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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
- Quick tour of Cytoscape
- tutorials.cytoscape.org
- Cytoscape YouTube channel
- Published figures using Cytoscape
Automation and Scripting
Readings about Cytoscape
- Nature Protocols sample workflow paper by Cytoscape Consortium - a quick overview of Cytoscape functions.
- Cytoscape Automation by Cytoscape Consortium - empowering workflow-based network analysis.
- Nature Methods paper by Cytoscape Consortium - a quick overview of Cytoscape App (Plugin) universe.
- Original Cytoscape paper (2003)
User Manual
Presentations
- Introduction to Cytoscape (Latest)
- 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.
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