Bounded Model Checking Using Satisfiability Solving
Formal Methods in System Design
Modeling and querying biomolecular interaction networks
Theoretical Computer Science - Special issue: Computational systems biology
On the Merits of Temporal Testers
25 Years of Model Checking
Executing multicellular differentiation
Bioinformatics
The Equivalence between Biology and Computation
CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
Decision diagrams for the representation and analysis of logical models of genetic networks
CMSB'07 Proceedings of the 2007 international conference on Computational methods in systems biology
Proving stabilization of biological systems
VMCAI'11 Proceedings of the 12th international conference on Verification, model checking, and abstract interpretation
Probabilistic model checking of complex biological pathways
CMSB'06 Proceedings of the 2006 international conference on Computational Methods in Systems Biology
Transactions on Computational Systems Biology XII
BMA: visual tool for modeling and analyzing biological networks
CAV'12 Proceedings of the 24th international conference on Computer Aided Verification
Hi-index | 0.00 |
We consider model checking of Qualitative Networks, a popular formalism for modeling signal transduction networks in biology. One of the unique features of qualitative networks, due to them lacking initial states, is that of "reducing reachability sets". Simply put, a state that is not visited after i steps will not be visited after i′ steps for every i′i. We use this feature to create a compact representation of all the paths of a qualitative network of a certain structure. Combining this compact path representation with LTL model checking leads to significant acceleration in performance. In particular, for a recent model of Leukemia, our approach works at least 5 times faster than the standard approach and up to 100 times faster in some cases. Our approach enhances the iterative hypothesis-driven experimentation process used by biologists, enabling fast turn-around of executable biological models.