Bringing Advanced Computational Techniques to Environmental Research (BACTER) offers a new paradigm for computational biology research and education. BACTER will engage students in project oriented computational biology from the outset of their graduate studies. The research will focus on two model organisms, Rhodobacter sphaeroides and Shewanella oneidensis, which are key to DOE Genomics: GTL program goals in bioremediation and energy production. Our objective is to train students to uncover biological mechanisms and pathways within these organisms using computational biology and synergistic collaboration with experimental groups.

The BACTER Institute is located at the University of Wisconsin-Madison. In achievement and prestige, UW-Madison has long been recognized as one of America's great universities. Many of its programs are hailed as world leaders in instruction, research and public service. Since 1849, the university has grown into a large, diverse community, with about 40,000 students enrolled each year. These students represent every state in the nation, and many countries from around the globe, making for a truly international population. Outside sources have traditionally identified UW-Madison as one of the leading institutions in the nation for educational quality. Many departments are routinely ranked among the nation's best. U.S. News and World Report lists 46 UW-Madison program areas among the top 10 in their fields.

The BACTER project will provide a "crash course" in nearly all aspects of computational biology research. Students will begin by using existing software tools to actively explore the relationship between genome sequence, protein structure and macromolecular function. The BACTER team will predict the genes and their implied protein sequences, the structures of the proteins, the pairwise interactions, the interaction network and finally whole cell and community models. Upon seeing the successes and limitations of current methodology, they will pursue specialized research projects able to advance the state of the art. Coursework will be designed to help students understand the nuts and bolts of biocomputing software and get them thinking about developing their own tools. The final stage of BACTER will have students plan and develop their own software for the analysis of microbial genomes, molecular interactions and signaling pathways. Because of the way BACTER is structured, students will gain a broad knowledge of computational methods and understand how their particular research fits into the big picture. They will also gain experience in working with interdisciplinary groups comprised of people trained in the physical, biological, computational, mathematical and engineering sciences.