Statecharts: A visual formalism for complex systems
Science of Computer Programming
The algorithmic beauty of plants
The algorithmic beauty of plants
Theoretical Computer Science
Journal of Computer and System Sciences
LSCs: Breathing Life into Message Sequence Charts
Formal Methods in System Design
Information Processing Letters
Membrane Computing: An Introduction
Membrane Computing: An Introduction
Formal Modeling of C. elegans Development: A Scenario-Based Approach
CMSB '03 Proceedings of the First International Workshop on Computational Methods in Systems Biology
The Immune System as a Reactive System: Modeling T Cell Activation With Statecharts
HCC '01 Proceedings of the IEEE 2001 Symposia on Human Centric Computing Languages and Environments (HCC'01)
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
A Simple Calculus for Proteins and Cells
Electronic Notes in Theoretical Computer Science (ENTCS)
An Intermediate Language for the Simulation of Biological Systems
Electronic Notes in Theoretical Computer Science (ENTCS)
Bisimulations in calculi modelling membranes
Formal Aspects of Computing
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 grand challenge: full reactive modeling of a multi-cellular animal
HSCC'03 Proceedings of the 6th international conference on Hybrid systems: computation and control
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
P systems, a new computational modelling tool for systems biology
Transactions on Computational Systems Biology VI
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
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
Translating Stochastic CLS into Maude
Electronic Notes in Theoretical Computer Science (ENTCS)
Control Flow Analysis for Brane Calculi
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
An intermediate language for the stochastic simulation of biological systems
Theoretical Computer Science
Spatial Calculus of Looping Sequences
Theoretical Computer Science
Probabilistic model checking of biological systems with uncertain kinetic rates
Theoretical Computer Science
Bio-PEPAd: A non-Markovian extension of Bio-PEPA
Theoretical Computer Science
Foundational aspects of multiscale modeling of biological systems with process algebras
Theoretical Computer Science
Simulating Signalling Pathways With BioWayS
Electronic Notes in Theoretical Computer Science (ENTCS)
An Analysis for Causal Properties of Membrane Interactions
Electronic Notes in Theoretical Computer Science (ENTCS)
An Algorithm for the Identification of Components in Biochemical Pathways
Electronic Notes in Theoretical Computer Science (ENTCS)
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We describe the Calculus of Looping Sequences (CLS) which is suitable for modeling microbiological systems and their evolution. We present two extensions, CLS with links (LCLS) and Stochastic CLS. LCLS simplifies the description of protein interaction at a lower level of abstraction, namely at the domain level. Stochastic CLS allows us to describe quantitative aspects of the modeled systems, such as the frequency of chemical reactions. As examples of application to real biological systems, we show the simulation of the activity of the lactose operon in E.coli and the quorum sensing process in P.aeruginosa, both described with Stochastic CLS.