Title: Computational Systems Biology with Constraints: Stochastic Modeling of Biological Systems withConcurrent Constraint Programming
Publisher: VDM Verlag
Publication Date: 2008
Language: English
ISBN 10: 3639088751
ISBN 13: 9783639088755
Binding: Soft cover
Condition: New

About this title

Synopsis

Recently, stochastic process algebras have been usedfor modeling biological systems, as they provide asimple, compositional language to define biologicalmodels. Classical process algebras, however, requireto express everything in terms of communications, alimiting restriction when structured informationneeds to be processed.In this book, we tackle this problem using a moregeneral language and programming it to deal with thedomain of interest. Specifically, we introduce astochastic extension (sCCP) of Concurrent ConstraintProgramming. It is precisely the use of constraintsthat gives flexibility and extendibility to thelanguage, together with the presence ofcontext-dependent stochastic rates. To prove this, weshow how sCCP can be used to model a wide range ofbiological systems, from biochemical networks to theprocess of folding of a protein, providing evidencethat the use of constraints simplifiesthe process of modeling and allows to incorporateexternal knowledge. Many analysis tools are developed: stochastic simulation, model checking,ODE-based approximations. The book can be ofinterest to researchers working in the field ofcomputational systems biology.

About the Author

Luca Bortolussi graduated in Mathematics at University of Triestein 2003 and he got a phd in Computer Science at University ofUdine in 2007. Since 2006, he is associate researcher at theDepartment of Maths and Computer Science at the University ofTrieste. His work is focussed mainly in algorithmic and modelingissues in computational biology.

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