Physico-Chemical Prokaryote Models: Stand-Alone Modules and Karyote Integration
Abstract
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.
Document Details
- Document Type
- Technical Report
- Publication Date
- Mar 01, 2006
- Accession Number
- ADA446908
Entities
Organizations
- Indiana University Bloomington