Bioinformatics Advance Access published online on September 13, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm416
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Cyto-Sim: A Formal Language Model and Stochastic Simulator of Membrane-Enclosed Biochemical Processes
aMicrosoft Research - University of Trento Centre for Computational & Systems Biology, Italy.
bDepartment of Experimental & Clinical Medicine, Magna Græcia University of Catanzaro, Italy.
To whom correspondence should be addressed. Dr. Tommaso Mazza, E-mail: t.mazza{at}unicz.it
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Abstract |
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Motivation: Compartments and membranes are the basis of cell topology and more than 30% of the human genome codes for membrane proteins. It is possible to represent compartments and membrane proteins in a nominal way with many mathematical formalisms used in systems biology, however few explicitly model the topology of the membranes themselves.
Discrete stochastic simulation of molecular kinetics potentially offers the most accurate representation of cell dynamics. Since the details of every molecular interaction in a pathway are often not known, the relationship between chemical species in not necessarily best described by simple mass action chemistry. Moreover, modelling every individual molecular interaction in the cell is probably unnecessary and currently impractical.
Simulation is a form of computer aided analysis, relying on human interpretation to derive meaning. To improve efficiency and gain meaning in an automatic way, it is necessary to have a formalism based on a model which has decidable properties.
Results: We present Cyto-Sim, a stochastic simulator of membrane-enclosed hierarchies of biochemical processes, where the membranes comprise an inner, outer and integral layer. The underlying model is based on well-established formal language theory and has been shown to have decidable properties (1), allowing formal analysis in addition to simulation. The simulator provides arbitrary levels of abstraction based on chemical kinetics and ordinary differential equations; these latter providing a further dimension of analysability.
The paradigm is flexible and extensible, permitting adaptation to other types of simulation and analysis and integration within standard platforms. In addition to its compact native syntax, based on stoichiometric equations and reaction kinetics, Cyto-Sim currently supports models described as Petri nets, can import all versions of SBML and can export SBML and MATLAB® m-files.
Availability: Cyto-Sim is available free, either as an applet or a standalone Java program via the web page (6). Other versions can be made available upon request.
Contact: sedwards{at}cosbi.eu
Associate Editor: Dr. Trey Ideker
Received on June 8, 2007; revised on July 25, 2007; accepted on August 9, 2007
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