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BioInform s Funding Update: Some Recent NSF Awards in Bioinformatics: Dec 2, 2002


A Database for Modeling Protein Spatial Geometry: Discovering Protein Functions. Start date: Sept. 1, 2002. Expires: July 31, 2007. Expected total amount: $651,826. Principal investigator: Jie Liang. Sponsor: University of Illinois, Chicago.

Project aims to develop tools using computational geometry for the discovery of similar protein surface patterns, as well as a databases of libraries of similar protein surfaces for biological querying and understanding. The search tools will be developed using an informatics approach for discovery of statistically significant similarity relationships of protein surfaces, combining sequence, physicochemical, and shape information.


Computational Capability for Fast and Reliable Characterization of Protein Complexes. Start date: Sept. 1, 2002. Expires: July 31, 2005. Expected total amount: $888,614. Principal investigators: Ying Xu, Dong Xu, Gregory Hurst, Edward Uberbacher. Sponsor: University of Tennessee, Knoxville.

Project will develop an integrated computational capability for the characterization of protein complexes in a cell by analyzing mass spectrometry data and chemical cross-linking information, as well as protein docking prediction under geometric constraints derived from these experimental data. Developed methods will be used for genome-scale cataloging of protein complexes in yeast and other genomes. Computer software and databases developed for the project will be made freely available to the academic and government organizations via the internet.


MOBY: A World-Wide Distributed Bioinformatics Analysis System. Start date: Sept. 1, 2002. Expires: August 31, 2004. Expected total amount: $596,028. Principal investigators: Lincoln Stein, Damien Gessler. Sponsor: Cold Spring Harbor Lab.

Project will provide a general architecture for integrating disparate biological data sources using a combined client/server, peer-to-peer implementation of the web service broker model. A core of model organism database developers already supports the architecture. The project will deliver a graphical implementation and annotation source as well as an application programming interface and proof of principle for four model organisms.


Bioinformatics of Alternative Splicing in the Nervous System. Start date: Sept. 15, 2002. Expires: August 31, 2004. Expected total amount: $1,786,058. Principal Investigators: Christopher Burge, Phillip Sharp, Tomaso Poggio. Sponsor: MIT.

Project aims to understand the signals in a gene that determine how that gene will be spliced when it is expressed in a particular part of the brain, and how alternative splicing is used to modulate brain function.


Exploring Approaches for Microarray Databases that Enable Flexible Design and Integrative Analysis. Start date: Nov. 1, 2002. Expires: October 31, 2004. Expected total amount: $479,985. Principal investigator: Kei-Hoi Cheung. Sponsor: Yale University.

Project will explore technologies for representing, storing, and processing microarray data for the Yale Microarray Database. MAGE-ML will be used as as a common data exchange mechanism between YMD and other MIAME-compliant microarray data repositories.


Data Squashing for Massive Data Analysis. Start date: Jan. 1, 2003. Expires: June 30, 2003. Expected total amount: $99,999. Principal investigator: Nandini Raghavan. Sponsor: Ornarose.

SBIR Phase I grant supports project development of “squashing” algorithms to compress massive datasets into much smaller ones so that outputs from statistical analyses carried out on the smaller datasets reproduce outputs from the same analyses carried out on the original datasets. The objective of the research is to critically evaluate squashing and, eventually, develop a commercial data squashing software product for use in computational biology, medical surveillance systems, telecommunications, or astronomy.


HIVbase, Data Integration Software to Support the Study of Chronic Viruses. Start date: Jan. 1, 2003. Expires: June 30, 2003. Expected total amount: $100,000. Principal investigator: Susanna Lamers. Sponsor: GJI.

SBIR Phase I grant supports the development of software, called HIVbase, that will integrate multiple sources of disparate data into an automated high-dimensional warehouse and also perform repetitious tasks common to genetic and clinical research projects. Applications will include protein identification tools, the ability to create user-defined searches based on specific genetic attributes, and the ability to efficiently share information with outside collaborators.

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