- Area of Interest: Data Integration & Visualization - University of California, San Diego Trey Ideker Lab - This presentation file will be available on my Speaker Deck account - speakerdeck.com/keiono
visualization only when it is necessary - Animation, 3D, charts on nodes, etc. - You can do a lot of things with basic set of Visual Properties - Use minimal set of visual channels to make the visualization understandable - Define story (or goal) before creating actual visualization - Understand human perception
is that they increasingly use programmers to abstract data so that mundane information looks visually appealing - this is motivated by the desire to appear on the cover of the glossy life sciences journals. - Comment from Wired Magazine article “Circle of Life: The Beautiful New Way to Visualize Biological Data” http://www.wired.com/wiredscience/2013/11/wired-data-life-martin-krzywinski/
strongest visual channels for mapping your data - Use these two for your important data - Automatic layout algorithms can be applied only to selected group of nodes
— You can analyze network with hundreds of Apps and Cytoscape built-in features - Now you need to publish your results - As PDF (Static Image) - As Interactive Web Page (New!)
real-world problems, National Resources for Network Biology (NRNB) is always open for collaboration! - NRNB Provides support for both of - Scientific Research - Application / Tool Development - nrnb.org
Protein–Protein Interactions. Part I. Experimental Techniques and Databases Shoemaker BA, Panchenko AR (2007) Deciphering Protein–Protein Interactions. Part I. Experimental Techniques and Databases. PLoS Comput Biol 3(3): e42.doi:10.1371/journal.pcbi.0030042 - Deciphering Protein–Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners Shoemaker BA, Panchenko AR (2007) Deciphering Protein–Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners. PLoS Comput Biol 3(4): e43. doi:10.1371/ journal.pcbi.0030043
A travel guide to Cytoscape plugins Rintaro 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 - Sample Protocol − Integration of biological networks and gene expression data using Cytoscape Cline, et al. Nature Protocols, 2, 2366-2382 (2007).