Physico-Chemical Prokaryote Models: Stand-Alone Modules and Karyote Integration
Final technical rept. Sep 2002-Sep 2005
INDIANA UNIV AT BLOOMINGTON THEORETICAL CHEMISTRY LAB
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At the Center for Cell and Virus Theory CCVT several types of systems biology modules were developed for the Bio- SPICE project. The cell modeling modules account for metabolic, proteomic and genomic kinetics and their spatially localized, multiple scale character. Modules for model development, calibration and multiplex e.g. genome-wide expression data interpretation are also provided. Models are made available via three complementary mechanisms 1 the Bio-SPICE system 2 open source stand-alone code and 3 a website sysbio.indiana.edu run by CCVT. The latter can also be run through the Bio-SPICE Dashboard. CCVT software has been demonstrated in a variety of contexts including transcriptional regulatory networks in prokaryotes and B cells, self-organized division mechanisms in E. coli, glycolysis in yeast and T. brucei, and the transcriptional response of human cells subjected to toxins. As CCVT also has an educational function, a number of graduate and undergraduate students have been trained as the next generation of systems biologists.
- Genetic Engineering and Molecular Biology