project-discovery-dashboard

iGEM project discovery and parts registry exploration

Installation

Use mamba/conda to install the environments:

mamba create -f env.yaml

# activate environment
mamba activate project_discovery_dashboard

Usage

Scrape team data using the old igem portal

python script_name.py --start_year 2008 --end_year 2023 --outfile data/raw/team_list_2008_2023.csv

Exploring Parts Registry

• mysqldump of the parts registry was downloaded from http://parts.igem.org/partsdb/download.cgi?type=parts
• the sqldump are then converted to sqlite using mysql2sqlite
• to ease analytics using streamlit, the sqlite file is converted to duckdb
• the converted sqlite and duckdb files are now available in zenodo: https://zenodo.org/records/10067040
• download the zenodo sqlite:

mkdir -p "data/raw"
wget -P data/raw https://zenodo.org/records/10067040/files/igem_parts_registry.sqlite

Notebooks

There are several notebooks provided to explore both the wiki and parts registry. You can run Jupyter with jupyterlab and explore the notebooks located in the notebooks folder

Streamlit

• Download the duckdb file to data/processed

mkdir -p "data/processed"
wget -P data/raw https://zenodo.org/records/10071080/files/duck.db

• Run streamlit with: streamlit run home.py

Development

Using pre-commits

Activate pre-commit by:

pre-commit

Google Colaboratory notes (data viz): https://colab.research.google.com/drive/1O6zHdq1NvdNuM-UcIzns9Kid71uYKZQZ?usp=sharing