CyChat puts a chat assistant inside Cytoscape Desktop. You describe what you want in plain
language, like "build a PPI network for these genes" or "export a PNG", and
CyChat writes the Cytoscape Automation code, runs it in your open session, and shows you
each step. No scripting, no jumping to a separate chat window, and you keep a record of
everything that was done so your analysis stays reproducible.
CyChat comes with its own Python runtime built in, so there is nothing extra to install.
It works with the major cloud LLM providers and with local models through Ollama, so you
can keep your data and keys on your own machine if you prefer. The agent can only download files/data through py4cytoscape and pandas after your approval.
> ⚠️ **Heads up on size.** CyChat bundles its own Python runtime, so the app is fairly large
> and can take a bit of time to download and install. That is normal, just give it a moment
> on the first install.
### Citation
Accepted as Short Paper at CIBB 2026:
Liebold J, Stahl M, Schulze J-O, Razavi MM, Bader GB, Kurtz S, Baumbach J.
**CyChat: a conversational Cytoscape app for no-code, reproducible network analysis.** bioRxiv. 2026. [https://doi.org/10.64898/2026.08.28.747833](https://doi.org/10.64898/2026.08.28.747833)
