Russel Smithies (of AgResearch) suggested using Galaxy assisting in setting up a local GBrowse service (fetching UCSC Btau4 data, converting to a format compatible with GBrowse) at work (CIGENE, Centre for Integrative Genetics).
Galaxy is a web application that deserves attention! Fetching data, sorting data, combining data sets, alignments, manipulations, fetching other data resulting from manipulations, statistics, ++. All with a very-very nice, simplistic interface.
“It is designed to help two communities that often have difficulty communicating:
- Experimental biologists: “I really have no time to program but I want to do whole-genome analyses to find targets for experimental validation”.
- Computational biologists: “I develop algorithms but have no time to develop interfaces”.
There are also a number of screencasts available.
Example of usage:
“Suppose you want to find top hundred protein-coding exons in human genome with the highest density of single nucleotide polymorphisms (SNPs). Answering this question is not trivial. To do so one needs to compare all human exons to all human SNPs. To put this into perspective the current version of human genome (hg18) includes 357,517 known exons and 12,351,941 SNPs.”
Elegantly solved, using Galaxy, in this screencast.
Galaxy also lets you create workflows (screencast).
I’m very impressed, and I’m already planning a local Galaxy server integrating our local data sources and tools.
Now, all that’s needed is to teach people how to use Galaxy. Hm. And I probably have to look for a new job…