Modeling formalisms for dynamic structure systems
ACM Transactions on Modeling and Computer Simulation (TOMACS)
Theory of Modelling and Simulation
Theory of Modelling and Simulation
Causal pi-Calculus for Biochemical Modelling
CMSB '03 Proceedings of the First International Workshop on Computational Methods in Systems Biology
Dynamic structure multiparadigm modeling and simulation
ACM Transactions on Modeling and Computer Simulation (TOMACS)
BioAmbients: an abstraction for biological compartments
Theoretical Computer Science - Special issue: Computational systems biology
Probabilistic representation of gene regulatory networks
Bioinformatics
Encoding Catalytic P Systems in π@
Electronic Notes in Theoretical Computer Science (ENTCS)
Semantics of dynamic structure event-based systems
Proceedings of the second international conference on Distributed event-based systems
An Abstract Machine for the Stochastic Bioambient calculus
Electronic Notes in Theoretical Computer Science (ENTCS)
Bio-PEPA: A framework for the modelling and analysis of biological systems
Theoretical Computer Science
HYPE: A Process Algebra for Compositional Flows and Emergent Behaviour
CONCUR 2009 Proceedings of the 20th International Conference on Concurrency Theory
Rule-based programming for integrative biological modeling
Natural Computing: an international journal
A Petri net model for membrane systems with dynamic structure
Natural Computing: an international journal
Efficient Formulations for Exact Stochastic Simulation of Chemical Systems
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Achieving reuse with pluggable software units
ICSR'11 Proceedings of the 12th international conference on Top productivity through software reuse
Beta binders for biological interactions
CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
Gene regulation in the pi calculus: simulating cooperativity at the lambda switch
Transactions on Computational Systems Biology VII
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The simulation of biological systems is a challenge to modeling methodologies. Living entities are supported by a complex hierarchical network of chemical reactions. The accurate representation of organisms require the use of stochastic chemical equations (SCE) organized into compartments in order to reflect the organization into cells, tissues and organs. In this paper we introduce a modeling and simulation framework based on the Heterogeneous Flow System Specification formalism (HFSS). HFSS provides an hybrid representation of dynamic systems, being able to describe sampled and discrete event systems. These features enable a modular representation of stochastic chemical reactions. In particular, we show that SCE require only two types of HFSS models defined in this paper: molecule holders, and chemical reactors. We provide a description of a HFSS implementation based on pluggable software units (PUs), a component-based framework that supports the development of SCE libraries.