A Stochastic Concurrent Constraint Based Framework to Model and Verify Biological Systems (original) (raw)
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Timed Concurrent Constraint Programming for Analysing Biological Systems
Electronic Notes in Theoretical Computer Science, 2007
In this paper we present our rst approach to model and verify biological systems using ntcc, a concurrent constraint process calculus. We argue that the partial information constructs in ntcc can provide a suitable language for such systems. We also illustrate how ntcc may provide a unied framework for the analysis of biological systems, as they can be described, simulated and veried using the elements available in the calculus.
Timed concurrent constraint programming in systems biology
2006
Systems biology aims at getting a higher-level understanding of living matter, building on the available data at the molecular level. In this field, theories and methods from computer science have proven very useful, mainly for system modeling and simulation. Here we argue that languages based on timed concurrent constraint programming (timed ccp)-a well-established model for concurrency based on the idea of partial information-have a place in systems biology. We summarize some works in which our group has tried to assess the possibilities/limitations of one such formalisms in this domain. Our base language is ntcc, a non-deterministic, timed ccp process calculus that provides a unified framework for modeling, simulating and verifying several kinds of biological systems. We discuss how the interplay of the operational and logic perspectives that ntcc integrates greatly favors biological systems analysis. £ http://avispa.puj.edu.co 2 Systems Biology Recent progresses in molecular biology have allowed to describe the structure of many components making up biological systems (e.g., genes and proteins) as isolated entities. Instead of being alone, these entities are part of complex biological networks present at the cellular environment (such as, e.g., genetic regulatory networks) which define and regulate cellular processes. The current challenge is to move from molecular biology to systems biology [14, 15], in order to understand how these individual components and entities integrate to each other in the networks they shape. Once this integration has been understood, it will be then possible to discover how these entities perform their tasks. Systems biology then aims at studying the mechanisms by which genes and proteins integrate and interact among them inside an organism. That is, systems biology studies in an integrated way both the structure and expression of a gene or a set of genes. The notions of system and multilevel interaction are crucial in this
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The tcc model is a formalism for reactive concurrent constraint programming. We present a model of temporal concurrent constraint programming which adds to tcc the capability of modeling asynchronous and nondeterministic timed behavior. We call this tcc extension the ntcc calculus. We also give a denotational semantics for the strongestpostcondition of ntcc processes and, based on this semantics, we develop a proof system for linear-temporal properties of these processes. The expressiveness of ntcc is illustrated by modeling cells, timed systems such as RCX controllers, multi-agent systems such as the Predator/Prey game, and musical applications such as generation of rhythms patterns and controlled improvisation.