Quick Start Guides
Introduction to Cytoscape (3.x)
Introduction to Cytoscape (2.x)
Tutorials
Open Tutorials: for 3.x
Open Tutorials: for 2.x
Readings 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.
- Original Cytoscape paper (2003)
- Updated Cytoscape paper (2011)
User Documents
User Manual for the latest version of Cytoscape
Manuals for older versions
Presentations
- Introduction to Cytoscape
- Basic Tutorial
- Advanced Tutorial
- International Conference on Systems Biology Demos
- Cytoscape presentation slides at Speaker Deck
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