Frequently when we go to a site to do workshops, we get requests about other workshops that they might host at their site. Last week at the workshop we did (UCSC Genome Browser, GenoCAD), I was asked again about tools for cancer genomics–such as TCGA and ICGC. This is a pretty common request, and I’ve contacted some resource providers to see if they have an outreach team for training so I can pass along the word to requestors.
But there are going to be some resources who won’t have the capacity to run regular workshops. And there are limitations to workshops as well–computer training rooms can only hold so many folks. If it’s held on a day you can’t get to it, there’s not much you can do about that.
We’ve been highlighting useful tools on cancer genomics this over the years. But this recent request reminded me of one I wanted to show and hadn’t had a chance to cover yet: canEvolve. Increasingly the big data projects will deliver more and more samples into the repositories–and it will require useful integration, curation, and analysis tools to dig out the details.
CanEvolve describes themselves as such:
Genome-wide profiles of tumors obtained using functional genomics platforms are being deposited to the public repositories at an astronomical scale, as a result of focused efforts by individual laboratories and large projects such as the Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium. Consequently, there is an urgent need for reliable tools that integrate and interpret these data in light of current knowledge and disseminate results to biomedical researchers in a user-friendly manner. We have built the canEvolve web portal to meet this need.
It came up in my recent explorations of StratomeX, and around the same time I noticed someone else talking about it:
— Jason H. Moore, Ph.D (@moorejh) February 28, 2014
You can read their paper for details on their goals and their foundations (linked below). Also when you go over to their site there’s a tab with some documentation. But they also have a set of tutorials to illustrate what they are describing, which I found helpful. You can follow along and try out the steps yourself.
I’ll post one of the videos here for you to get a sample of them and see what they can do. There’s no audio, but there’s text with the actions. And you can also see in their documentation area more guidance on what’s going on.
canEvolve site: http://www.canevolve.org/
canEvolve tutorials: https://www.youtube.com/user/canEvolve
Samur M.K., Yan Z., Wang X., Cao Q., Munshi N.C., Li C., Shah P.K. & Colak D. (2013). canEvolve: A Web Portal for Integrative Oncogenomics, PLoS ONE, 8 (2) e56228. DOI: 10.1371/journal.pone.0056228