Tuesday, 28 May 2013 at 12:02 pm

I am in the middle of my last year as a PhD student, working on my thesis and trying to get some last minute analysis finished. I've also decided to start building up a github profile by working on a few visualization web tools. Hopefully it will add to my CV. The goal of these tools will be to:

  • Client-side html/javascript/css only web tools. No server required.
  • Clean and minimalistic design
  • Help bioinformaticians who work at sequencing facilities by giving them an interactive output to give to clients

The only javascript dependency I'll be using is D3.js

The first tool I'll be making is an annotation viewer for visualizing features on a set of sequences. Something that's useful for people who want to load 50-100 sequences with protein domain annotations and look at the domain compositions; or for loading various genomic loci with transcript annotations.  

I've been working on it past couple of days and I've got most of the feature rendering code finished. You can check out a very preliminary demo here. The sample data is a bunch of SET domain containing genes and PFAM domain annotations:

http://htmlpreview.github.io/?https://github.com/damiankao/seeker/blob/master/test.html

It might not look like much, but coding contextual menus that will respond smartly to edge of the window and refactoring the code for loose coupling took some effort.

It will probably only work on Chrome/Safari/Firefox. There are contextual menus for each feature and sequence for the user to manipulate what features they want shown (left click on features and sequence names). The end goal is to let the user save the rendering as a svg file for further editing.

Here is my github page.




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