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.

“This workshop was one of the most successful ever. It was astonishing to see researchers get their apps up and running on the platform,” said Steve Mock, TACC’s director of Advanced Computing Interfaces.

“Similar to how smartphone users can configure apps to meet their individual needs, our portal allows researchers to configure their workspace by developing apps and taking advantage of apps developed by other users. This tool will serve as a central location to integrate all of the diverse data types for the Arabidopsis community,” said project PI Chris Town of the JCVI.

AIP is the first and only Arabidopsis resource that enables researchers to collect all of their data from the same source. This innovative platform also engages the Arabidopsis community by allowing users to access publications, visualisations, discussion forums, and job postings.

To begin educating researchers on the platform, the AIP team hosted bioinformatics scientists from research labs and database providers across the U.S., Canada, and Europe. The two-day workshop offered attendees the opportunity to begin building the foundation necessary to develop their own web applications for the portal.

During the first day, lectures and tutorials by AIP developers introduced attendees to web app architecture and development using the Science Apps Software Development Kit and the Agave API. Attendees then applied that knowledge to develop science apps under the guidance of AIP staff on the second day. To end the workshop, students discussed the design and implementation details of their science apps and received feedback from the class and AIP staff. Once back at their home institutions, they will implement their app design on the portal for community use.

“This workshop was one of the most successful ever,” Steve Mock said. “It was astonishing to see researchers get their apps up and running on the platform. And not only did the attendees walk away with nearly-functional apps that can be hosted on AIP, but we learned a lot from them in the process.”

Due to its success and to generate continued momentum, the AIP team plans to replicate the developer’s workshop at JCVI and host additional workshops at TACC in 2015. As more researchers learn about AIP and its value to Arabidopsis research, the AIP team will work to ensure that everyone has access to training opportunities and engagement.

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