Wednesday, January 2, 2013

Blog Series: Workshop on Genomics, Cesky Krumlov; Preparation--Galaxy

Section 5: Galaxy

This will be a short one (and the people rejoiced!).

Galaxy is an open source, web-based platform designed to assist in computational analysis for researchers. It helps in data management and contains analysis tools in the framework ranging from converting from one data format to another, manipulating fasta files, fetching sequence data, calculating statistics as well as conducting some evolutionary analyses and metagenomic analyses. It also has a link to the ENCODE projects tools.

Nuff dive in see the suggested readings:
  1. Goecks, J; A Nekrutenko and J Taylor. 2010. Galaxy: a comprehensive approach for supporting accessible, reproducible and transparent computational research in the life sciences. Genome Biology. 11:R86.
  2. Blankenberg, D et al., Integrating diverse databases into an unified analysis framework: a Galaxy approach. Database (Oxford) 2011:bar011.
  3. J Goecks also has a slideshare up on Galaxy that shows some of the nifty graphics that can be generated from some of the tools.
  4. 2 years ago David Coil put up a series of tutorials using Galaxy to visualize various datasets. Not sure how up to date the push to click operation is (Galaxy in 2010 versus 2013), but worth a view. Below is the first video in the set. David Coil actually has a nice set of videos on his profile all less than 10 min long so the commitment is minimal, see if any are of interest--most deal with sequencing and programs for analysis.

Or just hop to the website directly: Galaxy and perhaps take a tutorial on how to get started.

Next Up: Preparation--GMOD/Gbrowse