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AIC Seminar Series

little b: A Language for Building Mathematical Models of Biological Systems

Aneil MallavarapuHarvard University

Notice:  hosted by Richard Waldinger

Date:  2007-04-19 at 16:00

Location:  EJ228  (Directions)

   Abstract

Systems biology is increasingly turning to mathematical modeling to understand the dynamics of molecular pathways. A model builder translates a high-level description couched in terms of biology and mechanistic assumptions into one of mathematical variables and functions. Typically a modeller will need to prepare several related models. Complexity arising from molecular complex formation and reaction mechanics means that even small conceptual changes can require numerous modifications at the mathematical level, making model preparation both time consuming and error prone. Little b is a Lisp-based modeling language designed to solve such problems. Current work focuses on generating ordinary differential equation systems of single or multi-compartment molecular systems. The core language provides reasoning and symbolic mathematics capabilities with an object-oriented framework, enabling users to extend the base libraries, or develop modeling frameworks of their own. http://littleb.org

   Bio for Aneil Mallavarapu

Aneil Mallavarapu is Senior Research Scientist at Harvard Department of Systems Biology, where I helped start the Virtual Cell Program, and currently lead the little b project. I worked in the technology group of Millennium Pharmaceuticals, developing software and hardware for genomics research, and initiated pathway-centered knowledge management efforts there. I did my PhD in Cell Biology and Biochemistry at UCSF. There and later at Harvard Medical School, I studied cytoskeletal dynamics and developed a number of optical technologies for marking, perturbing and visualizing proteins in living cells.

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