proteins

...now browsing by tag

 
 

ProteinVis: Visualizing a large tree in Haskell and OpenGL

Sunday, January 18th, 2009

The following is a screenshot of ProteinVis, a tree viewer for hierarchical clusterings of proteins in the human Genome.  I did this project a while back with a colleague, Xiaojun Guan, and a professor of biology at UNC Chapel Hill, Dr William Kaufman.  Clicking on a node in the tree builds a set (actually, these are lazily computed from sets that are declared to be part of the tree at load time) of proteins that share Gene Ontology terms.

ProteinVis: A viewer for clusterings of human proteins

Click for a larger view

The basic idea is to look at the Gene Ontology terms that have been assigned to individual proteins in context of other similar proteins to see if the Gene Ontolog terms make sense in context. This was one of my first visualizations in OpenGL using Haskell, and so the code isn’t what I’d call pretty.  In any case, I’m releasing the source code here under Renci’s open source license, which is included in the source distribution.  I don’t really expect it to be of much interest, though, except to see what I did to get the visualization up and running.  These days I’m writing much better code.

ProteinVis, for win32 environments

ProteinVis, for Linux x86_64 environments

ProteinVis darcs repository