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CLEI Electronic Journal
Article . 2006 . Peer-reviewed
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CLEI Electronic Journal
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CLEI Electronic Journal
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A Stochastic Concurrent Constraint Based Framework to Model and Verify Biological Systems

إطار عمل قائم على القيود المتزامنة العشوائية لنمذجة الأنظمة البيولوجية والتحقق منها
Authors: Carlos Olarte; Camilo Rueda;

A Stochastic Concurrent Constraint Based Framework to Model and Verify Biological Systems

Abstract

Abstract Concurrent process calculi are powerful formalisms for modelling concurrent systems. The mathematical style underlying process cal- culi allow to both model and verify properties of a system, thus pro- viding a concrete design methodology for complex systems. ntcc , a constraints-based calculus for modeling temporal non-deterministic and asynchronous behaviour of processes has been proposed recently. Process interactions in ntcc can be determined by partial informa- tion (i.e. constraints) accumulated in a global store. ntcc has also an associated temporal logic with a proof system that can be conve- niently used to formally verify temporal properties of processes. We are interested in using ntcc to model the activity of genes in biological systems. In order to account for issues such as the basal rate of re- actions or binding affinities of molecular components, we believe that stochastic features must be added to the calculus. In this paper we propose an extension of ntcc with various stochastic constructs. We describe the syntax and semantics of this extension together with the new temporal logic and proof system associated with it. We show the relevance of the added features by modelling a non trivial biological system: the gene expression mechanisms of the λ virus. We argue that this model is both more elaborate and compact than the stochastic πcalculus model proposed recently for the same system.

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Keywords

Artificial intelligence, Geometry, Temporal logic, Model Checking, Theoretical computer science, Temporal Logic, Probabilistic Systems, Biochemistry, Genetics and Molecular Biology, FOS: Mathematics, Syntax, Constraint (computer-aided design), Molecular Biology, Rotation formalisms in three dimensions, Process calculus, Computer network, Extension (predicate logic), Life Sciences, Biochemical Modeling, Semantics (computer science), QA75.5-76.95, Reconfigurable Computing Systems and Design Methods, Computer science, Programming language, Process (computing), Stochasticity in Gene Regulatory Networks, Computational Theory and Mathematics, Hardware and Architecture, Electronic computers. Computer science, Asynchronous communication, Computer Science, Physical Sciences, Reconfigurable Computing, Mathematics, Formal Methods in Software Verification and Control

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
1
Average
Average
Average
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