Arabidopsis Informatics

IAIC Publication: Arabidopsis bioinformatics resources: The current state, challenges, and priorities for the future

Blake — Thu, 07 Mar 2019 21:23:03 +0000

The IAIC held a workshop (May, 2018): “2018 – the Future of Arabidopsis Bioinformatics” to evaluate the current status of Arabidopsis informatics and chart a course for future research and development. The workshop focused on several challenges, including the need for reliable and current annotation, community‐defined common standards for data and metadata, and accessible and user‐friendly repositories/tools/methods for data integration and visualization.

The workshop publication “Arabidopsis bioinformatics resources: The current state, challenges, and priorities for the future” can be found here.

Blake Meyers, IAIC Director, introducing the workshop’s objectives

Solutions envisioned included (a) a centralized annotation authority to coalesce annotation from new groups, establish a consistent naming scheme, distribute this format regularly and frequently, and encourage and enforce its adoption; (b) community-established guidelines and standards for data and metadata formats; (c) a searchable, central repository for analysis and visualization tools. Improved versioning and user access to make tools more accessible. Finally, workshop participants proposed a “one‐stop shop” website, an Arabidopsis “Super‐Portal” to link tools, data resources, programmatic standards, and best practice descriptions for each data type, while emphasizing such a portal must have community buy‐in and participation in its establishment and development to encourage adoption.

Plant scientists and computer scientists working together to provide relevant resources to the plant biology community

New IAIC Collaboration

Joanna — Sun, 14 Feb 2016 21:23:18 +0000

New IAIC Community Collaboration with NAASC via ART-21 award
The IAIC is partnering with a new education and training initiative led by the North American Arabidopsis Steering Committee:
Advancing Arabidopsis Research and Training for the 21st Century (ART-21) is an NSF-funded Research Coordinated Network to enable research and training activities for the Arabidopsis and broader plant science community.
You can get an overview of this new 5 year networking award from this presentation at PAG XXIV and from the NAASC webpage at Araport.

Araport and ThaleMine updates

Joanna — Thu, 05 Mar 2015 22:22:03 +0000

Araport, the new Arabidopsis information portal, was funded by NSF as a new model for assimilation and integration of a wide range of data types pertaining to Arabidopsis thaliana, the model flowering plant. Now entering its second year, the web site (www.araport.org) hosts instances of JBrowse and InterMine containing genomic, expression and proteomic data.

A key part of Araport is ThaleMine which enables you to analyze gene and protein data from TAIR, expression and interaction data from BAR, ortholog data from Panther, and more.
You use plain text or structured queries for interactive gene and protein reports.

First-ever AIP Developer Workshop

Blake — Mon, 19 Jan 2015 17:47:53 +0000

Nov. 2014- TACC, JCVI, and Cambridge University hosted an NSF-funded AIP developer workshop in Austin, Texas, USA. 20 plant scientists from the US and Europe participated.
See: https://www.tacc.utexas.edu/-/first-ever-aip-developer-workshop-a-success

AIP will host a developer workshop: Nov. 5-6, 2014

Blake — Thu, 11 Sep 2014 22:20:10 +0000

The Arabidopsis Information Portal (Araport.org) is a new kind of science resource, where the community is not only invited to contribute functionality, but is empowered to do so. To facilitate community participation, AIP will host a developer workshop oriented toward Arabidopsis researchers and students on Nov. 5-6, 2014. The goals are to provide instruction on how to make data available via web services and how to display data in an science app hosted at AIP. Participants should have some experience in development of interactive web applications and/or web services. Further information will be available at (https://www.araport.org/devzone). Please contact the organizers by email (araport@jcvi.org) with “WORKSHOP – YOURNAME” in the subject line, your CV and a brief description of your objectives in attending the workshop. We will contact prospective participants to ascertain their goals and level of relevant experience. All expenses will be covered for course participants.

Arabidopsis data gets new home via NSF-funded Arabidopsis Information Portal

Joanna — Thu, 26 Sep 2013 17:54:10 +0000

A new article entitled ‘Arabidopsis Data Gets New Home at JCVI’s AIP as TAIR Turns to Subscriptions to Stay Afloat‘ by Uduak Grace Thomas describes the three+ year process by members of the international Arabidopsis community to (1) maintain continuity in housing vital Arabidopsis data (2) expand capabilities to store and manage vast new datasets and datatypes (3) develop new resources and integrate resources developed (or to be developed) by the global community and (4) share the burden of supporting community resources across a potentially wider range of funding agencies and countries. These efforts culminated recently in an NSF award to PI Chris Town (J. Craig Venter Institute) to develop a new Arabidopsis Information Portal (AIP).

Town and colleagues from the Texas Advanced Computing Center and Cambridge University expect to produce a functioning portal prototype by the end of year. The project will leverage significant NSF investments in plant bioinformatics via the iPlant Collaborative. It will also sub-contract with TAIR staff to migrate exisiting data into an open source relational database.

The AIP will be structured in three tiers including a ‘user interface, a database structure, and a web-services layer that will pull information from JCVI-hosted data warehouses and external databases through third-party applications.’

AIP development plans include:

An implementation of an Arabidopsis-specific instance of InterMine, a data integration platform that is widely accepted in the animal model organism database community
The design and construction of a web services layer that facilitates data access
Integration with iPlant Collaborative resources
Federation with other data providers
Development of analytical workflows

The article also describes the new subscription model planned by TAIR staff and differences between the two resources.

NSF funds J. Craig Venter Institute to develop the Arabidopsis Information Portal (AIP)

Joanna — Sun, 22 Sep 2013 21:37:56 +0000

The National Science Foundation has announced that it will fund for five years a group led by Chris Town at the J. Craig Venter Institute to develop the Arabidopsis Information Portal (AIP). The Arabidopsis Information Portal will use a combination of data federation and web services technologies to provide the Arabidopsis community with integrated views of a wide range of relevant data types. The AIP concept was developed in a series of workshops organized by the International Arabidopsis Informatics Consortium (IAIC) following the announcement that NSF funding for TAIR (The Arabidopsis Information Resource) would terminate in August 2013. In addition to hosting all the data currently in TAIR, the AIP will provide access to and integration of a more diverse set of data types, such as expression data, protein interaction data and data from the 1001 genomes project.

The AIP will have a modular design that will allow community members worldwide to develop and plug in both data and analysis modules, thus allowing costs to be distributed across multiple countries and funding agencies. Collaborating institutions in this project are the Texas Advanced Computing Center (TACC) and the Cambridge Systems Biology Centre, UK. Staff from TAIR will assist in providing data from the current TAIR database to the AIP in year 1.

AIP development will be in consultation with the AIP Scientific Advisory Board consisting of representatives of the global Arabidopsis and bioinformatics communities.

AIP NSF award link

TAIR to charge users via subscription model

Joanna — Sat, 31 Aug 2013 22:00:39 +0000

The IAIC formed in 2010 order to maintain and expand vital Arabidopsis community resources in response to the the NSF’s decision to reduce, and then cease, funding for TAIR, the main Arabidopsis database since 1999.

For more than two years international IAIC participants convened meetings and workshops to strategize how to fund and develop this new, expanded resource, now called the AIP, including to leverage international resources and expertise.

These collective community efforts culminated in the submission of an AIP funding proposal that was informed in large part by an IAIC-organized design workshop in December 2011 which brought together plant researchers and computational experts to hash out the needs of the community and how they would best translate into a revitalized bioinformatics resource. The AIP proposal was submitted in fall 2012 and has been in discussions for the last 6+ months, with a final funding decision expected at any time. An international Scientific Advisory Board has also been in place since early 2012.

Below is a Nature news release about the new path chosen by TAIR members, to maintain TAIR under a new subscription service:

http://www.nature.com/news/popular-plant-database-set-to-charge-users-1.13642

Presentation from ICAR 2013- Blake Meyers

Joanna — Thu, 08 Aug 2013 21:53:45 +0000

The opening presentation from ICAR 2013- by Blake Meyers, Interim IAIC Director, has been posted to the meeting page.

Presentations from Plant and Animal Genome- 2013

Blake — Thu, 14 Feb 2013 00:14:40 +0000

Presentations at the recent IAIC workshop entitled ‘The International Arabidopsis Informatics Consortium (IAIC) and development of the Arabidopsis Information Portal (AIP)‘ are available for viewing.