Earlier this month, the US Department of Energy’s Genomes to Life Initiative awarded 26 new grants for the 2004 fiscal year. Of those, seven computational projects were awarded a total of $7.2 million over the next three years.
A summary of the Genomes to Life computational projects follows, and further details are available at http://www.doegenomestolife.org/pubs/2004abstracts/html/ModelComp.shtml.
Development of Advanced Tools for Data Management, Integration, Analysis and Visualization through a Comprehensive Systems Analysis of the Halophilic Archaeon. Principal investigator: Leroy Hood, Institute for Systems Biology. Collaborator: the Keck Institute. Start date: May 2004. Total funding: $1.2 million. Supports the development of software tools for data integration, network inference, database mining, and network comparisons.
Rapid Reverse Engineering of Genetic Networks via Systematic Transcriptional Perturbations. Principal investigator: J.J. Collins, Boston University. Start date: April 2004. Total funding: $1.6 million.
Project to develop a procedure called real competitive PCR (rcPCR), that will provide proteomics data to reconstruct microbial regulatory networks. The team has used the method to model an E. coli system and proposes to expand it to Shewanella.
Computational Hypothesis Testing: Integrating Heterogeneous Data and Large-Scale Simulation to Generate Pathway Hypotheses. Principal investigator: Mike Shuler, Gene Network Sciences. Collaborators: Wadsworth Center; Washington University , St. Louis; Cybercell consortium. Start date: April 2004. Total funding: $2.2 million.
Funds development of a dynamic simulation of E. coli and Shewanella using published literature, databases, and high-throughput E. coli experimental data from the Cybercell consortium.
Computational Resources for GTL. Principal investigator: Herbert M. Sauro, Keck Graduate Institute; Claremont College. Start date: April 2004. Total amount: $460,000.
Supports enhancements for the Biospice software package for network modeling.
Development of Bioinformatics and Experimental Technologies for Identification of Prokaryotic Regulatory Networks. Principal investigator: Charles Lawrence, Wadsworth Center. Collaborator: Washington University, St. Louis. Start date: April 2004. Total amount: $1.9 million.