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Transactions on Computational Systems Biology XII - Special Issue on Modeling Methodologies (Paperback, Edition.)
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Transactions on Computational Systems Biology XII - Special Issue on Modeling Methodologies (Paperback, Edition.)
Series: Transactions on Computational Systems Biology, 5945
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Inspired by the interesting contributions to the 6th Conference on
Compu- tional Methods in Systems Biology (CMSB 2008) and the
Dagstuhl Seminar 09091on"FormalMethods inMolecular
Biology"inFebruary2009, papershave been selected for this special
issue of the journal TransactionsonComputational Systems Biology,
under the title Modeling Methodologies. The special issue starts
with a position paper on "Biomodel Engineering - from Structure to
Behavior," which discusses the potential that concepts from
traditional computing science hold for creating more powerful
models of biol- ical systems and identi?es venues for challenging
future research. The technical contributions of the special issue
covera broadrangeof mod- ing methodologies that have recently been
developed in computational systems biology. First,
twonewmodelinglanguagesarepresented.The"Attributed?-Calculus
withPriorities"presentsacombinationofaconcurrentprocesslanguage,
i.e., the ?-calculus, and a sequential core language, i.e., the
?-calculus; being equipped
withprioritiesthelanguageenablesthedescriptionofdiversespatialphenomena,
di?erent kinetics, as well as an individual-based and
population-based modeling of biological systems. It is shown how
the di?erent dialects of the ? calculus, including the
pi@-calculus, can be expressed. Its stochastic semantic is ?rmly
rooted in CMTC's and is re?ected in the stochastic simulator.
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