Reachability Analysis of Delta-NotchLateral Inhibition Using Predicate Abstraction
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
Symbolic Model Checking of Biochemical Networks
CMSB '03 Proceedings of the First International Workshop on Computational Methods in Systems Biology
Visual Programming for Modeling and Simulation of Biomolecular Regulatory Networks
HiPC '02 Proceedings of the 9th International Conference on High Performance Computing
Dynamic Algorithm for Inferring Qualitative Models of Gene Regulatory Networks
CSB '04 Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference
Bounded Asynchrony: Concurrency for Modeling Cell-Cell Interactions
FMSB '08 Proceedings of the 1st international workshop on Formal Methods in Systems Biology
A Uniform Approach to Three-Valued Semantics for μ-Calculus on Abstractions of Hybrid Automata
HVC '08 Proceedings of the 4th International Haifa Verification Conference on Hardware and Software: Verification and Testing
Property Driven Three-Valued Model Checking on Hybrid Automata
WoLLIC '09 Proceedings of the 16th International Workshop on Logic, Language, Information and Computation
ATVA'05 Proceedings of the Third international conference on Automated Technology for Verification and Analysis
Type inference in systems biology
CMSB'06 Proceedings of the 2006 international conference on Computational Methods in Systems Biology
The biochemical abstract machine BIOCHAM
CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
Feedback from nature: an optimal distributed algorithm for maximal independent set selection
Proceedings of the 2013 ACM symposium on Principles of distributed computing
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Biological cell networks exhibit complex combinations of both discrete and continuous behaviors: indeed, the dynamics that govern the spatial and temporal increase or decrease of protein concentration inside a single cell are continuous differential equations, while the activation or deactivation of these continuous dynamics are triggered by discrete switches which encode protein concentrations reaching given thresholds. In this paper, we model as a hybrid system a striking example of this behavior in a biological mechanism called Delta-Notch signaling, which is thought to be the primary mechanism of cell differentiation in a variety of cell networks. We present results in both simulation and reachability analysis of this hybrid system. We emphasize how the hybrid system model is computationally superior (for both simulation and analysis) to other nonlinear models in the literature, without compromising faithful modeling of the biological phenomena.