In transition from global to modular temporal reasoning about programs
Logics and models of concurrent systems
Programming and Verifying Real-Time Systems by Means of the Synchronous Data-Flow Language LUSTRE
IEEE Transactions on Software Engineering - Special issue: specification and analysis of real-time systems
ACM Transactions on Programming Languages and Systems (TOPLAS)
A Mechanically Checked Proof of a Multiprocessor Result via a Uniprocessor View
Formal Methods in System Design
Bounded Model Checking Using Satisfiability Solving
Formal Methods in System Design
POPL '77 Proceedings of the 4th ACM SIGACT-SIGPLAN symposium on Principles of programming languages
Circular Compositional Reasoning about Liveness
CHARME '99 Proceedings of the 10th IFIP WG 10.5 Advanced Research Working Conference on Correct Hardware Design and Verification Methods
Practical Methods for Proving Program Termination
CAV '02 Proceedings of the 14th International Conference on Computer Aided Verification
NuSMV 2: An OpenSource Tool for Symbolic Model Checking
CAV '02 Proceedings of the 14th International Conference on Computer Aided Verification
Modeling and querying biomolecular interaction networks
Theoretical Computer Science - Special issue: Computational systems biology
Proving that programs eventually do something good
Proceedings of the 34th annual ACM SIGPLAN-SIGACT symposium on Principles of programming languages
Proceedings of the 38th conference on Winter simulation
The temporal logic of programs
SFCS '77 Proceedings of the 18th Annual Symposium on Foundations of Computer Science
Spin model checker, the: primer and reference manual
Spin model checker, the: primer and reference manual
CMSB '08 Proceedings of the 6th International Conference on Computational Methods in Systems Biology
Decompositional Construction of Lyapunov Functions for Hybrid Systems
HSCC '09 Proceedings of the 12th International Conference on Hybrid Systems: Computation and Control
The Equivalence between Biology and Computation
CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
What Can Formal Methods Bring to Systems Biology?
FM '09 Proceedings of the 2nd World Congress on Formal Methods
A sound and complete proof rule for region stability of hybrid systems
HSCC'07 Proceedings of the 10th international conference on Hybrid systems: computation and control
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
TACAS'08/ETAPS'08 Proceedings of the Theory and practice of software, 14th international conference on Tools and algorithms for the construction and analysis of systems
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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
Multiple verification in complex biological systems: the bone remodelling case study
Transactions on Computational Systems Biology XIV
At the interface of biology and computation
Proceedings of the SIGCHI Conference on Human Factors in Computing Systems
Model-Checking signal transduction networks through decreasing reachability sets
CAV'13 Proceedings of the 25th international conference on Computer Aided Verification
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We describe an efficient procedure for proving stabilization of biological systems modeled as qualitative networks or genetic regulatory networks. For scalability, our procedure uses modular proof techniques, where state-space exploration is applied only locally to small pieces of the system rather than the entire system as a whole. Our procedure exploits the observation that, in practice, the form of modular proofs can be restricted to a very limited set. For completeness, our technique falls back on a non-compositional counterexample search. Using our new procedure, we have solved a number of challenging published examples, including: a 3-D model of the mammalian epidermis; a model of metabolic networks operating in type-2 diabetes; a model of fate determination of vulval precursor cells in the C. elegans worm; and a model of pair-rule regulation during segmentation in the Drosophila embryo. Our results show many orders of magnitude speedup in cases where previous stabilization proving techniques were known to succeed, and new results in cases where tools had previously failed.