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Technical Help

Bioinformatics StackExchange -- Search and ask questions about software installation, operation and troubleshooting. On this forum, you can also 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

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  • Write information about your platform: OS/Java version, memory size, etc.
  • Add example files: network/attribute files