Handbook of theoretical computer science (vol. B)
Model checking
Introduction To Automata Theory, Languages, And Computation
Introduction To Automata Theory, Languages, And Computation
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
Hybrid Modeling and Simulation of Biomolecular Networks
HSCC '01 Proceedings of the 4th International Workshop on Hybrid Systems: Computation and Control
CAV '01 Proceedings of the 13th International Conference on Computer Aided Verification
Design and Synthesis of Synchronization Skeletons Using Branching-Time Temporal Logic
Logic of Programs, Workshop
Causal pi-Calculus for Biochemical Modelling
CMSB '03 Proceedings of the First International Workshop on Computational Methods in Systems Biology
LICS '96 Proceedings of the 11th Annual IEEE Symposium on Logic in Computer Science
Hybrid modeling and simulation of genetic regulatory networks
HSCC'03 Proceedings of the 6th international conference on Hybrid systems: computation and control
Spatial Networks of Hybrid I/O Automata for Modeling Excitable Tissue
Electronic Notes in Theoretical Computer Science (ENTCS)
Modeling and simulation of cardiac tissue using hybrid I/O automata
Theoretical Computer Science
HYPE: A Process Algebra for Compositional Flows and Emergent Behaviour
CONCUR 2009 Proceedings of the 20th International Conference on Concurrency Theory
Algebraic systems biology: theses and hypotheses
AB'07 Proceedings of the 2nd international conference on Algebraic biology
Hierarchical modeling for computational biology
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
An agent-oriented conceptual framework for systems biology
Transactions on Computational Systems Biology III
Abstract machines of systems biology
Transactions on Computational Systems Biology III
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Many biological systems can be modeled using systems of ordinary differential algebraic equations (e.g., S-systems), thus allowing the study of their solutions and behavior automatically with suitable software tools (e.g., PLAS, Octave/Matlab驴). Usually, numerical solutions (traces or trajectories) for appropriate initial conditions are analyzed in order to infer significant properties of the biological systems under study. When several variables are involved and the traces span over a long interval of time, the analysis phase necessitates automation in a scalable and efficient manner. Earlier, we have advocated and experimented with the use of automata and temporal logics for this purpose (XS-systems and Simpathica) and here we continue our investigation more deeply.We propose the use of hybrid automata and we discuss the use of the notions of bisimulation and collapsing for a "qualitative" analysis of the temporal evolution of biological systems. As compared with our previous proposal, hybrid automata allow maintenance of more information about the differential equations (S-system) than standard automata. The use of the notion of bisimulation in the definition of the projection operation (restrictions to a subset of "interesting" variables) makes possible to work with reduced automata satisfying the same formulae as the initial ones. Finally, the notion of collapsing is introduced to move toward still simpler and equivalent automata taming the complexity of the automata whose number of states depends on the level of approximation allowed.