since 2005 - Core modules design & implementation - Release management - Area of Interest: Data Integration & Visualization - University of California, San Diego Trey Ideker Lab
Protein - DNA - Genetic (Epistasis) - Synthetic lethality - Biochemical Reactions - Compound - Enzyme - Compound Cartoon representation of a complex between DNA and the protein p53 Node Node Edge
networks) 3.Analyze and Visualize Networks 4.Prepare for Publication - A specific example of this workflow: − Cline, et al. “Integration of biological networks and gene expression data using Cytoscape”, Nature Protocols, 2, 2366-2382 (2007). Cytoscape Workflow
to get biologically meaningful analysis result only from network topology (= structure) - Meaningful Visualization - Expression values - Node Color - Gene Function - Node Shape - etc.
- Emphasize what you want to tell by the image - Use color, shape, size of objects effectively! - Excellent resource for data visualization - Tamara Munzner’s Web Site: http://www.cs.ubc.ca/~tmm/
Saito, Michael E Smoot, Keiichiro Ono, Johannes Ruscheinski, Peng- Liang Wang, Samad Lotia, Alexander R Pico, Gary D Bader, Trey Ideker (2012) Nature Methods 9 (11) p. 1069-1076
Bend, Background Images - Server-side applications - Headless Mode (Command-line) - More advanced visualization by new rendering engines - For developers: Cleaner API
the web browsers - Take advantage of HTML5/Canvas - Sharing core concepts - Visual Style, Layouts, etc. - A building block for web apps, NOT a complete web application