2011 Annual Report
1a.Objectives (from AD-416)
Serve as the information system for the documentation of plant, insect, animal, and microbial germplasm maintained by the U.S. National Genetic Resources program. Operate and enhance existing databases, create and improve linkages to other genetic resources databases, and share information and technology on documentation of genetic resources collections.
1b.Approach (from AD-416)
Support will be provided to the existing GRIN databases that serve the National
Genetic Resources Program to ensure that they are functional and relevant to the
needs of collection managers and curators and to the germplasm user community.
Upgrades will be made to the highly specialized application software, as
appropriate, to ensure that it remains compatible with hardware upgrades and that it meets the requirements for germplasm maintenance and documentation and information exchange. Appropriate measures will be taken to ensure security of the databases and the data they contain. The next version of the GRIN software will be developed as a scalable portable system capable of being transfered to other genebanks in addition to allowing greater interoperability between genetic resources and biodiversity databases.
The Database Management Unit (DBMU) of the National Germplasm Resources Laboratory provides a central database for the germplasm collections within the National Plant Germplasm System (NPGS). This central database provides curator software for managing the collections as well as a portal for public access and requesting material. An essential task for the DBMU is to maintain near 24/7 availability of the system. A 98% availability target was met. A new application server was purchased and installed. The GRIN (Germplasm Resources Information Network) system was recently moved from a 10 Mb commercial internet service provider to the 600 Mb USDA telecommunications network (UTN).
In addition to maintaining the servers and current GRIN software, the DBMU is contributing to the development of a new version of the GRIN software (GRIN-Global) with ARS collaborators from the North Central Regional Plant Introduction Station (Ames, IA), Global Crop Diversity Trust, and Bioversity International. This will be a scalable version of GRIN using open source technology to better service the needs of both the NPGS and the international genetic resource management community. The 2011 phase of the project consisted of refining both the curator tool and public Web site features and functions of the system, rigorously documenting and testing the system, securing an external code review for possible security vulnerabilities, and releasing a 0.9 (advanced test) version to domestic and international clients.
Enhancements to current GRIN. Improvements were made to the existing Germplasm Resources Information Network curator and public software, including the ability to download an entire evaluation (all traits), improved marker data displays and additional query options on the crop query pages. Hardware and network enhancements include purchase and installation of a new application server and movement from a commercial internet server to the USDA network.
Participate in development of GRIN-Global. Most of the staff time for the Database Management Unit (DBMU) in 2011 has been oriented toward GRIN-Global development and deployment efforts. Major accomplishments of the DBMU have been in web development, schema review, training documentation, installation and testing of the GRIN-Global software. This ongoing effort is also described in the progress report.
Coordinate the activities of the Crop Germplasm Committees (CGC). There are 42 CGCs, comprised of public and private sector scientists for a given crop, that comprise a support network for the National Plant Germplasm System (NPGS). Included among their activities are preparing and updating status/vulnerability reports for their crop(s) and serving as peer reviewers for USDA-funded plant exploration and characterization proposals. Twenty-three committees have met (in person or by teleconference) as of July 2011. These CGCs are an integral part of the overall effectiveness of the NPGS.
GRIN availability. The Germplasm Resources Information Network (GRIN) database was available on a nearly 24/7 basis throughout 2011. Access to the web pages for GRIN included about 2 million visits for the past year. Our statistics also indicated the average visitor spent 7 minutes at the site and viewed more than 9 different pages. As of July 2010, more than 129,000 germplasm samples have been distributed from the National Plant Germplasm System genebanks, most of them requested on the basis of information made available through GRIN. This ensures timely and comprehensive information on the vast collections of the U.S. National Plant Germplasm System are available to researchers worldwide.