Prediction of Conserved Alternative Splicing Events. Start date: Feb 1, 2005. Expires: Jan. 31, 2007. Amount: $80,000. Principal investigator: Christopher Burge. Institution: Massachusetts Institute of Technology. NIH institute: NLM.
Proposal to develop a pair hidden Markov model to identify conserved alternative splicing events, which have so far gone undetected by the standard approach of aligning cDNAs and expressed sequence tags to the genomic sequence.
Cross-experiment Microarray Data Normalization. Start date: Feb. 1, 2005. Expires: Jan. 31, 2008. Amount: $151,534. Principal investigator: Terri Ni. Institution: Vanderbilt University. NIH institute: NLM.
Supports continued development of a nonparametric microarray data normalization method called MDA (Maximal Density Approximation), which is based on classification and approximation theory. The aim of the project is to extend the MDA method from intra- to inter-experiment data application and to derive an optimal standardized approach to meet the additional difficulties encountered in the analysis of inter-experiment data.
Computational Tools for T- and B-Cell Epitope Prediction. Start date: Feb. 1, 2005. Expires: Jan. 31, 2010. Amount: $264,250. Principal investigator: Werner Braun. Institution: University of Texas Medical Branch Galveston. NIH institute: NIAID.
Funds development of software tools to predict T- and B-cell epitopes of allergenic and viral proteins. The approach is based on novel quantitative descriptors of the physical-chemical properties of amino acids developed recently the grantees. The novel descriptors of physical-chemical properties of amino acids will be used in combination with a partial-least-squares approach to reduce the number of variables in the discriminant analysis and in artificial neural networks. Algorithms based on multivariate classification, K-nearest-neighbor methods, support vector machines and neural networks will be developed and assessed by cross-validation for their ability to predict T- and B-cell epitopes in proteins.
Database-Driven Software for Biological NMR Analysis. Start date: Feb. 10, 2005. Expires: Jan. 31, 2007. Amount: $170,998. Principal investigator: Michael Gryk. Institution: University of Connecticut School of Medicine and Dentistry. NIH institute: NIBIB.
Project aims to develop a conceptual data model for both raw and analyzed NMR spectroscopy data, which is “required to provide a database system capable of format conversion among the codependent software,” according to the grantees. The implementation of the model will be supported by a multi-platform software application, which will integrate the NMR data model and existing NMR data processing and analysis software (free and commercial products) to improve productivity at the data collection, data assignment, data analysis, and structure determination phases.
Effective Outsourced Training for Biomedical Software. Start date: March 1, 2005. Expires: Aug. 31, 2005. Amount: $99,997. Principal investigator: Warren Lathe. Institution: OpenHelix. NIH institute: NIGMS.
Supports development of a training program “to bridge the gap between bioinformatics tools and under-trained users,” according to the grantees. Through collaboration with software providers, OpenHelix will develop training programs on the three main genome browsers. Next, the company will present those programs using three methods: on-site training at customer facilities; live web-conference training, and pre-recorded, on-demand web courses.
Rosetta: An Integrated Protein Structure Modeling Suite. Start date: March 1, 2005. Expires: Feb. 29, 2008. Amount: $612,495. Principal investigator: Carol Rohl. Institution: University of California, Santa Cruz. NIH Institute: NIGMS.
Proposal to modernize the Rosetta software package for protein structure modeling in order to facilitate its continued development in parallel in multiple research groups and to promote the widespread use of the software in the scientific community. Rosetta currently contains modules for de novo protein structure prediction, protein design, protein-protein docking, protein-protein and protein-DNA interface design, protein-protein and protein-DNA interaction specificity prediction, loop modeling, and high-resolution protein structure refinement. To facilitate further integration of the different modules to attack problems such as flexible backbone protein-protein docking, and to facilitate the continued development of new features and functionality, the Rosetta package will be ported to C++ and modernized to an object-oriented design. In addition, a Rosetta web server will be developed, and the source code will be made freely available to the scientific community with extensive documentation.
Integrated Resource for Protein Recognition Studies. Start date: March 1, 2005. Expires: Feb. 28, 2009. Amount: $284,876. Principal investigator: Ilya Vakser. Institution: University of Kansas Lawrence. NIH institute: NIGMS.
Project aims to improve the understanding of fundamental properties of protein interaction in order to facilitate development of better tools for prediction of protein complexes. Specific aims include: development of an advanced docking algorithm; development of a database of protein-protein co-crystallized structures, a database of protein-protein simulated unbound structures, a database of protein-protein models, and a database of docking decoys; and development of an integrated web-based public resource for studying protein recognition.
Computational Biology Resources. Start date: March 1, 2005. Expires: Feb. 28, 2009. Amount: $342,225. Principal investigator: Gary Churchill. Institution: Jackson Laboratory. NIH institute: NIGMS.
Funds development of software for mouse-colony management and the tracking and analysis of data associated with mouse colonies. The centerpiece of this proposal is an existing mouse colony management system, called MTS, which was developed by researchers at the Jackson Laboratory. This proposal focuses on extending the current capabilities of MTS and the development of a robust software product for wider distribution.
Biomedical Ontology and Tools for Database Curation. Start date: March 11, 2005. Expires: March 10, 2006. Amount: $99,250. Principal investigator: Colleen Crangle. Institution: ConverSpeech. NIH institute: NHGRI.
Proposal to extend an existing biomedical language ontology to include genomic and linguistic data from the Saccharomyces Genome Database, and to use the ontology to discover, in full-text articles made available by SGD, information about the molecular function of yeast gene products that can be inferred from direct experimental assays.