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BioInform s Funding Update: Some Recent NIH Awards in Bioinformatics: Apr 26, 2004

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Plasmodium Genome Database. Start date: March 2004. Expires: Feb. 2009. Amount: $629,123. Principal investigator: Christian Stoekert. Institution: University of Pennsylvania. NIH institute: NIAID.

Supports ongoing development of the Plasmodium Genome Database (PlasmoDB), a reference database for the malaria-causing parasite P. falciparum. Project plans include an improved web interface for relational queries, and a mechanism for community input and response, including implementation of comment forms, tracking responses to comments, and posting comments and responses at PlasmoDB.


Pattern Recognition Software for Single Cell Proteomics. Start date: April 2004. Expires: Oct. 2004. Amount: NA. Principal investigator: Erik Nilsson. Institution: Insilicos. NIH institute: NIGMS.

Proposes a new method for analyzing proteins in single cells based on a software platform that classifies samples processed on a capillary-electrophoresis proteomics instrument that measures proteins in single cells.


Shared Computational Resource for Functional Genomics. Start date: April 2004. Expires: March 2005. Amount: $270,064. Principal investigator: Roger Bumgarner. Institution: University of Washington. NIH institute: NCRR.

Funds the purchase of a Sun V880 server and a 1-terabyte disk array and tape backup system for the University of Washington functional genomics computing center, which currently supports 53 PIs and 152 researchers.


Linux Computational Cluster. Start date: April 2004. Expires: March 2005. Amount: $458,124. Principal investigator: Mahum Michael Barmada. Institution: University of Pittsburgh. NIH institute: NCRR.

Funds a 200-processor Linux cluster with 2 terabytes of disk space. The major user group for the shared resource will be the Department of Human Genetics at the University of Pittsburgh.


Computeserver Structural & Functional Image Analysis. Start date: April 2004. Expires: March 2005. Amount: $495,990. Principal investigator: Bruce Fischl. Institution: Massachusetts General Hospital. NIH institute: NCRR.

Supports a new 344-node cluster of 2.8-GHz Xenon processors to support structural and functional image analysis.


System for the Stanford Microarray Database. Start date: April 2004. Expires: March 2005. Amount: $440,621. Principal investigator: Gavin Sherlock. Institution: Stanford University. NIH institute: NCRR.

Provides funding to purchase a new computer system for the Stanford Microarray Database. The grant will fund a server to accommodate the database, a server to provide additional computational power, a RAID array for data storage, three RAIDs for image storage and backup, a backup library, a partitioning license from Oracle, and the appropriate uninterruptable power supplies and storage racks for the machines.


Joint Modeling of Genomic and Functional Genomic Data. Start date: April 2004. Expires: March 2006. Amount: NA. Principal investigator: Mario Medvedovic. Institution: University of Cincinnati. NIH institute: NLM.

Proposal to develop novel mathematical models and corresponding computational tools to extract relevant expression patterns, related regulatory motifs, and genomic aberrations by jointly modeling genomic and functional genomic data. The procedures will be based on the context-specific Bayesian infinite mixture model.


COMKAT: Compartment Model Kinetic Analysis/Imaging. Start date: April 2004. Expires: March 2007. Amount: $326,453. Principal investigator: Raymond Muzic. Institution: Case Western Reserve University. NIH institute: NCI.

Funds development of new software tools for in vivo characterization of molecular and cellular events based on the previously developed image analysis package COMKAT (Compartment Model Kinetic Analysis Tool). New features will include co-registration, fusion, and visualization of multi-modality data; region-of-interest specification and time-activity curve creation; and a library of examples.


Genomic Reconstruction of Yeast Transcription Networks. Start date: April 2004. Expires: March 2008. Amount: $268,267. Principal investigator: Hao Li. Institution: University of California, San Francisco. NIH institute: NIGMS.

Supports development of theoretical models and computational algorithms to reconstruct the transcription networks in Saccharomyces cerevisiae. Project will map the DNA recognition sites and target genes of transcription factors in the genome; identify environmental and genetic perturbations under which each transcription factor is activated or deactivated; and build databases and online tools for analyzing gene expression data and transcriptional regulation.


Novel Algorithms for Crystallographic Computing. Start date: April 2004. Expires: March 2009. Amount: $393,216. Principal investigator: Nikolaos Sahinidis. Institution: University of Illinois Urbana-Champaign. NIH institute: NIGMS.

Project to develop improved computational methods to identify the phases of the diffracted rays from measurements of intensities alone in X-ray crystallography. Mathematical models for determining three-dimensional crystal structures from single crystal X-ray diffraction measurements will be developed, along with mathematical optimization algorithms to solve those models.


Cytoscape: A Modeling Platform for Biomolecular Networks. Start date: June 2004. Expires: May 2009. Amount: $369,894. Principal investigator: Trey Ideker. Institution: University of California San Diego. NIH institute: NIGMS.

Funds development of Cytoscape, an open source software project for integrating biomolecular interaction networks with genome-scale expression data and other molecular states. Funding will support improvements to the Cytoscape core architecture and user interface; construction of a data services layer with access to multiple biological databases hosted on the Internet; and a “substantial” increase in the number of publicly available plug-in analyses.

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