visualization problems: interesting research problems for postgraduate thesis [request for experts/researchers]

Question

[a.jeffery.ca]

Hello everyone!

what I'm going to ask for might sound a little bit broad and not too specific, and that is because I'm new to bioinformatics (my background is in computer science). I'm now interested in building some software tool for analysis/visualization purposes for my thesis, and I'm carious to know what are some of the "hot" or recent research topics/challenges in proteomics or genomics pertaining data analysis and visualization that can be solved computationally. I read Francisco Azuaje and Joaqu ́ın Dopazo's book "Data Analysis and Visualization in Genomics and Proteomics" and was just an excellent starting point. Even though I narrowed my search to proteomics and particularly to protein structure patterns, I still, however, unable to pin down a specific problem to tackle.

any insight will be really appreciated.

[pld]

I would personally love to see some better visualizations of transcriptome assembly quality.

Answer 1

[Lars Juhl Jensen]

There are numerous challenges to pick from:

• Visualization of site data onto protein networks (MS often gives site-specific regulation information, but edges are between proteins).
• Comparative visualization of networks across conditions or species (for N>2 simple color-coding of nodes works poorly).
• Visualization of time course data (for nodes) onto networks (relates to dynamic networks, but edges are not dynamic).
• Giving a meaningful overview of a hairball (not sure there is a good solution)

One piece of advise: Please do not make yet another stand-alone tool for this purpose. Join an existing effort by implementing your new functionality as a plugin/extension/app for a popular network tool such as Cytoscape.

Answer 2

[Jean-Karim Heriche]

As far as I know, there's still no good visualization tool for hairballs (aka big networks) but I would be particularly interested in visualization of dynamic networks.