Information Processing Letters
Membrane Computing: An Introduction
Membrane Computing: An Introduction
Hybrid Modeling and Simulation of Biomolecular Networks
HSCC '01 Proceedings of the 4th International Workshop on Hybrid Systems: Computation and Control
Modeling and querying biomolecular interaction networks
Theoretical Computer Science - Special issue: Computational systems biology
Theoretical Computer Science - Special issue: Computational systems biology
Modelling biochemical pathways through enhanced π-calculus
Theoretical Computer Science - Special issue: Computational systems biology
BioAmbients: an abstraction for biological compartments
Theoretical Computer Science - Special issue: Computational systems biology
A Calculus of Looping Sequences for Modelling Microbiological Systems
Fundamenta Informaticae - SPECIAL ISSUE ON CONCURRENCY SPECIFICATION AND PROGRAMMING (CS&P 2005) Ruciane-Nide, Poland, 28-30 September 2005
Bio-PEPA: An Extension of the Process Algebra PEPA for Biochemical Networks
Electronic Notes in Theoretical Computer Science (ENTCS)
Decision problems in membrane systems with peripheral proteins, transport and evolution
Theoretical Computer Science
Membrane systems with proteins embedded in membranes
Theoretical Computer Science
Electronic Notes in Theoretical Computer Science (ENTCS)
HYPE Applied to the Modelling of Hybrid Biological Systems
Electronic Notes in Theoretical Computer Science (ENTCS)
Type Disciplines for Analysing Biologically Relevant Properties
Electronic Notes in Theoretical Computer Science (ENTCS)
Stochastic Calculus of Looping Sequences for the Modelling and Simulation of Cellular Pathways
Transactions on Computational Systems Biology IX
CoBiC: Context-dependent Bioambient Calculus
Electronic Notes in Theoretical Computer Science (ENTCS)
Rule-based programming for integrative biological modeling
Natural Computing: an international journal
RTA'03 Proceedings of the 14th international conference on Rewriting techniques and applications
Extending the calculus of looping sequences to model protein interaction at the domain level
ISBRA'07 Proceedings of the 3rd international conference on Bioinformatics research and applications
Hybrid dynamics of stochastic programs
Theoretical Computer Science
Scalable simulation of cellular signaling networks
APLAS'07 Proceedings of the 5th Asian conference on Programming languages and systems
CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
Modelling ecological systems with the calculus of wrapped compartments
CMC'12 Proceedings of the 13th international conference on Membrane Computing
Electronic Notes in Theoretical Computer Science (ENTCS)
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The modelling and analysis of biological systems has deep roots in Mathematics, specifically in the field of Ordinary Differential Equations (ODEs). Alternative approaches based on formal calculi, often derived from process algebras or term rewriting systems, provide a quite complementary way to analyse the behaviour of biological systems. These calculi allow to cope in a natural way with notions like compartments and membranes, which are not easy (sometimes impossible) to handle with purely numerical approaches, and are often based on stochastic simulation methods. Recently, it has also become evident that stochastic effects in regulatory networks play a crucial role in the analysis of such systems. Actually, in many situations it is necessary to use stochastic models. For example when the system to be described is based on the interaction of few molecules, when we are at the presence of a chemical instability, or when we want to simulate the functioning of a pool of entities whose compartmentalised structure evolves dynamically. In contrast, stable metabolic networks, involving a large number of reagents, for which the computational cost of a stochastic simulation becomes an insurmountable obstacle, are efficiently modelled with ODEs. In this paper we define a hybrid simulation method, combining the stochastic approach with ODEs, for systems described in the Calculus of Wrapped Compartments (CWC), a calculus on which we can express the compartmentalisation of a biological system whose evolution is defined by a set of rewrite rules.