Our Center will attack the challenges created by the large quantity of data generated from new high throughput technologies. We have teamed biologists, computer scientists and computational scientists from several Universities to build an experienced and distinguished team. Our first major tool building project will be an Object Oriented Framework for the integration of data and tools for genomics, proteomics, DNA arrays and protein-protein interactions. This tool will follow the data from the source through model building. It will build on existing open source tools such as a data acquisition package from particle physics (ROOT), a public database system (MYSQL or PostgreSQL), statistics tools (""""""""R""""""""), graphics libraries, a variety of software tools that have been developed at ISB and new tools needed for the new technologies. We stress the use of an open source system as a means to build the community, creating a functioning system that can be tailored for research and education. We then propose to augment this system with tools for analysis, visualization and model building. We will use yeast as a model system owing to the wide range of data that it available for it. Finally, we propose some novel educational programs designed to put graduate students together into interdisciplinary teams for problem solving.
| Marzolf, Bruz; Deutsch, Eric W; Moss, Patrick et al. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:286 |
| Bonneau, Richard; Reiss, David J; Shannon, Paul et al. (2006) The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo. Genome Biol 7:R36 |
| Drees, Becky L; Thorsson, Vesteinn; Carter, Gregory W et al. (2005) Derivation of genetic interaction networks from quantitative phenotype data. Genome Biol 6:R38 |
| Shannon, Paul; Markiel, Andrew; Ozier, Owen et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13:2498-504 |
