ICAR 2014- Vancouver, Canada

Two IAIC/AIP workshops were held in conjunction with ICAR 2014:

  1. Arabidopsis Information Portal (AIP) Developer and User Workshop (Leads: Chris Town and Matt Vaughn)
  2. The International Arabidopsis Informatics Consortium: Community Research and Resources, including the Arabidopsis Information Portal and Module (Leads: Blake Meyers, Erich Grotewold, and Nick Provart)

Detailed programs and descriptions:

(1) Arabidopsis Information Portal Developer and User Workshop: The workshop was divided into two parts. The first and longer part was oriented to the users of ARAPORT. The second was an informal discussion aimed at potential developers. Within the user-oriented part, the introductory session introduced the AIP team to the community and provided an overview of the project and its technical implementation. The second section on user-interface presentations provided a walk-through of the entire ARAPORT site and its current functionalities and previewed a new interface being developed by the Provart group. This was followed by hands-on tutorials on the two main user interfaces – JBrowse and ThaleMine. This user-oriented part concluded with an open period for comments, questions and suggestions. Part 2 was a shorter, technical session in which potential developers had the opportunity to learn how to develop app and/or provide their data sets to AIP via web services.

PART I: Introductory session

  1. Meet the AIP team (Chris Town, JCVI)
  2. Overview of the AIP project (Chris Town, JCVI)
  3. Technical implementation – what’s under the hood (Jason Miller, JCVI)

User interface presentations

  1. An overview of the ARAPORT site (Matt Vaughn, TACC)
  2. A zoomable user interface for the AIP (Jamie Waese, University of Toronto)

Hands-on tutorials

  1. An introduction to JBrowse (led by Ben Rosen, JCVI; assists by other team members)
  2. An introduction to ThaleMine (led by Ben Rosen, JCVI; assists by other team members)

Both the JBrowse and ThaleMine sessions consisted of a live demo and walk through of the main features from the podium interspersed with interactive exercises for the participants to work through.

Questions and Suggestions

PART II- Informal Discussion for Developers (Matt Vaughn, TACC): A high-level overview of AIP’s development road map was presented, including and how they anticipate users will be able to provide apps and/or data sources for inclusion in AIP. This was a prelude to a developer workshop planned for Fall 2014.

(2) The International Arabidopsis Informatics Consortium: Community Research and Resources, including the Arabidopsis Information Portal and Modules

Workshop Organizers: Blake Meyers, University of Delaware; Erich Grotewold, Ohio State University; Nick Provart, University of Toronto

This workshop, developed by members of the International Arabidopsis Informatics Consortium (IAIC), presented a brief overview of the efforts underway internationally to support development of the new information repository and informatics resource, the AIP. Speakers provided an overview of the international development of the IAIC, and the AIP and its components, its plan for sustainability, recent progress, and planned connections with a broad array of community-generated modules and their associated data. Presentations by plant biologists and computational experts highlighted resources that are, or will be, connecting with the AIP.

A key goal of the workshop was to connect with researchers who (1) are developing tools and resources (potential ‘modules’), and who are wondering how they might fit with the AIP, or (2) are not developing modules but want to learn of features of the new portal (AIP) and modules that might accelerate and enhance their research.

This workshop complemented the longer and more hands-on user/developer workshop described above. Members of the IAIC and the AIP participated, presenting an excellent opportunity to connect with potential collaborators. The IAIC is supported by a Research Coordination Network (RCN) award from the US National Science Foundation (NSF).

Background: The IAIC was initiated following two community-organized workshops held in 2010. This international consortium is addressing growing bioinformatics needs for Arabidopsis data, with the goal of coordinating the management of data and leveraging growth in resources, knowledge, and collaborations. The IAIC’s first major task was to facilitate the establishment of the Arabidopsis Information Portal (AIP), the underlying infrastructure to integrate Arabidopsis data on a global scale. Following establishment of the AIP, its connections to additional community-led will facilitate data integration. The IAIC Steering Committee organized an ‘AIP Design Workshop’ in December 2011, to solicit input from an international group of Arabidopsis researchers and computational experts on the functionalities of the AIP. The NSF funded the AIP in September 2013, a five-year award made to a group led by Chris Town at the J. Craig Venter Institute.

Program

  1. 5:15-5:20: Introduction to the IAIC. Blake Meyers, University of Delaware, USA
  2. 5:20-5:32: Data Sets, Webservices and Visualization Apps from the Bio-Analytic Resource for use in the AIP and other Cyberinfrastructure Assets. Nick Provart, University of Toronto, Canada
  3. 5:32-5:42: Small RNA informatics resources at the University of Delaware, Mayumi Nakano, University of Delaware
  4. 5:42-5:54: AIP and Araport: Overview/introduction and module integration and development. Matt Vaughn, Texas Advanced Computing Center, USA
  5. 5:54-6:04: How TAIR could incorporate into the Arabidopsis Information Portal (AIP) as a module. Eva Huala, TAIR, USA
  6. 6:04-6:15: Group and presenter discussion/Q &A on AIP, IAIC, Modules, etc.