Set up
Skills are installed by placing their folder where your agent loads skills.
The download comes from github.com/pnnl/ChatGEM itself, not from our server, so what you get is exactly what its author published.
Install instructions come from the README
Skills do not use an MCP config. Follow the steps in the README below.
README
synced Oct 22, 2026ChatGEM
Code and data files accompanying the chatGEM manuscript.
chatGEM accelerates genome scale metabolic modeling workflows via a grounded coding agent
Repository layout
RAG_COBRApy_codes/ # 52 numbered COBRApy scripts + model files and data assets
ecGEM_ChatGEM/ # per-experiment enzyme-constrained GEM runs for P. putida KT2440 OPAL strains
iBAQ/ # iBAQ proteomics processing scripts and raw data
/skills/chatgem/ # ChatGEM agent skill --> move to .claude to use with Claude code
Setup
git clone https://github.com/pnnl/ChatGEM
cd ChatGEM
uv sync
Related Work
ADEPT agentic platform and core system: https://github.com/pnnl/adept-agentic and https://github.com/pnnl/adept-agentic-framework-core
ChatGEM preprint: https://www.biorxiv.org/content/10.64898/2026.07.20.739662v2
Niaz Chowdhury & August George, 2026, PNNL