Membrane Computing: An Introduction
Membrane Computing: An Introduction
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 Probabilistic Model for Molecular Systems
Fundamenta Informaticae - Concurrency Specification and Programming (CS&P 2004)
CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
An Intermediate Language for the Simulation of Biological Systems
Electronic Notes in Theoretical Computer Science (ENTCS)
Systemic computation: A model of interacting systems with natural characteristics
International Journal of Parallel, Emergent and Distributed Systems - Emergent Computation
Electronic Notes in Theoretical Computer Science (ENTCS)
nanoK: A calculus for the modeling and simulation of nano devices
Theoretical Computer Science
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
Spatial Calculus of Looping Sequences
Electronic Notes in Theoretical Computer Science (ENTCS)
An intermediate language for the stochastic simulation of biological systems
Theoretical Computer Science
From Biochemistry to Stochastic Processes
Electronic Notes in Theoretical Computer Science (ENTCS)
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
The calculus of looping sequences for modeling biological membranes
WMC'07 Proceedings of the 8th international conference on Membrane computing
The calculus of looping sequences
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
Modular Verification of Interactive Systems with an Application to Biology
Electronic Notes in Theoretical Computer Science (ENTCS)
Fundamenta Informaticae - From Mathematical Beauty to the Truth of Nature: to Jerzy Tiuryn on his 60th Birthday
Modelling ammonium transporters in arbuscular mycorrhiza symbiosis
Transactions on computational systems biology XIII
Spatial Calculus of Looping Sequences
Theoretical Computer Science
Bisimulation congruences in the calculus of looping sequences
ICTAC'06 Proceedings of the Third international conference on Theoretical Aspects of Computing
Simulation techniques for the calculus of wrapped compartments
Theoretical Computer Science
Typed stochastic semantics for the calculus of looping sequences
Theoretical Computer Science
Electronic Notes in Theoretical Computer Science (ENTCS)
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The paper presents the Calculus of Looping Sequences (CLS) suitable to describe microbiological systems and their evolution. The terms of the calculus are constructed by basic constituent elements and operators of sequencing, looping, containment and parallel composition. The looping operator allows tying up the ends of a sequence, thus creating a circular sequence which can represent a membrane. We show that a membrane calculus recently proposed can be encoded into CLS. We use our calculus to model interactions among bacteria and bacteriophage viruses, and to reason on their properties.