Progress 05/07/08 to 04/04/13
Outputs
Progress Report 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. 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. Develop the next version of the GRIN software as a scalable portable system capable of being transfered to other genebanks in addition to allowing greater interoperability between genetic resources and biodiversity databases. Over the duration of the project, the plant pages of the Germplasm Resources Information Network (GRIN) received almost 9 million visits. Researchers, breeders, and educators worldwide accessed the database, which resulted in more than 1.2 million samples being distributed from the U.S. National Plant Germplasm System (NPGS). The number of active plant accessions curated in the NPGS and documented in GRIN grew from about 500,000 to more than 560,000 over the duration of this project. The amount and types of data on the collections grew significantly, which represented a major commitment on the part of ARS scientists and collaborating partners to characterize and evaluate the collections more thoroughly. For example, at the beginning of this project there were about 6.8 million characterization records and 165,000 digital images on NPGS accessions; those numbers increased to more than 8.7 million and 255, 000, respectively, by the end of the project. These efforts provided more detailed and specific information to assist stakeholders and users. The project maintained its collaboration with colleagues at Agriculture and Agri-Food Canada, the U.S. Forest Service, the USDA Plant Variety Protection Office, and USDA-APHIS to provide GRIN services to their agencies. GRIN was maintained in compliance with USDA information security practices and there were no significant security incidents over the life of the project. The staff maintained a long-standing track record of > 98% 24/7/365 availability of the GRIN system, commensurate with its importance as a global research tool. GRIN documented the activities of 42 Crop Germplasm Committees, whose consultations on a range of issues provide invaluable assistance to the NPGS curators and genebanks. The system also documented USDA animal, microbial, and invertebrate germplasm collections whose impact is similarly significant and documented in other reports. For example, the number of units in the animal germplasm collection at the National Center for Genetic Resources Preservation in Ft. Collins, CO increased from about 560,000 to 760,000 over the five year span of this project. Finally, a major collaborative effort was initiated during this project to develop a new version of the plant GRIN system, while maintaining and enhancing the current one. The new plant component of GRIN is called GRIN-Global and will be deployed to the NPGS in late 2013. GRIN-Global will use the superior data structure of GRIN, refined over several decades, in combination with upgraded and more flexible information technology tools. The public website will be redesigned to be more user friendly, and contain more features and functions. GRIN-Global will capably serve the NPGS, and offer unprecedented opportunities for global collaboration in the conservation, documentation, and utilization of plant genetic resources for food and agriculture.
Impacts
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Progress 10/01/11 to 09/30/12
Outputs
Progress Report 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. 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. Develop the next version of the GRIN software 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. 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 2012 phase of the project consisted of refining both the curator tool and public Web site features. This culminated in the release of the first production version 1.0 that was made available to the international community on December 19, 2011. Current efforts are focusing on additional improvement and enhancements that will constitute version 2.0 of the system. Plans are also underway to migrate the NPGS to GRIN Global. Webinar based training sessions are being conducted for NPGS genebank staff and a gap analysis process is underway to determine the unique needs that must be addressed for the NPGS sites to implement GRIN Global. Accomplishments 01 GRIN database available. The GRIN database was available on a nearly 24 basis throughout 2012. Access to the web pages for GRIN included about 2 million visits for the past year, similar to 2011. Our statistics also indicated the average visitor spent 8 minutes at the site and viewed mor than 9 different pages. As of June 2012 more than 152,000 germplasm samples have been distributed from the NPGS 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. 02 Improvements to GRIN software. Improvements were made to the existing GRIN curator and public software, including the ability to download a spreadsheet of evaluation data (user selected traits). Most of the staf time for DBMU in 2012 has been oriented toward GRIN-Global development a deployment efforts. Major efforts of the DBMU have been in web developme schema review, training documentation, installation, server hosting and testing of the GRIN-Global software. This ongoing effort is also describ in the progress report. A major milestone was the release of the first production version 1.0 on December 19, 2011. 03 Crop Germplasm Committees. There are 42 CGCs, comprised of public and private sector scientists for a given crop, that comprise a support network for the 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-two committees have met (in person or by teleconferenc as of July 2012. These CGCs are an integral part of the overall effectiveness of the NPGS.
Impacts
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Progress 10/01/10 to 09/30/11
Outputs
Progress Report 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. 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. Accomplishments 01 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. 02 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. 03 Participate in development of GRIN-Global. Most of the staff time for t 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 effor is also described in the progress report. 04 Coordinate the activities of the Crop Germplasm Committees (CGC). There are 42 CGCs, comprised of public and private sector scientists for a giv crop, that comprise a support network for the National Plant Germplasm System (NPGS). Included among their activities are preparing and updatin status/vulnerability reports for their crop(s) and serving as peer reviewers for USDA-funded plant exploration and characterization proposa Twenty-three committees have met (in person or by teleconference) as of July 2011. These CGCs are an integral part of the overall effectiveness the NPGS.
Impacts
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Progress 10/01/09 to 09/30/10
Outputs
Progress Report 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. 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. Develop the next version of the GRIN software 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 supports National Program 301 by providing 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 ordering of 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 system was 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 collaborators from ARS, 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 the NPGS and the breeding and research community. In addition it will be made available to interested genetic resource managers worldwide, especially in the developing countries where there is a serious need for a genebank management system. The 2010 phase of the project involved the writing of the base software code, a new version of the public interface and a complete review of the GRIN-Global schema. Accomplishments 01 GRIN Availability. The GRIN database was available on a nearly 24/7 bas throughout 2010. Access to the web pages for GRIN averaged over 1.5 million hits per month for 2010. As of July 2010 more than 118,000 samples of germplasm have been distributed from the NPGS genebanks, most of them requested on the basis of information made available through GRI 02 Enhancements to current GRIN. Improvements were made to the existing GR 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 moveme from a commercial internet server to the USDA network. 03 Participate in development of GRIN-Global. Most of the efforts of the Database Management Unit (DBMU) have been switched from the existing GRI system to participating in the GRIN-Global development and deployment efforts. Major efforts of the DBMU have been in web development, schema review, training documentation, installation and testing of the GRIN- Global software.
Impacts
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Publications
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Progress 10/01/08 to 09/30/09
Outputs
Progress Report 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. 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. Develop the next version of the GRIN software as a scalable portable system capable of being transfered to other genebanks in addition to allowing greater interoperability between genetic resources and biodiversity databases. Significant Activities that Support Special Target Populations The Database Management Unit (DBMU) supports NP 301 by providing a central database for the germplasm collections within the National Plant Germplasm System (NPGS). This central database provides curator tools for managing the collections as well as a portal for public access and ordering of 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. Preparations were made to move from a 10 Mb commercial internet service provider to the 600 Mb USDA telecommunications network. 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 collaborators from ARS, 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 the NPGS and the breeding and research community. In addition, it will be made available to interested genetic resource managers worldwide, especially in the developing countries where there is a serious need for a genebank management system. The initial phases of the project that have been completed are: designation of the development team, several team meetings, selection of the Technical Steering Committee, conversion of the Oracle database to open source MySQL, training and initialization of the development work. Technology Transfer Number of Web Sites managed: 5
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