Welcome to Berkeley BioSpice

Berkeley BioSpice

This is the home page for the Berkeley BioSpice effort. This site describes research and sofware development by BioSpice project participants primarily working at Lawrence Berkeley National Laboratory (LBNL), the University of California at Berkeley (UCB), and Stanford Research Institute International (SRI) as well as collaborations with scientists at other institutions and in industry. (Links to participating institutions are listed at the bottom of this page.) Berkeley BioSpice researchers include biologists, computer scientists, engineers, mathematicians, and software developers. Their research programs include

• development of high through-put profiling techniques to study microorganisms such as Escherichia coli and Bacillus subtilis;

• experimental studies of sporulation initiation control mechanisms in response to environmental signals;

• experimental studies of the timing of cell-type-specific gene expression relative to septum formation and chromosome translocation in B. subtilis undergoing sporulation;

• development of software that integrates models of cellular phenomena, such as sporulation and chemotaxis, into 3D fluid-mechanical models of cellular behavior;

• development of automated sensitivity analysis of biological kinetics modeling and application to bacterial chemotaxis;

• development of software tools to graphically represent cellular pathways, define conceptual and mathematical models of processes in the pathway, and link databases to biological entities in the pathway.

DARPA BioSpice

In 2001, the Defense Advanced Research Projects Agency (DARPA) launched a new computational biology initiative known as BioSpice. The main focus of BioSpice is to develop computational models of intracellular processes. The models will be experimentally validated and will serve as the core of a simulation environment that will include tools for analysis, knowledge representation, and visualization, as well as links to essential biological databases.

DARPA's goals for BioSpice are further described in Section II of the Bio-Computation Information Pamphlet. Software developed as part of DARPA's BioSpice project will be released to the BioSpice community, membership in which is described on http://www.biospice.org.

Participating Institutions

Defense Advanced Research Projects Agency (DARPA)  |  Howard Hughes Medical Institute (HHMI)
Lawrence Berkeley National Laboratory (LBNL)  |  SRI International (SRI)
University of California, Berkeley (UCB)

Last modified: July 26, 2002