Video Tip of the Week: DNA Subway

At a recent training workshop on the UCSC Genome Browser, I spoke with an educator who is using a custom local installation of the browser to work with students on bioinformatics lessons. It’s a project called the Genomics Education Partnership at WashU, and students learn by annotating regions of the genome with bioinformatics tools. You can see the team’s installation of the browser here. It sounded like an enjoyable and effective method and useful to students.

So the other day when I was exploring some of the resources available from the iPlant Collaborative, I was reminded of the annotation educational method by their very cool DNA Subway project. It’s another strategy to educate students with genome annotation tools–but I also think there might be some scientists who might want to use it beyond formal educational settings. It’s not new–I can remember reading about it in the past, but looking at it again with fresh eyes after that other conversation was worthwhile. And they’ve added new features since I last explored.

Student annotation projects are widespread, and there are probably numerous different successful strategies that local folks have implemented to set this up. But I suspect that more folks who are teaching bioinformatics might find the workflow infrastructure of the DNA Subway system a useful mechanism to use themselves, rather than setting up their own. So this week’s video tip of the week highlights the DNA Subway. Oh–and by the way: just because it’s at iPlant doesn’t mean it’s restricted to plants. You can go over there and see the various species options.

The providers of the Subway describe it as:

DNA Subway makes high-level genome analysis broadly available to students and educators and provides easy access to the types of data and informatics tools that drive modern biology. Using the intuitive metaphor of a subway map, DNA Subway organizes research-grade bioinformatics analysis tools into logical workflows and presents them in an appealing interface.”

I thought this was a really effective way to conceptualize the tasks that need to occur on a project. And it’s integrated with the tools you need at each “stop” to accomplish the tasks. The new “green line” in Beta that they have created isn’t shown in the video, but you should have a look at the site. It’s got tools for NGS RNA-seq data analysis, integrating the Tuxedo workflow protocol that includes TopHat, Bowtie, and Cufflinks, and is a really good thing for students to be exposed to. If you go over to the DNA Subway site itself and choose the “green line” to explore, you can see more information.

I can’t seem to embed their video, so I’d recommend you look at the larger size version on a separate page, and to go over and have a look for yourself at the DNA Subway.

Go over to their site by clicking on the image to access the video.

Go over to their site by clicking on the image to access the video.

Quick links:

DNA Subway main description page: http://www.iplantcollaborative.org/discover/dna-subway

DNA Subway installation: http://dnasubway.iplantcollaborative.org/

DNA Subway video tour (larger size): http://dnasubway.iplantcollaborative.org/files/tour/index.html

References:

Goff S.A., Vaughn M., McKay S., Lyons E., Stapleton A.E., Gessler D., Matasci N., Wang L., Hanlon M. & Lenards A. & (2011). The iPlant Collaborative: Cyberinfrastructure for Plant Biology, Frontiers in Plant Science, 2 34. DOI:

Trapnell C., Roberts A., Goff L., Pertea G., Kim D., Kelley D.R., Pimentel H., Salzberg S.L., Rinn J.L. & Pachter L. & (2012). Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks, Nature Protocols, 7 (3) 562-578. DOI: