Gramene: A Platform for Comparative Cereal Genomics. Start date: Dec. 15, 2003. Expires: Nov. 30, 2007. Amount: $5,500,235. Principal investigator: Lincoln Stein. Sponsor: Cold Spring Harbor Laboratory.
Supports expanded operations of Gramene (http://www.gramene.org), a comparative mapping database for rice and other cereals. The project uses controlled vocabularies to describe rice genes, mutants, and varieties; high-throughput analytic techniques to annotate features on the genome; and a combination of automatic and manual annotation to discover relationships between genetic and physical maps. Specific aims include mapping between the rice and maize genomes; developing an open source genome annotation pipeline; beginning a pilot project to annotate maize mutants with the Plant Ontology; and adding advanced query tool and report functionality to the Gramene web site.
Summer Research Projects in Biosystems Modeling and Analysis. Start date: Nov. 1, 2003. Expires: Oct. 31, 2006. Amount: $335,029. Principal investigator: Satish Nair. Sponsor: University of Missouri, Columbia.
Supports a three-year Research Experience for Undergraduates (REU) site at the University of Missouri Columbia for twelve students per year during ten weeks in the summer to focus on research in the area of mathematical modeling and analysis in the biosciences. Students will work with an interdisciplinary team of faculty researchers to learn how to explore biosystems using quantitative modeling and system theory analysis.
Macromolecular Structure Database (MSD). Start date: Jan. 1, 2004. Expires: Dec. 31, 2008. Amount: $28,794,057. Principal Investigator: Helen Berman. Sponsor: Rutgers University, New Brunswick.
Funds continued development of the Protein Data Bank (http://www.rcsb.org/pdb/), including improved data processing and automated data deposition and exchange functions. Data archiving, distribution, and query capabilities will also be improved via a new system for distribution and archiving of all PDB data, enabling comprehensive structural data analyses regardless of geographic location, local hardware, or software configuration. Finally, completion and maintenance of a comprehensive physical archive is being undertaken to ensure the preservation of primary data and of all records associated with the transactions of the database including documents describing its evolution and maintenance.