Monday, May 21, 2012

v3 code release - Maize genome supported

Version 3 of the Wash U Epigenome Browser source code is available now! Follow this link to download. Following is an account of what's new.


New genome assembly
We're very happy to support the maize genome (from the B73 strain, assembly version 2).

 (from Wikipedia)


Corn is nutritious and makes healthy food. While in industrial countries, maize is grown to feed the livestock and produce biofuel, maize researchers all know how important maize is as a staple food for people in many parts of the world.

So we are now supporting maize genome in our Browser with the hope that maize researcher and breeders can benefit from browsing maize genomic data using our service.

Data including genome sequence, gene and repeat prediction was downloaded from http://www.maizesequence.org/index.html. Apart from a few genome annotation tracks, the maize genome database is currently empty. We will certainly add public maize data sets here (let us know what you would like to see), but you can always view your own data sets via the custom track and Data Hub functions. Click following link to open the browser showing maize genome and tracks from a sample data hub:

http://epigenomegateway.wustl.edu/browser/?genome=AGPv2&coordinate=1:11499583-11999166&datahub=http://epigenomegateway.wustl.edu/browser/b73/testhub.txt&gftk=AGPv2_5a,full

You can find a sketch of the procedures for making maize database here.


Bug fixes
  1. At the heatmap track facet browsing panel, clicking the ⊞ or ⊟ will correctly open or fold the contents (it used to generated an error).
  2. When the correlation function is in use, any heatmap tracks newly added with have their correlation coefficients properly computed and displayed.
  3. Occasional error encountered when clicking some items in gene track is now eliminated.


Minor improvements
To make it easier to configure metadata color map, the button  is added at right side of metadata color map:

Clicking this button will display a panel containing the metadata vocabulary. You can browse through the vocabulary and add/remove terms from the color map by toggling the checkboxes: