| --- |
| license: mit |
| language: |
| - en |
| --- |
| # FPbase: The Fluorescent Protein Database |
| More than 1000 experimental fluorescent proteins with structured and searchable fluorescence polarization (FP) data |
| https://www.fpbase.org. |
|
|
| ## Quickstart Usage |
|
|
| ### installation |
| Clone repo and cd into directory |
|
|
| $git clone https://github.com/tlambert03/FPbase.git |
| $cd FPbase |
| |
| Create and activate environment using python 3.13 with conda |
| |
| $conda create -n FPbase python=3.13 |
| $conda activate FPbase |
| |
| (optional) Install uv |
| |
| $curl -LsSf https://astral.sh/uv/install.sh | sh |
| |
| Install python requirements for local development |
| |
| $uv sync |
| $sudo apt install postgresql postgresql-contrib -y |
| $curl -fsSL https://deb.nodesource.com/setup_20.x | sudo -E bash - |
| $sudo apt install -y nodejs |
| $npm i -g pnpm |
| |
| Install frontend requirements |
| |
| $pnpm install |
| |
| Create database, and apply migrations |
| |
| $createdb fpbase |
| $python backend/manage.py migrate |
| |
| Start and test dev servers |
| |
| $pnpm dev |
| |
| ### fetch database information |
| Run the [pull_fpbase.py](https://huggingface.co/datasets/Kaleychinoy/FPbase_databazaar_2026/blob/main/src/pull_fpbase.py) |
| |
| $python /src/pull_fpbase.py |
| |
| ## Output description |
| Check the [fpbase_raw.csv](https://huggingface.co/datasets/Kaleychinoy/FPbase_databazaar_2026/tree/main/data) |
| - **name: protein name** |
| - **fpbase_id: ID in FPbase** |
| - **ex_max: excitation maximum** |
| - **em_max: emission maximum** |
| - **emhex: emission color** |
| - **exhex: emission color** |
| - **ext_coeff: extinction coefficient** |
| - **qy: quantum yield** |
| - **lifetime_ns: lifetime(ns)** |
| - **pdb: PDB ID**: |
| - **genbank: genbank ID** |
| - **uniprot: Uniprot ID** |
| - **aggregation: oligomeric state** |
| - **switch_type: photo-switching types** |
| |
| ### Dataset Description |
| (https://github.com/tlambert03/FPbase) |
| FPbase is a free and open-source, community-editable database for fluorescent proteins (FPs) and their properties. |
| The primary objective is to aggregate structured and searchable FP data that is of interest to the imaging community and FP developers. |
| Each protein in the database has a dedicated page showing amino acid sequence, accession IDs (e.g. GenBank, UniProt), evolution lineages and mutations, fluorescence attributes, structural data, references that introduced or characterized the protein, |
| and more. Excerpts from primary literature can be entered to store key information about a protein that is otherwise difficult to capture within the current database schema. |
