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Objective 2.3 GCP-iPlant Collaboration Agreement 201010

The Integrated Breeding Platform and iPlant - Overview October 1st, 2010


The iPlant Collaborative hosted a workshop from September 29th to October 1st, 2010 with managers and developers of the Integrated Breeding Platform (IBP) project which is managed by the Generation Challenge Program (GCP) and supported by the Bill & Melinda Gates Foundation as well as other GCP donors. The workshop was also attended by representatives from USDA, NCGR, Agriculture and Agri-food Canada (AAFC) and the Bill & Melinda Gates Foundation. The objective of the workshop was to investigate the possibility of collaborating on the development of an Integrated Breeding Workbench - a configurable suite of logistic, analytic and decision support tools to facilitate modern plant breeding.

This workshop followed a face-to-face meeting between the IBP Management (Graham McLaren, Diego Gonzales-de-Leon, and Guy Davenport) and iPlant management on May 19th 2010 in Tucson AZ and a conference call on August 10th 2010 with a larger number of participants from both the IBP and iPlant. The purpose of these previous meetings was to explore if iPlant and the IBP could create a mutually beneficial collaboration with coordinated development efforts. It was clear from these meetings and discussions that IBP could focus on the creation and development of breeding tools specific for their needs and build them on the iPlant Cyberinfrastructure (CI) platform.

iPlant will benefit by having a close interaction with the highly experienced breeders from centers of the Consultative Group on International Agricultural Research (CGIAR) which are geographically dispersed around the world and concentrate on agricultural research for food security and development. The IBP will benefit by building on the iPlant CI platform that many plant biology researchers will use for discovery research. Academic researchers and breeders are likely to be stimulated to work with the IBP given the GCP's humanitarian objectives. iPlant collaborators will benefit by gaining access to the users in the CGIAR and academic research organizations interested in supporting the humanitarian applications of the IBP and to rich resources of biological data which will be accessible through the iPlant CI for collaborative biological research. Taken together, such a coordinated effort will be mutually advantageous.

The CGIAR and other partners have been working on developing the International Crop Information System (ICIS) and a field book system for maize breeding for over a decade, and the IBP managers have expressed their desire and willingness to update and merge these systems to be compatible with iPlant's design and to be scalable to the CGIAR's new needs. iPlant is building a software developer toolkit (SDK) and an application programming interface (API) and will work closely with IBP developers to facilitate building the Integrated Breeding Workbench on the iPlant CI.

The iPlant Grand Challenge Project (Genotype to Phenotype) agreed that the Workbench and the data that will be generated through the workbench will be valuable components. The representatives of USDA and AAFC agreed that the workbench would provide a valuable tool for breeding and agricultural research in the public sector in developed as well as developing countries.
Participants from iPlant and IBP were introduced to each other and spent the first days describing their needs and technologies to each other. The decision was made to work on developing a basic field notebook system and a statistical analysis pipeline based on existing R scripts as a first step in the collaboration. These will be refined and further modules added in a staged collaboration. On the last day of the workshop two groups were formed and started to develop the work plans for the two first modules. The background documents, presentations and a summary of the workshop are being posted on the iPlant wiki.

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