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NSF Bioinformatics Grants Awarded Sept. 12 — Oct. 14, 2008

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Collaborative Research: Phylogenetic Trees for Comparative Biology. Start date: Oct. 1, 2008. Expires: Sept. 30, 2011. This award was granted to two investigative teams:
  • Principal investigator: David Fernandez-Baca. Awarded amount to date: $800,000. Sponsor: Iowa State University. 
  • Principal investigator: Michael Sanderson. Sponsor: University of Arizona. Awarded amount to date: $450,000.
Proposal to use data in GenBank, which currently includes sequences from 185,000 species, to build an electronic repository of one billion phylogenetic trees. The goal of the project is to build a large number of phylogenetic trees and then construct search and retrieval tools to match these trees to “any query list of species in which a user may be interested,” according to the grant abstract.
 

 
The Generation of Complex Epistasis by Metabolic Networks. Start date: Sept. 15, 2008. Expires: Aug. 31, 2012. Awarded amount to date: $1,314,084. Principal investigator: Daniel Kliebenstein. Sponsor: University of California-Davis.
 
This project will use the rice and Arabidopsis metabolomes as model systems to identify mechanisms by which metabolomic quantitative trait loci form an epistatic network that constrains potential variation in the metabolome. Among other goals, the data generated will be used to develop a metabolic network de novo using a logic-based algorithm that has identified novel metabolic networks in other metabolomics data, according to the grant abstract. This information “will allow for the development of models that integrate natural variation in plant metabolic networks to potentially predict phenotypic diversity,” the abstract states. All data will be available through the project website and through the Arabidopsis Information Resource and Gramene.
 

 
Grid, Public, and GPU Computing for the Tree of Life. Start date: Sept. 15, 2008. Expires: Aug. 31, 2009. Awarded amount to date: $442,700. Principal investigator: Michael Cummings. Sponsor: University of Maryland College Park.
 
Supports a project to create tools that expand the computing power freely available to all researchers involved in the Assembling the Tree of Life project, as well as other phylogenetic researchers. The goal of the project is to combine grid and graphics-processing-unit computing “to take better advantage of a diversity of computing resources, particularly existing desktop processing capacity available through public-computing,” according to the grant abstract. The main product will be a grid system, customized for phylogenetic tree search and accessed through a web interface that links thousands of individual computers worldwide. The likelihood-based tree search program GARLI (Genetic Algorithm for Rapid Likelihood Inference) will be the initial application for the system.
 

 
ALFRED: Making Very High Throughput Data Accessible. Start date: Sept. 15, 2008. Expires: Aug. 31, 2009. Awarded amount to date: $200,000. Principal investigator: Kenneth Kidd. Sponsor: Yale University.
 
Supports a project to update the Allele Frequency Database, or ALFRED, to integrate information from high-throughput SNP projects that study up to about 2 million SNPs. The first aim is to expand the contents of ALFRED by automating the curation processing order to facilitate the addition of these very large data sets. The second aim is to enhance the educational and research value of ALFRED by improving the geographic information system interface. The third aim is to improve the interface in order to help users access the expanded content. Currently, ALFRED includes nearly 280,000 gene frequency tables based on more than 650 human populations studied very unevenly on more than 14,700 polymorphisms along with population and marker descriptions and links to other informative databases.

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