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 the steps and results. You can refine the analysis through follow-up messages without writing scripts or leaving Cytoscape. Export your requests and the executed workflow code as a Jupyter notebook to review, rerun, and share your analysis.
CyChat downloads and sets up its Python runtime automatically, so there is no separate Python environment to install. It works with major cloud LLM providers and with local models through Ollama if you prefer to run the LLM on your own machine. Chat histories and memory are stored locally. You can let routine steps run automatically or choose to review and edit generated code before running it.
### 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)
