Galaxy For Interactive Visual Analysis

Posted on 20 November 2012 by Jeremy Goecks

Our latest publication on using Galaxy for interactive visual analysis is out in this month’s Nature Biotechnology.

This Galaxy Page includes the RNA-seq analyses described in the paper and visualizations that can used for visual analysis of Cufflinks transcript assemblies. In this paper, visual analysis was used to find good parameter settings.

Encode phase two papers now out

Posted on 5 September 2012 by James Taylor

A massive number of publications, along with an iPad application, some great web-based visualizations, etc. landed today from the ENCODE project. This is a monumental contribution, which Ewan summarized masterfully. We were much less involved than during the life-consuming pilot phase, but one interesting piece we (specifically Dannon) were contributed to was the production of a virtual machine image (available as a downloadable image and for instantiation on AWS) that allows direct inspection and rerunning of the analysis that generated all the figures in the main paper. This is a great example of one technique we can use to achieve greater transparency and reproducibility in computationally intensive science.

Galaxy Conference and reproducibility review

Posted on 1 September 2012 by James Taylor

A meeting report on the highly successful Galaxy Community Conference 2012 has now been published in Genome Biology. Slides and video for the entire conference and training day are now availalble.

Our review/perspective on enhancing transparency and reproducibility has appeared in Nature Reviews Genetics.

The Mouse ENCODE consortium (in which we participate) has published a maker paper in Genome Biology.