Timed Concurrent Constraint Programming in Systems Biology

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.

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