Arabidopsis Information Portal at PAGXXIII

Last Monday the Arabidopsis community gathered for the Arabidopsis Information Portal workshop at PAG XXIII. The Arabidopsis Informatics Portal (AIP) was funded by NSF and BBSRC to move beyond the Arabidopsis genome resource provided by TAIR toward linking the genome to the epigenome, proteome, transcriptome and interactome.

AraportThe first talk was a short update from Eva Huala, formerly of TAIR and now of Phoenix Bioinformatics, the nonprofit company she started in order to keep TAIR going. Huala explained that after TAIR’s NSF funding ended, the pay-to-access model was chosen over the alternative pay-to-submit (open access) approach. This means TAIR is focussed on ensuring the subscribers get the best possible value for money by providing the best possible database curation, manual annotation and user experience. Most TAIR subscription fees are paid by libraries, as if it was a journal, but researchers from institutions whose libraries do not pay the fee will be able to access TAIR’s manual annotation after a year’s embargo.

Next, Sean May (NASC, University of Nottingham) explained that NASC is a module of AIP and is currently integrating with the ABRC. He is consulting the community about the development of NASC, so make sure you have your say in the NASC Strategy Survey: http://bit.ly/1J24Hgk

Chia-yi Cheng (JCVI) gave an overview of Araport, the online home of the AIP. Araport federates diverse datasets from other places, for example TAIR, UniProt and BAR, and maintains the Col-0 ‘gold standard’ annotation. It uses JBrowse as the default genome browser and hosts datasets including the CoGe epigenomics resource, which I blogged about last week. (more…)

First Arabidopsis Information Portal developer workshop a success

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Published on: December 4, 2014

The Arabidopsis Information Portal (AIP) was funded in 2013 by NSF, and co-funded this year by BBSRC. The UK team is led by Gos Micklem at the University of Cambridge. AIP provides the Arabidopsis thaliana Col-0 reference genome sequence with associated annotation, including gene structure, gene expression, protein function, and interaction networks. It is much more than this however: an open-access online community resource for Arabidopsis research. AIP is intended to be full of resources and tools to navigating the genome, all built by community developers as part of their own research and shared with the rest of the community via AIP. 

Here Makeda Easter blogs about the first AIP developer workshop, which was hosted by TACC, JCVI, and the University of Cambridge. This post was originally published on the news pages at the Texas Advanced Computing Centre

 

AIP dev workshop 1000

Last month, a group of 20 plant scientists from the U.S. and Europe convened at the Texas Advanced Computing Center (TACC) in Austin to participate in the Arabidopsis Information Portal (AIP) Developer Workshop.

“Our key goal with this workshop was to onboard a group of developers with varying degrees of experience with web technologies to contribute web apps and APIs to our platform,” said TACC Life Sciences Computing Director Matthew Vaughn, co-PI of the project. “With the growing number and diversity of data types available for Arabidopsis, effective developer engagement is crucial to making it all available in a single place. No one group can do it all.

The Arabidopsis Information Portal is an open-access, community extensible, online resource for Arabidopsis research. AIP is an international effort from collaborators TACC, J. Craig Venter Institute (JCVI), and Cambridge University and is powered by cutting edge technologies such as InterMine, Jbrowse, Drupal, and the iPlant Agave API.

The portal not only provides users access to genomic information, but it also allows researchers to contribute their own data through developing scientific applications.

(more…)

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