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Video Tip of the Week: Araport, Arabidopsis Portal

The recent Plant Biology 2015 conference tweets were full of delightful morsels (). Some of them edible. I am very psyched to learn of the Legume Federation. Legumes are *way* at the top of my list of favorite organisms. I think it was their tweet of the Araport data that led to this week’s video tip of the week.

Araport was new to me. I had been familiar with TAIR, and I knew of some of their changes after the funding went away. But this got me looking into how the community was re-organizing to support the plant model organism data, and also providing supporting tools and new directions.

The paper (below, 2014) describes the foundations and some of the transition issues from TAIR. And it also describes some of the tools that they are making available going forward. They have a customized InterMine called ThaleMine that can help you make customized queries to mine the data. There’s a JBrowse for visual browsing of the genome data. They are also maintaining a GBrowse with the Arabidopsis data, and they have a page of browser comparisons. There’s BLAST for sequence-based searching.

But what’s also very cool is that they are also making this a framework for people to build their own apps around. This “community contributed modules” is a great idea. So tools that folks may need for their particular research directions can be built right on top of the Araport setup.

This week’s tip is the ThaleMine intro video that they have provided.

I would keep an eye out for more videos from them in the future as well. There’s also a   Presentations page, and if you want more of an overall look at their foundations and plants there’s a nice overview slide deck from the ICAR 2015 conference.

Check out the Araport resources for arabidopsis and plant genomics tools.

Quick links:

Araport: http://www.araport.org/

References:

Hanlon, M., Vaughn, M., Mock, S., Dooley, R., Moreira, W., Stubbs, J., Town, C., Miller, J., Krishnakumar, V., Ferlanti, E., & Pence, E. (2015). Araport: an application platform for data discovery Concurrency and Computation: Practice and Experience DOI: 10.1002/cpe.3542

Krishnakumar, V., Hanlon, M., Contrino, S., Ferlanti, E., Karamycheva, S., Kim, M., Rosen, B., Cheng, C., Moreira, W., Mock, S., Stubbs, J., Sullivan, J., Krampis, K., Miller, J., Micklem, G., Vaughn, M., & Town, C. (2014). Araport: the Arabidopsis Information Portal Nucleic Acids Research, 43 (D1) DOI: 10.1093/nar/gku1200