BNMC Seminar:  Modular Software and Modular Biology

Herbert Sauro
Keck Graduate Institute

Modularity is a key concept that pervades both software
engineering and biological systems. In this talk I will
discuss two things: the Systems Biology Workbench (SBW),
which is an extensible and modular software framework for
systems biology, and modularity in biological networks. I
will discuss strategies for searching for functional motifs
in networks, including work we have done in the evolution of
in silico functional motifs.

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About Dr. Sauro: Herbert Sauro was originally educated as a
biochemist/microbiologist but became interested in the use
of simulation and theory to understand cellular networks
after accidently coming across a paper by David Garkfinkel
on the simulation of glycolysis. He wrote one of the first
biochemical simulators for the PC (SCAMP) in the 1980s in
order to assist work on extending metabolic control analysis
(A theory closely related to biochemical systems
theory). However, with the lack of community interest in
systems biology during the late 80s and early 90s, he left
science to start a software company and offer consultancy
work to finance firms in the UK. With the surge in interest
in systems biology in the US in the late 90s, he secured a
position at Caltech to assist in the devleopment of the
Systems Biology Markup Language. Since then he moved to a
faculty position at the Keck Graduate Institute where he
continues to do research on network motifs, theory and
software.

About the BNMC: The Beckman Institute Biological Network
Modeling Center (BNMC; http://bnmc.caltech.edu) is an
interdisciplinary effort whose goal it is to bring together
Caltech biologists, bioengineers, mathematicians, and
computer scientists to develop and apply state-of-the-art
computational tools for modeling and analyzing complex
biological systems.  Its key members come from multiple
Caltech divisions and groups, including Biology, Control and
Dynamical Systems, and CACR (the Center for Advanced
Computing Research).  As part of its mission, the BNMC holds
a regular seminar series on topics relevant to computational
modeling in biology.