Colloquia, Seminars and Conference News
Title : Models of protein-protein interactions: language, compilation and executable
Date : November 9, 2007. (11:00 am) Tea starts half an hour before each seminar
Location: ITEB 336
Speaker : Prof. Michael Blinov
Abstract:
A mathematical model of protein-protein interaction system is often specified in the form of a reaction network comprising a list of molecular species (proteins, their modification states, and complexes of several proteins) and reactions among them. However, multiple ways that proteins can combine and be modified cause the problem of combinatorial complexity. For example, a protein that contains n sites at which phosphate can be added can occupy 2n different states. Furthermore, proteins may interact with multiple binding partners, combining dynamically to form various heterogeneous complexes. Even when only a few proteins are considered, their activities, potential modifications and interactions imply a very large number of possible molecular species, thousands to millions for systems we have considered. Models of such scope are relevant for analysis of proteomic data and mechanistic studies of signal transduction systems.
Reaction networks are commonly specified in XML formats (SBML, CellML). These formats can be described as “low-level programming language” as they specify each and every species and reactions in a reaction network. However, because of combinatorial complexity, this approach is often impractical or impossible. Thus, a model can be specified in a “high-level programming language” that describes the main features of a system. A compiler can be then used to generate a “low-level code” (reaction network) and an “executable” (system of equations). I will be talking about a rule-based approach for model specification. In this approach, the high-level description is in the form of rules specifying main features of proteins and protein activities and interactions. The compiler is a recursive engine that generates a reaction network. I will describe BioNetGen scripting language (BNGL) and BioNetGen compiler that were developed by author and coworkers, and provide an overview of other “high-level” biological modeling languages (little B, Maude, Biosham) and open problems.
References (available at http://www.ccam.uchc.edu/mblinov/):
1. http://vcell.org/bionetgen/
2. http://www.sbml.org
3. M. L. Blinov, J. Yang, J. R. Faeder and W. S. Hlavacek (2006) Graph theory for rule-based modeling of biochemical networks. Transact. Computat. Syst. Biol. VII in the series Lect. Notes Comput. Sci. 4230, 89-106.
4. W. S. Hlavacek, J. R. Faeder, M. L. Blinov, R. G. Posner, M. Hucka and W. Fontana (2006) Rules for modeling signal-transduction systems. Sci. STKE 2006, re6.
5. M. L. Blinov, J. R. Faeder, B. Goldstein and W. S. Hlavacek (2004) BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains. Bioinformatics 20, 3289-3291.
Bio: Michael L. Blinov received his Ph.D. in mathematics from the Weizmann Institute of Science and did postdoctoral work in the Theoretical Biology and Biophysics Group at Los Alamos National Laboratory. He is currently Assistant Professor at the University of Connecticut Health Center in the Center for Cell Analysis and Modeling (http://www.ccam.uchc.edu/mblinov/). His research has involved developing and analyzing detailed models of signal transduction. He is now focused on mechanistic computational modeling of complex biochemical systems, developing algorithms and software for rule-based modeling and exchange and visualization of biological data.
[Back]
