A calculus of mobile processes, I
Information and Computation
A calculus of mobile processes, II
Information and Computation
Embedding as a tool for language comparison
Information and Computation
Comparing the expressive power of the synchronous and the asynchronous &pgr;-calculus
Proceedings of the 24th ACM SIGPLAN-SIGACT symposium on Principles of programming languages
Communicating and mobile systems: the &pgr;-calculus
Communicating and mobile systems: the &pgr;-calculus
What is a “good” encoding of guarded choice?
Information and Computation - Special issue on EXPRESS 1997
Information Processing Letters
On the expressive power of polyadic synchronisation in π-calculus
Nordic Journal of Computing
Theoretical Computer Science - Special issue: Computational systems biology
BioAmbients: an abstraction for biological compartments
Theoretical Computer Science - Special issue: Computational systems biology
A time-dependent extension of gillespie algorithm for biochemical stochastic π-calculus
Proceedings of the 2006 ACM symposium on Applied computing
A Simple Calculus for Proteins and Cells
Electronic Notes in Theoretical Computer Science (ENTCS)
Bio-PEPA: An Extension of the Process Algebra PEPA for Biochemical Networks
Electronic Notes in Theoretical Computer Science (ENTCS)
Efficient Stochastic Simulation of Biological Systems with Multiple Variable Volumes
Electronic Notes in Theoretical Computer Science (ENTCS)
Bio-PEPA: A framework for the modelling and analysis of biological systems
Theoretical Computer Science
A core calculus for a comparative analysis of bio-inspired calculi
ESOP'07 Proceedings of the 16th European conference on Programming
A stochastic pi calculus for concurrent objects
AB'07 Proceedings of the 2nd international conference on Algebraic biology
Stochastic simulation of biological systems with dynamical compartment structure
CMSB'07 Proceedings of the 2007 international conference on Computational methods in systems biology
π@: a π-based process calculus for the implementation of compartmentalised bio-inspired calculi
SFM'08 Proceedings of the Formal methods for the design of computer, communication, and software systems 8th international conference on Formal methods for computational systems biology
Tau leaping stochastic simulation method in p systems
WMC'06 Proceedings of the 7th international conference on Membrane Computing
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 semantics for bioambients
PaCT'07 Proceedings of the 9th international conference on Parallel Computing Technologies
Dynamic Compartments in the Imperative Π-Calculus
CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
Spatial Calculus of Looping Sequences
Theoretical Computer Science
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The application of concurrent calculi to the formalisation of biological systems constitutes a promising approach to the analysis of biological phenomena in silico. The peculiar nature of such systems inspired the introduction of specific features in biologically-oriented calculi, such as compartments to model more faithfully their highly organised structure. In this paper we present S@p@, a conservative extension of the stochastic @p-calculus which allows an intuitive and concise formalisation of multi-compartment systems with dynamic structure, despite retaining the simplicity of the original @p-calculus. The possibility to encode into S@p@ several bio-inspired, compartmentalised languages demonstrates its expressive power and flexibility. The calculus is accompanied by an extended version of Gillespie's stochastic simulation algorithm, able to handle multiple compartments with varying volumes. An enhanced formalisation of the algorithm is also presented, in order to provide efficient simulation in the presence of a high number of compartments and reactions.