NSF Bioinformatics Grants Awarded April 15 — May 13, 2010
Computational Modeling and Analysis of Gene Expression Patterns from Microscopy Image Data
Start date: June 1, 2010
Expires: May 31, 2011
Awarded amount to date: $155,068
Principal investigator: Uwe Ohler
Sponsor: Duke University
Supports a project to develop an integrated framework for analyzing and interpreting biological image data. "With recent advances in microscopy technology, as well as means to visualize biological molecules, the growing amount of available data has turned images into a new data type for computational biology with new and exciting challenges and possibilities," according to the grant abstract. "Algorithms to extract, represent, and compare spatial and temporal expression patterns from images are still in early stages, and are often tailored to a particular scenario." The project aims to develop a "principled probabilistic framework" that uses "top-down generative strategies" to extract samples from images, model gene expression patterns from microscopy data, and integrate image expression data with other genomic data to understand gene regulation.
ChemMine Tools: an Open Source Framework for Chemical Genomics
Start date: May 15, 2010
Expires: April 30, 2011
Awarded amount to date: $219,275
Principal investigator: Thomas Girke
Sponsor: University of California, Riverside
Funds development of ChemMineTools, a software environment for analyzing and modeling large sets of small molecules along with their bioactivity data. The software will provide "unrestricted access to a scalable set of open source tools that integrates novel and existing algorithms," according to the grant abstract. The analysis modules will be available as part of the R statistical software environment. The researchers specifically aim to develop "accelerated compound search and clustering algorithms that scale to today's large databases with millions of entries." This task will focus on expanding two existing algorithms — EI-Search and EI-Clustering — which "will be adopted to advanced similarity measures that can currently not be used for processing large databases due their insufficient speed performance."
From Zero to Genome in Two Years: Transformative Techniques for Evolutionary Genetics
Start date: May 15, 2010
Expires: April 30, 2012
Awarded amount to date: $155,958
Principal investigator: William Cresko
Sponsor: University of Oregon, Eugene
Funds a project "to develop a clear set of protocols and computational software to rapidly produce genomic analysis tools for just about any organism." The investigators plan to first test the protocols on Caenorhabditis elegans, and then to "further refine" the techniques by applying them to a non-model vertebrate organism, the pipefish Syngnathus scovelli. "The research on these two organisms will serve as test cases from which an easily followed set of methods will be created and distributed widely, including the wet lab procedures for data generation and the software for the analysis of these data," the grant abstract states.
Acquisition of High Performance Computer and Microarray Scanner for Interdisciplinary Research in Computer Science and Biology at St. Lawrence University
Start date: May 1, 2010
Expires: April 30, 2013
Awarded amount to date: $179,336
Principal investigator: Richard Sharp
Sponsor: Saint Lawrence University
The project, funded under the American Recovery and Reinvestment Act of 2009, provides a microarray scanner and a "high-end compute server" to support the research of twelve faculty members at St. Lawrence University. Projects include "image synthesis, comparative genome analysis in yeast, phylogenetic analysis of microbial communities and comparative analysis of bacterial genomes, microarray analysis of gene expression, and bird foraging studies," according to the grant abstract. The awardees said they chose a server instead of a compute cluster, "due to the simpler programming model inherent in one machine versus many." In addition, "most of the St. Lawrence users employ software tools that are parallel, but not distributed, and hence would not benefit from a cluster."
Algorithmic Problems in Protein Structure Studies
Start date: Sept. 17, 2009
Expires: Aug. 31, 2012
Awarded amount to date: $225,001
Principal investigator: Gopal Pandurangan
Sponsor: Brown University
Supports the design of "efficient algorithms for fundamental problems that arise in studies of the three-dimensional structures of proteins." The project addresses two specific algorithmic problems, according to the grant abstract: "identifying correspondences between a pair of graphs where one is a significantly corrupted version of the other, and determining three-dimensional coordinates for the vertices of a graph, given approximate, noisy distance measurements for its edges."