Theoretical Computer Science
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
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
Theory of Self-Reproducing Automata
Theory of Self-Reproducing Automata
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 Spatial Extension to the π Calculus
Electronic Notes in Theoretical Computer Science (ENTCS)
Bisimulations in calculi modelling membranes
Formal Aspects of Computing
Electronic Notes in Theoretical Computer Science (ENTCS)
A P-Lingua Programming Environment for Membrane Computing
Membrane Computing
Stochastic Calculus of Looping Sequences for the Modelling and Simulation of Cellular Pathways
Transactions on Computational Systems Biology IX
Stochastic biological modelling in the presence of multiple compartments
Theoretical Computer Science
Dynamic Compartments in the Imperative Π-Calculus
CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
A core calculus for a comparative analysis of bio-inspired calculi
ESOP'07 Proceedings of the 16th European conference on Programming
Psim: a computational platform for metabolic P systems
WMC'07 Proceedings of the 8th international conference on Membrane computing
Membrane computing as a modeling framework: cellular systems case studies
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
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
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
WMC'09 Proceedings of the 10th international conference on Membrane Computing
Modelling ecological systems with the calculus of wrapped compartments
CMC'12 Proceedings of the 13th international conference on Membrane Computing
An Algorithm for the Identification of Components in Biochemical Pathways
Electronic Notes in Theoretical Computer Science (ENTCS)
Simulation of Spatial P system models
Theoretical Computer Science
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This paper presents Spatial CLS, an extension of the Calculus of Looping Sequences (CLS) with spatial features. Spatial CLS allows keeping track of the position of biological elements in a continuous space (2D or 3D) as time passes. The movement of elements in the space can be precisely described, and elements can interact when constraints on their positions are satisfied such as, for example, if two elements are close enough. As for CLS, membranes and elements inside them can be directly modeled in the syntax. Spatial CLS allows describing the space occupied by elements and membranes. The space occupied by different objects is always kept disjoint. The validity of this constraint is ensured at all times by the semantics of the calculus. In order to model specific behaviors, the modeler can provide an algorithm to rearrange the position of objects in case of a space conflict. Being an extension of CLS, Spatial CLS provides a simple and powerful syntax, based on rewrite rules, for describing the possible reactions among elements of a system. Moreover, rewrite rules are endowed with a stochastic reaction rate parameter. The aim of Spatial CLS is to enable a more accurate description of those biological processes whose behavior depends on the exact position of the elements. As example applications of the calculus, we present a model of cell proliferation, and a model of the quorum sensing process in Pseudomonas aeruginosa.