Communicating sequential processes
Communicating sequential processes
Statecharts: A visual formalism for complex systems
Science of Computer Programming
The algorithmic analysis of hybrid systems
Theoretical Computer Science - Special issue on hybrid systems
Proceedings of the DIMACS/SYCON workshop on Hybrid systems III : verification and control: verification and control
The Unified Modeling Language user guide
The Unified Modeling Language user guide
Modular Specification of Hybrid Systems in CHARON
HSCC '00 Proceedings of the Third International Workshop on Hybrid Systems: Computation and Control
XS-systems: eXtended S-Systems and Algebraic Differential Automata for Modeling Cellular Behavior
HiPC '02 Proceedings of the 9th International Conference on High Performance Computing
XS-systems: eXtended S-Systems and Algebraic Differential Automata for Modeling Cellular Behavior
HiPC '02 Proceedings of the 9th International Conference on High Performance Computing
Using Hybrid Concurrent Constraint Programming to Model Dynamic Biological Systems
ICLP '02 Proceedings of the 18th International Conference on Logic Programming
A Framework for Reasoning about Animation Systems
IVA '01 Proceedings of the Third International Workshop on Intelligent Virtual Agents
Modeling Cellular Behavior with Hybrid Automata: Bisimulation and Collapsing
CMSB '03 Proceedings of the First International Workshop on Computational Methods in Systems Biology
Symbolic Model Checking of Biochemical Networks
CMSB '03 Proceedings of the First International Workshop on Computational Methods in Systems Biology
Dynamic Algorithm for Inferring Qualitative Models of Gene Regulatory Networks
CSB '04 Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference
HSCC '08 Proceedings of the 11th international workshop on Hybrid Systems: Computation and Control
Bounded Asynchrony: Concurrency for Modeling Cell-Cell Interactions
FMSB '08 Proceedings of the 1st international workshop on Formal Methods in Systems Biology
Stochastic Calculus of Looping Sequences for the Modelling and Simulation of Cellular Pathways
Transactions on Computational Systems Biology IX
Local Identification of Piecewise Deterministic Models of Genetic Networks
HSCC '09 Proceedings of the 12th International Conference on Hybrid Systems: Computation and Control
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
Bisimulation congruences in the calculus of looping sequences
ICTAC'06 Proceedings of the Third international conference on Theoretical Aspects of Computing
Abstract machines of systems biology
Transactions on Computational Systems Biology III
The biochemical abstract machine BIOCHAM
CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
Simulation techniques for the calculus of wrapped compartments
Theoretical Computer Science
Typed stochastic semantics for the calculus of looping sequences
Theoretical Computer Science
A box-based distance between regions for guiding the reachability analysis of spaceex
CAV'12 Proceedings of the 24th international conference on Computer Aided Verification
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 Probabilistic Model for Molecular Systems
Fundamenta Informaticae - Concurrency Specification and Programming (CS&P 2004)
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In a biological cell, cellular functions and the genetic regulatory apparatus are implemented and controlled by a network of chemical reactions in which regulatory proteins can control genes that produce other regulators, which in turn control other genes. Further, the feed-back pathways appear to incorporate switches that result in changes in the dynamic behavior of the cell. This paper describes a hybrid systems approach to modeling the intra-cellular network using continuous differential equations to model the feedback mechanisms and mode-switching to describe the changes in the underlying dynamics. We use two case studies to illustrate a modular approach to modeling such networks and describe the architectural and behavioral hierarchy in the underlying models. We describe these models using CHARON [2], a language that allows formal description of hybrid systems. We provide preliminary simulation results that demonstrate how our approach can help biologists in their analysis of noisy genetic circuits. Finally we describe our agenda for future work that includes the development of models and simulation for stochastic hybrid systems.