Journal of Computer and System Sciences
Information Processing Letters
Membrane Computing: An Introduction
Membrane Computing: An Introduction
Probabilistic symbolic model checking with PRISM: a hybrid approach
International Journal on Software Tools for Technology Transfer (STTT) - Special section on tools and algorithms for the construction and analysis of systems
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)
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
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
A study of the robustness of the EGFR signalling cascade using continuous membrane systems
IWINAC'05 Proceedings of the First international conference on Mechanisms, Symbols, and Models Underlying Cognition: interplay between natural and artificial computation - Volume Part I
Bisimulation congruences in the calculus of looping sequences
ICTAC'06 Proceedings of the Third international conference on Theoretical Aspects of Computing
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
An Intermediate Language for the Simulation of Biological Systems
Electronic Notes in Theoretical Computer Science (ENTCS)
An intermediate language for the stochastic simulation of biological systems
Theoretical Computer Science
Measurable stochastics for Brane Calculus
Theoretical Computer Science
Modelling ecological systems with the calculus of wrapped compartments
CMC'12 Proceedings of the 13th international conference on Membrane Computing
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We survey the formalism Calculus of Looping Sequences (CLS) and a number of its variants from the point of view of their use for describing biological membranes. The CLS formalism is based on term rewriting and allows describing biomolecular systems. A first variant of CLS, called Stochastic CLS, extends the formalism with stochastic time, another variant, called LCLS (CLS with links), allows describing proteins interaction at the domain level. A third variant is introduced for easier description of biological membranes. This extension can be encoded into CLS as well as other formalisms capable of membrane description such as Brane Calculi and P Systems. Such encodings allow verifying and simulating descriptions in Brane Calculi and P Systems by means of verifiers and simulators developed for CLS.