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Computational Systems Biology with Constraints. Edition No. 1
VDM Publishing House, Oct 2008, Pages: 248
Recently, stochastic process algebras have been used
for modeling biological systems, as they provide a
simple, compositional language to define biological
models. Classical process algebras, however, require
to express everything in terms of communications, a
limiting restriction when structured information
needs to be processed.
In this book, we tackle this problem using a more
general language and programming it to deal with the
domain of interest. Specifically, we introduce a
stochastic extension (sCCP) of Concurrent Constraint
Programming. It is precisely the use of constraints
that gives flexibility and extendibility to the
language, together with the presence of
context-dependent stochastic rates. To prove this, we
show how sCCP can be used to model a wide range of
biological systems, from biochemical networks to the
process of folding of a protein, providing evidence
that the use of constraints simplifies
the process of modeling and allows to incorporate
external knowledge. Many analysis tools are
developed: stochastic simulation, model checking,
ODE-based approximations. The book can be of
interest to researchers working in the field of
computational systems biology.
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