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Intuitive formal modelling of biological systems: From an intuitive narrative description of biological systems to their formal ,Used
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Like distributed systems of computers, biological systems are made of many interacting concurrent entities. Because of this similarity, the application of techniques coming from concurrency theory to the modelling of biological systems has become increasingly popular in recent years. One of the major challenges in this context is the definition of suitable modelling languages that are formal and executable but also easy to understand by noncomputer scientists, together with the development of user friendly tools for modelling, analysis and simulation of biological systems. In this book we present a high level textual modelling language (called Narrative Language), its automatic translation into a formal language belonging to the family of process algebras (called Betabinders), and the definition of rules to infer causal and spatial dependencies between model reactions. The approach is illustrated on a model of the widely studied Gp130/JAK/STAT signalling pathway. This work is a step towards the definition of a framework which allows scientists to easily describe biological systems and automatically perform simulation and formal analysis of models.
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