Quick Start Guides

Tutorials

Papers about Cytoscape

Nature Protocols sample workflow paper by Cytoscape Consortium - a quick overview of Cytoscape functions.

Nature Methods paper by Cytoscape Consortium - a quick overview of Cytoscape App (Plugin) universe.

User Documents

User Manual for the latest version of Cytoscape

Manuals for older versions

Presentations

User FAQ at Biostar

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.

Getting Help

Still cannot find answer for your question? Ask your question in the mailing list.


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