Progress 10/01/10 to 09/30/11
Outputs
Progress Report Objectives (from AD-416) Grass species are integral to U.S. future plans for sustainable food and biofuels development. To meet anticipated demands, it is necessary to fully apply all modern technologies to these grasses. This project will develop and coordinate genomic and bioinformatic technologies and protocols to grass food and biofuels crops, and will make these resources available to all U.S. researchers and other relevant sectors. Approach (from AD-416) 1) Contribute to the maintenance and development of databases and electronic resources for important data sources to include information on genetics, germplasms, and genomics of wheat, barley, rye, oats, switchgrass, Brachypodium, and related species. 2) Develop software tools for processing of data. 3) Collaborate in the development and distribution of molecular markers, maps, and other resources. 4) Collaborate with other bioinformatics projects to enhance the availability and interconnectedness of all relevant data. Cooperation continues to facilitate the coordination of data accumulation from laboratory sites worldwide. The website for the US Wheat and Barley Scab Initiative, www.scabusa.org, was enhanced with additional features and redesign. The �Fusarium head blight (FHB) Alerts� regions were reconfigured and an administrative interface was created to manage the FHB Alert subscriptions; these updates were advertised by poster at a recent barley conference. Web site forms and server-side processing scripts used for authorized credit processing, database registration and procedure ordering, a tool vital towards organizing project activities, was updated. The US Wheat and Barley Scab Initiative (USWBSI) server was updated, and the scabsmart.org web-site was integrated into this resource. The GrainGenes project served to facilitate hosting of The Hordeum Toolbox (THT). The project is collaborating with a team of programmers to make adjustments to the THT database design for use in a continuing project, with combined efforts of wheat and barley CAP projects in a new venture know as the Triticeae CAP (TCAP). The collaboration continues to develop tools for a database known a The Triticeae Toolkit (T3). The above projects in their interactions with GrainGenes have contributed computer scripts and data formatting for the parent project, as well as software installation and computer systems administration. Software was upgraded for performance, compatibility, and security. Project progress is monitored by meetings, conference calls, site visits, e-mails and phone calls on a regular basis.
Impacts
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Progress 09/28/06 to 09/14/11
Outputs
Progress Report Objectives (from AD-416): Grass species are integral to U.S. future plans for sustainable food and biofuels development. To meet anticipated demands, it is necessary to fully apply all modern technologies to these grasses. This project will develop and coordinate genomic and bioinformatic technologies and protocols to grass food and biofuels crops, and will make these resources available to all U.S. researchers and other relevant sectors. Approach (from AD-416): 1) Contribute to the maintenance and development of databases and electronic resources for important data sources to include information on genetics, germplasms, and genomics of wheat, barley, rye, oats, switchgrass, Brachypodium, and related species. 2) Develop software tools for processing of data. 3) Collaborate in the development and distribution of molecular markers, maps, and other resources. 4) Collaborate with other bioinformatics projects to enhance the availability and interconnectedness of all relevant data. The GrainGenes project collected appropriate datasets from cooperating research projects to provide ongoing public access to the products of those projects' efforts. For example, a major cooperator was the NSF (National Science Foundation)-sponsored wheat D-genome physical mapping and sequencing project, http://avena.pw.usda.gov/wheatD/. As another part of this cooperation besides data exchange, the project's website was installed on one of GrainGenes's server machines. Other projects for which GrainGenes provided all of the server, system, software, network, and security support include The Triticeae Toolbox (T3) and the US Wheat and Barley Scab Initiative (USWBSI) projects, both USDA-sponsored. Major infrastructure enhancements improving service for all hosted projects as well as the GrainGenes Database itself included installation of a new hardware firewall and an iKVM (KVM over IP, a device allowing console- level access to multiple server machines remotely). The USWBSI site http://scabusa.org was completely re-programmed to convert from the Perl language to PHP, providing a friendlier interface, more features, better operating-system compatibility, and improved maintainability by the webmaster/administrator supported under this subproject. The resulting dissemination of data and information was a major contributor to the success of all four sub-objectives of parent project Objective 1, "Integrate small grains genetic and genomic data within the GrainGenes database and link to relevant external databases."
Impacts
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Progress 10/01/09 to 09/30/10
Outputs
Progress Report Objectives (from AD-416) Grass species are integral to U.S. future plans for sustainable food and biofuels development. To meet anticipated demands, it is necessary to fully apply all modern technologies to these grasses. This project will develop and coordinate genomic and bioinformatic technologies and protocols to grass food and biofuels crops, and will make these resources available to all U.S. researchers and other relevant sectors. Approach (from AD-416) 1) Contribute to the maintenance and development of databases and electronic resources for important data sources to include information on genetics, germplasms, and genomics of wheat, barley, rye, oats, switchgrass, Brachypodium, and related species. 2) Develop software tools for processing of data. 3) Collaborate in the development and distribution of molecular markers, maps, and other resources. 4) Collaborate with other bioinformatics projects to enhance the availability and interconnectedness of all relevant data. Replaces 5325- 21000-010-01S. Documents SCA with UC Davis. Formerly 5325-21000-010-02S (08/01/08). The cooperation continues to facilitate the coordination of data accumulation from laboratory sites worldwide. The cooperation is successfully managing the web site, www.scabusa.org, and databases for the US Wheat and Barley Scab Initiative (USWBSI) - a U.S. effort to combat the devastating disease of Fusarium head blight of the small grains crops. A system was set up to send �FHB alerts�, real-time disease updates and field reports, to users' cell phones. The credit card processing system was changed to a new vendor, Authorize.net, to meet the requirements for information security. New modules were added to the website for security and blocking spam. The software used to operate the website, Xoops, was upgraded to the latest version. This subordinate project has contributed computer scripts and data formatting for the parent project, as well as software installation and computer systems administration. The MySQL, PHP, and Perl software were upgraded for performance, compatibility, and security. One of the primary computation servers failed and was replaced, requiring installation of all the software. Scripts were developed to export the GrainGenes database and index it for full-text searching, to be executed at regular intervals as the database expands. Project progress is monitored by meetings, conference calls, site visits, e-mails and phone calls on a regular basis.
Impacts
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Progress 10/01/08 to 09/30/09
Outputs
Progress Report Objectives (from AD-416) Grass species are integral to U.S. future plans for sustainable food and biofuels development. To meet anticipated demands, it is necessary to fully apply all modern technologies to these grasses. This project will develop and coordinate genomic and bioinformatic technologies and protocols to grass food and biofuels crops, and will make these resources available to all U.S. researchers and other relevant sectors. Approach (from AD-416) 1) Contribute to the maintenance and development of databases and electronic resources for important data sources to include information on genetics, germplasms, and genomics of wheat, barley, rye, oats, switchgrass, Brachypodium, and related species. 2) Develop software tools for processing of data. 3) Collaborate in the development and distribution of molecular markers, maps, and other resources. 4) Collaborate with other bioinformatics projects to enhance the availability and interconnectedness of all relevant data. Replaces 5325- 21000-010-01S. Documents SCA with UC Davis. Formerly 5325-21000-010-02S (08/01/08). Significant Activities that Support Special Target Populations The cooperation continues to facilitate the coordination of data accumulation from laboratory sites worldwide. The cooperation is successfully managing the web site and databases for the US Wheat and Barley Scab Initiative (USWBSI) - a U.S. effort to combat the devastating disease of fusarium head blight of the small grains crops. A new service on this website is a system for submission and tracking of research proposals to be funded by the USWBSI. The cooperation has also collaborated in the organization and operations of several wheat genomics projects, data from which are included in publicly available database resources maintained and developed by the parent project. This subordinate project has contributed computer scripts and data formatting for the parent project, creation of curational tools for the parent database, and further enhancement of the parent relational database structure. In addition, activities have included collaboration in the physical mapping of wheat and Brachypodium genomes, use of large- insert library resources, and design and analysis of microarrays for wheat functional genomics research. Recent collections of DNA clones for the research of the new model species Brachypodium distachyon have been made available to the UC Davis strain collection site. The resources made available have included BAC derived genome libraries of Brachypodium Bd21. Within these libraries are clones from which BAC-end sequence data was derived and such sequence data was critical in the assembly of sequencing information for the Brachypodium distachyon genome which was conducted at the DOE JGI genome sequencing facility. Project progress is monitored by meetings, conference calls, site visits, e-mails and phone calls on a regular basis.
Impacts
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Progress 10/01/07 to 09/30/08
Outputs
Progress Report Objectives (from AD-416) Grass species are integral to U.S. future plans for sustainable food and biofuels development. To meet anticipated demands, it is necessary to fully apply all modern technologies to these grasses. This project will develop and coordinate genomic and bioinformatic technologies and protocols to grass food and biofuels crops, and will make these resources available to all U.S. researchers and other relevant sectors. Approach (from AD-416) 1) Contribute to the maintenance and development of databases and electronic resources for important data sources to include information on genetics, germplasms, and genomics of wheat, barley, rye, oats, switchgrass, Brachypodium, and related species. 2) Develop software tools for processing of data. 3) Collaborate in the development and distribution of molecular markers, maps, and other resources. 4) Collaborate with other bioinformatics projects to enhance the availability and interconnectedness of all relevant data. Replaces 5325- 21000-010-01S. Documents SCA with UC Davis. August 2006. Significant Activities that Support Special Target Populations This report documents research conducted under a specific cooperative agreement between the ARS and the University of California, Davis. This SCA is a continuation of 5325-21000-010-02S. Additional details of the research can be found in the report for the parent CRIS 5325-21000-014- 00D, Database and Bioinformatic Resources for Small Grains Research and Crop Improvement. The cooperative agreement continues to facilitate the coordination of data accumulation from laboratory sites worldwide. The agreement is successfully managing the web site and databases for the US Wheat and Barley Scab Initiative - a U.S. effort to combat the devastating disease of fusarium head blight of the small grains crops. A new service on this website is a system for submission and tracking of research proposals to be funded by the USWBSI. The agreement has also collaborated in the organization and operations of several wheat genomics projects, data from which is included in publicly available database resources maintained and developed by the parent project. This subordinate project has contributed computer scripts and data formatting for the parent project, creation of curational tools for the parent database, and further enhancement of the parent relational database structure. In addition, activities have included collaboration in the physical mapping of wheat and Brachypodium genomes, use of large-insert library resources, and design and analysis of microarrays for wheat functional genomics research. Project progress is monitored by meetings, conference calls, site visits, e-mails and phone calls on a regular basis. This research supports NP 301 Component 2: Crop Informatics, Genomics, and Genetic Analyses, Problem Statements A: Genome Database Stewardship and Informatics Tool Development, and B: Structural Comparison and Analysis of Crop Genomes.
Impacts
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Progress 10/01/06 to 09/30/07
Outputs
Progress Report Objectives (from AD-416) Grass species are integral to U.S. future plans for sustainable food and biofuels development. To meet anticipated demands, it is necessary to fully apply all modern technologies to these grasses. This project will develop and coordinate genomic and bioinformatic technologies and protocols to grass food and biofuels crops, and will make these resources available to all U.S. researchers and other relevant sectors. Approach (from AD-416) 1) Contribute to the maintenance and development of databases and electronic resources for important data sources to include information on genetics, germplasms, and genomics of wheat, barley, rye, oats, switchgrass, Brachypodium, and related species. 2) Develop software tools for processing of data. 3) Collaborate in the development and distribution of molecular markers, maps, and other resources. 4) Collaborate with other bioinformatics projects to enhance the availability and interconnectedness of all relevant data. Replaces 5325- 21000-010-01S. Documents SCA with UC Davis. BSL-1; August 2006. Significant Activities that Support Special Target Populations This report serves to document research conducted under a specific cooperative agreement between the ARS and the University of California, Davis and is a continuation of 5325-21000-010-01S. Additional details of research can be found in the report for the parent CRIS 5325-21000-010- 00D, Database and Bioinformatic Resources for Small Grains Research and Crop Improvement. The cooperative agreement continues to facilitate the coordination of data accumulation from laboratory sites worldwide. The agreement is successfully managing the web site and databases for the US Wheat and Barley Scab Initiative - a U.S. effort to combat the devastating disease of fusarium head blight of the small grains crops. The agreement has collaborated in the organization and operations of several wheat genomics projects, and has evaluated and included in publicly available database resources maintained and developed by the parent project. This subordinate project has contributed computer scripts and data formatting for the parent project, the creation of curational tools for the parent project database, and further enhancements of the parent relational database structure. In addition, activities have included collaboration in the physical mapping of wheat and Brachypodium genomes, using large- insert library resources and design and analysis of microarrays for wheat functional genomics research. Project progress is monitored by meetings, conference calls, site visits, e-mails and phone calls on a regular basis.
Impacts
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