Wednesday, January 2, 2013

Blog Series: Workshop on Genomics, Cesky Krumlov; Preparation--GMOD/Gbrowser

Section 6: GMOD/Gbrowse

GMOD was set up to be a kind of community for biologists to allow them to focus on research and 'the science' if you will instead of fretting over the nitty gritty application acrobatics they need to implement to obtain useful information from their data. It is a series of interconnected applications and databases for scientific use.

GBrowse is a component of GMOD that is for, as you might have guessed, Genome Browsing. I did see a magic word in the description that is dreaded by many who work at institutions with enhanced security protocols...'install'. Here's where the disclaimer from the first blog entry comes in...make sure of how it installs and that you've submitted all the proper paperwork and links so that information assurance can approve and install the program. Yep, it's doubtful you'll get to install in, your IT or IA department will usually take care of that either remotely or by coming to your computer. This of course applies to all of the programs mentioned in previous blogs as well.

Other components include: Community Annotation, Comparative Genome Visualization, Database tools, Gene expression visualization, Genome annotation, Molecular pathway visualization and Blast sequence alignment...I lifted all this from the GMOD wiki, so check it out, it is also one of the suggested 'readings'.

It will be interesting to explore Galaxy and GMOD and see how and if they overlap...they seem to target the same audience but potentially with different available functionality...

The other suggested reading focuses on GBrowse: Stein et al., 2002. The generic genome browser: a building block for a model organism system database. Genome Research. 12:1599-1610.

Looks like we'll be learning about some really interesting platforms and packages of tools available. Myself, I tend to gravitate toward the web-based platforms (I'm already clicking through Galaxy) as most of the time it doesn't require a software install which reduces my work headache by leaps and bounds and spares the bottle of wine at home that would've been in danger of being drank in one swallow the minute I walked in the door!

Next Up: Preparation--Metagenomics