The interdisciplinary study of coordination
ACM Computing Surveys (CSUR)
Communicating and mobile systems: the &pgr;-calculus
Communicating and mobile systems: the &pgr;-calculus
Information Processing Letters
Theoretical Computer Science - Special issue: Computational systems biology
BioAmbients: an abstraction for biological compartments
Theoretical Computer Science - Special issue: Computational systems biology
PML: Toward a High-Level Formal Language for Biological Systems
Electronic Notes in Theoretical Computer Science (ENTCS)
Cell Cycle Control in Eukaryotes: A BioSpi model
Electronic Notes in Theoretical Computer Science (ENTCS)
Modelling coordination in biological systems
ISoLA'04 Proceedings of the First international conference on Leveraging Applications of Formal Methods
Beta binders for biological interactions
CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
A stochastic pi calculus for concurrent objects
AB'07 Proceedings of the 2nd international conference on Algebraic biology
Simulating bacterial transcription and translation in a stochastic π calculus
Transactions on Computational Systems Biology VI
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In recent years, there has been increasing interest in computational models of biological systems based on various calculi of communicating processes, such as the stochastic pi-calculus. These models make it possible to simulate and eventually visualize the dynamic evolution of complex biosystems in time and under varying environmental conditions. While the elegance of the pi-calculus lies in its minimality, this is also a drawback when it comes to modeling because much effort must be devoted to encoding high-level ideas into the low-level means that the language affords us. In this paper, we describe an on-going effort to design a new higher-level programming language that provides direct ontological support for the concepts which are used to formulate, organize and structure models of biomolecular systems. Our language has an object-oriented flavour where we view molecular components as agents with finite sets of behaviours (states). Reactions are modeled as exchanges over connected ports that may cause agents to switch states.