Interactive Level-Set Modeling for Visualization of Biological Volume Datasets. Start date: Oct. 1, 2003. Expires: Sept. 30, 2005. Amount: $111,602. Principal investigator: David Breen. Sponsor: Drexel University.
Project to make level-set modeling — a computationally expensive visualization technique — interactive for use in 3D visualization of biological data sets. Researchers will design and implement a hardware and software system for interactive level-set surface model computation and display based on off-the-shelf PC hardware and graphics boards and new algorithms and software.
HIVbase, Data Integration Software to Support the Study of Chronic Viruses. Start date: March 1, 2004. Expires: Feb. 28, 2006. Amount: $499,812. Principal investigator: Susanna Lamers. Sponsor: GJI.
Phase II SBIR project to develop systems for managing and analyzing genetic data and unstructured information related to HIV research. the project will build on a Phase I feasibility study that developed software for data storage and integration with applications for data mining, analysis, and data retrieval.
Comparison and Annotation of Multiple Whole Genomes. Start date: March 15, 2004. Expires: Feb. 28, 2009. Amount: $400,000. Principal investigator: Lior Pachter. Sponsor: University of California, Berkeley.
Proposal to address the “algorithmic problems” of comparative genomics. Goals include developing accurate multiple alignment methods for whole genomes; incorporating phylogenetic models into whole-genome alignment and annotation strategies; discovering novel primate or human genes that may be related to disease; and developing a better understanding of the the regulatory code and the annotation of transcription factor binding sites and other regulatory elements. Research will build on the group’s previous comparative genomics algorithms using hidden Markov models (pairwise, generalized, and phylogenetic), which will be integrated with heuristics to process whole genomes.
Computational Investigation of Structural and Dynamical Mechanisms of Protein Regulation by Post-Translational Phosphorylation. Start date: May 1, 2004. Expires: April 30, 2009. Amount: $519,205. Principal investigator: Matthew Jacobson. Sponsor: University of California, San Francisco.
Proposal to develop a physics-based theory for predicting protein conformational change caused by phosphorylation. Computational methods employed will range from quantum mechanics to molecular mechanics with implicit solvation models. The research is expected to result in a computer program that is capable of predicting atomic-level response to phosphorylation for many proteins with known phosphorylation sites but no experimentally determined structure in the phosphorylated form.