CSB Assignment Week 6

Assignments for Week 6

Exercises for this week relate to this week's lecture.
Pre-reading for this week will prepare next week's lecture.
Exercises and pre-reading will be topics on next week's quiz.

Exercises

Cytoscape 3 tutorials ([1])

• Introduction to Cytoscape 3: User Interface
• Introduction to Cytoscape 3.1: Part 2 - importing networks
• Introduction to Cytoscape 3: Part 3 - Web import
• Cytoscape 3: Filtering and editing

Pre-reading

Fung et al. (2012) Visualization of the interactome: what are we looking at?. Proteomics 12:1669-86. (pmid: 22610544)

[ PubMed ] [ DOI ] Network visualization of the interactome has been become routine in systems biology research. Not only does it serve as an illustration on the cellular organization of protein-protein interactions, it also serves as a biological context for gaining insights from high-throughput data. However, the challenges to produce an effective visualization have been great owing to the fact that the scale, biological context and dynamics of any given interactome are too large and complex to be captured by a single visualization. Visualization design therefore requires a pragmatic trade-off between capturing biological concept and being comprehensible. In this review, we focus on the biological interpretation of different network visualizations. We will draw on examples predominantly from our experiences but elaborate them in the context of the broader field. A rich variety of networks will be introduced including interactomes and the complexome in 2D, interactomes in 2.5D and 3D and dynamic networks.