The bioinformatics ecosystem is challenging. There are so many tools, and so many different tasks, that it can be daunting to locate or create a workflow that you can use and re-use quickly and easily. A number of interfaces and sites are now available to help you wrangle this. This week’s tip highlights one of these–GenePattern–that has been helping researchers navigate this problem for a long time now.
It came to my attention again when I saw this terrific article about it: Bridging the Gap: Bring Genome Analysis Tools to the Masses with GenePattern. The new release of the GenePattern software has prompted the piece, and also got me to have a look at the tools again as well. And I especially appreciate that these interfaces can help people who have less local infrastructure and support–in our travels we see a lot of folks who just don’t have access to the help they need, and this type of tool–as well as Galaxy, Taverna, and others of that nature.
This video is the initial getting started one, but there are a lot of additional videos from this team as well. If you can’t watch the video right now, you can still go over to their Quick Start written guide to get a feeling for the features.
Reich M., Liefeld T., Gould J., Lerner J., Tamayo P. & Mesirov J.P. (2006). GenePattern 2.0, Nature Genetics, 38 (5) 500-501. DOI: 10.1038/ng0506-500