Looking for open visualization problems in bioinformatics

Question

[vbazurto]

Hi,

I'm a graduate computer science student interested in researching visualization in bioinformatics and currently I'm working on visualizations using mainly D3 and Lively Web Server as development platform.

I'm currently interested in open problems about web visualizations in bioinformatics in general. I have been working on genemaps viral visualizations.

Can anyone give me some ideas about where to start? I'm also interested in the development of dashboards of correlated biological data. Basically I would like to collaborate on an open problem in the previously mentioned area.

[Jean-Karim Heriche]

To see what people are doing in visualization of biological data, have a look at the VIZBI website.

Answer 1

[Michael]

How about a good visualization of biological networks? http://www.hiveplot.net/ explains very nicely the problem of the 'hairball'; whether the proposed hiveplot is really a break-through remains to be seen, but there must be more not yet invented alternatives to the hairball, there is definitely room for improvement.

Answer 2

[Madelaine Gogol]

Some kind of better-than-a-venn diagram way to represent set intersections for multiple sets. And yeah, there's this thing, but...

Answer 3

[DG]

Basically any biological problem where you think some cool visualizations could be helpful is open. The vast majority of visualizations for biological data is pretty rudimentary in my opinion. Complex networks like Micheal Dondrup suggested is a particularly striking example. I'm very interested in dashboards myself for exploring genomic variant information myself. Most of what I deal with is in databases and spreadsheets where we set filters and look through results but I've though many, many times about complex dashboards for visually filtering, sorting, and looking at the data in a variety of ways simultaneously. I'm very open to collaborating with new people on this sort of thing.

[Coryza]

Check http://www.croppedia.com/wp-content/themes/admium/images/benefits/CropPEdiaNG-variomics.png > Croppedia. Screen = example case of visualizing 131 Rice lines, with a powerful interface to extract all sorts of overlap/patterns.

Answer 4

[Alex Reynolds]

I tried coming up with a better Venn some years ago, called an "Eulergrid". I would love someone to make my Eulergrid plots d3-enabled, adding some event handlers to turn sets on and off, resort sets by various criteria, highlight subsets by some subgrouping, etc.