL database (for mac: [postgres.app](https://postgresapp.com/))
1. Create database, and apply migrations
```bash
createdb fpbase
python backend/manage.py migrate
```
1. start dev servers:
```bash
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](https://doi.org/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](https://www.fpbase.org/submit/)
[Submit spectral information](https://www.fpbase.org/spectra/submit/)
### Thank you to these providers for supporting open source projects
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