Characterizing finite Kripke structures in propositional temporal logic
Theoretical Computer Science - International Joint Conference on Theory and Practice of Software Development, P
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
NuSMV 2: An OpenSource Tool for Symbolic Model Checking
CAV '02 Proceedings of the 14th International Conference on Computer Aided Verification
Symbolic Model Checking of Biochemical Networks
CMSB '03 Proceedings of the First International Workshop on Computational Methods in Systems Biology
Causal pi-Calculus for Biochemical Modelling
CMSB '03 Proceedings of the First International Workshop on Computational Methods in Systems Biology
Graphs for Core Molecular Biology
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
SHIFT and SMART-AHS: a language for hybrid system engineering modeling and simulation
DSL'97 Proceedings of the Conference on Domain-Specific Languages on Conference on Domain-Specific Languages (DSL), 1997
Proceedings of the 38th conference on Winter simulation
Timed Concurrent Constraint Programming for Analysing Biological Systems
Electronic Notes in Theoretical Computer Science (ENTCS)
Inclusion dynamics hybrid automata
Information and Computation
Equivalence and Discretisation in Bio-PEPA
CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
Model checking genetic regulatory networks with parameter uncertainty
HSCC'07 Proceedings of the 10th international conference on Hybrid systems: computation and control
Model checking liveness properties of genetic regulatory networks
TACAS'07 Proceedings of the 13th international conference on Tools and algorithms for the construction and analysis of systems
Action-based analysis of discrete regulatory networks with short-term stimuli
Proceedings of the 8th International Conference on Computational Methods in Systems Biology
A semantic equivalence for Bio-PEPA based on discretisation of continuous values
Theoretical Computer Science
Equivalences for a biological process algebra
Theoretical Computer Science
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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/Matlabtm). 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 approach, 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 it 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 automaton taming the complexity in terms of states whose number depends on the attained level of approximation.