Advanced Topic: Automation

Slides: https://cytoscape.org/cytoscape-tutorials/presentations/advanced-automation-2026-ismb.html


Chris Churas, Jing Chen, John "Scooter" Morris

UCSD and UCSF (retired)
12 July 2026

Goals and Motivations

By the end of this workshop you should be able to:
  • Command programmatic control over Cytoscape
  • Agentic Integration
  • Integrate Cytoscape into your web applications
  • Extend Cytoscape Web with a Python Service App
Cytoscape Automation Agentic Integration Integrate Cytoscape with your Web Apps Service Apps Wrap-up

Automation Use Cases

Here are some common automation workflows. Pick one that is similar to the type of data you work with. Follow the steps to learn about package functions.

Ask questions if anything is unclear!

  1. Transcriptomic data: Rmd, ipynb
  2. Tumor expression and mutation data: Rmd, ipynb
  3. Proteomics data: Rmd, ipynb
Cytoscape Automation Agentic Integration Integrate Cytoscape with your Web Apps Service Apps Wrap-up
Cytoscape Automation Agentic Integration Integrate Cytoscape with your Web Apps Service Apps Wrap-up
Cytoscape Automation Agentic Integration Integrate Cytoscape with your Web Apps Service Apps Wrap-up
Cytoscape Automation Agentic Integration Integrate Cytoscape with your Web Apps Service Apps Wrap-up

Wrap-up

What have we learned?

  • Command programmatic control over Cytoscape
  • Agentic Integration
  • Integrate Cytoscape into your web applications
  • Extend Cytoscape Web with a Python Service App

Wrap-up

Don't forget about Notebooks!

  • Notebooks: ipynb and Rmd files
  • GitHub: ipynb and Rmd(nb.html) files
  • Google Colab: Python and R

Wrap-up

Questions and Discussion

  • Anything unclear?
  • Anything missing?

Thank You!

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