User Links

Have a Question?

Technical Help

StackOverflow -- Search and ask questions about software installation, operation and troubleshooting. Be sure to tag your question with "cytoscape" so we can find it!

Biology and Bioinformatics Help

BioStars -- Search and ask questions about data anaysis and visualization, including recommended apps, databases and workflows. Be sure to tag your question with "cytoscape" so we can find it!

Tutorials & Demos

Automation and Scripting

Readings about Cytoscape

Data Sources

Biological Networks

  • Pathguide - Comprehensive list of pathway/interaction databases
  • PSICQUIC - Standardized web service supported by most of the major data providers

Social Science

Social networking services are good data sources. You can write simple web crawler using scripting languages and save it as standard data format such as GML, GraphML, or simple tab-delimited text. Cytoscape supports many standard graph file formats.

Community Resources

Check out the other community resources for Cytoscape.

Tips for Asking Questions

  • Be specific: write down steps to reproduce your issues or details about new feature you want.
  • Write information about your platform: OS/Java version, memory size, etc.
  • Add example files: network/attribute files