Handbook of theoretical computer science (vol. B)
An introduction to assertional reasoning for concurrent systems
ACM Computing Surveys (CSUR)
Model checking
Using Hybrid Concurrent Constraint Programming to Model Dynamic Biological Systems
ICLP '02 Proceedings of the 18th International Conference on Logic Programming
Probabilistic Abstraction for Model Checking: An Approach Based on Property Testing
LICS '02 Proceedings of the 17th Annual IEEE Symposium on Logic in Computer Science
TACAS '99 Proceedings of the 5th International Conference on Tools and Algorithms for Construction and Analysis of Systems
Lateral Inhibition through Delta-Notch Signaling: A Piecewise Affine Hybrid Model
HSCC '01 Proceedings of the 4th International Workshop on Hybrid Systems: Computation and Control
Hybrid Modeling and Simulation of Biomolecular Networks
HSCC '01 Proceedings of the 4th International Workshop on Hybrid Systems: Computation and Control
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
Taming the complexity of biochemical models through bisimulation and collapsing: theory and practice
Theoretical Computer Science - Special issue: Computational systems biology
A Probabilistic Model for Molecular Systems
Fundamenta Informaticae - Concurrency Specification and Programming (CS&P 2004)
Parallel Model Checking Large-Scale Genetic Regulatory Networks with DiVinE
Electronic Notes in Theoretical Computer Science (ENTCS)
Abstract interpretation and types for systems biology
Theoretical Computer Science
On temporal logic constraint solving for analyzing numerical data time series
Theoretical Computer Science
CMSB '08 Proceedings of the 6th International Conference on Computational Methods in Systems Biology
CMSB '08 Proceedings of the 6th International Conference on Computational Methods in Systems Biology
Stochastic Analysis of Amino Acid Substitution in Protein Synthesis
CMSB '08 Proceedings of the 6th International Conference on Computational Methods in Systems Biology
Rule responder HCLS eScience infrastructure
Proceedings of the 3rd International Conference on the Pragmatic Web: Innovating the Interactive Society
On algorithmic analysis of transcriptional regulation by LTL model checking
Theoretical Computer Science
CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
A Bayesian Approach to Model Checking Biological Systems
CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
Algebraic systems biology: theses and hypotheses
AB'07 Proceedings of the 2nd international conference on Algebraic biology
On the analysis of numerical data time series in temporal logic
CMSB'07 Proceedings of the 2007 international conference on Computational methods in systems biology
Formal cell biology in biocham
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
Petri nets for systems and synthetic 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
From model-checking to temporal logic constraint solving
CP'09 Proceedings of the 15th international conference on Principles and practice of constraint programming
Model revision from temporal logic properties in computational systems biology
Probabilistic inductive logic programming
A new occurrence counting analysis for bioambients
APLAS'05 Proceedings of the Third Asian conference on Programming Languages and Systems
Temporal logic constraints in the biochemical abstract machine BIOCHAM
LOPSTR'05 Proceedings of the 15th international conference on Logic Based Program Synthesis and Transformation
Compositional reachability analysis of genetic networks
CMSB'06 Proceedings of the 2006 international conference on Computational Methods in Systems Biology
Analysis of signalling pathways using continuous time markov chains
Transactions on Computational Systems Biology VI
Machine learning biochemical networks from temporal logic properties
Transactions on Computational Systems Biology VI
Building and analysing an integrative model of HIV-1 RNA alternative splicing
CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
CMSB'04 Proceedings of the 20 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
Black box checking for biochemical networks
CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
From syntax to semantics in systems biology towards automated reasoning tools
Transactions on Computational Systems Biology IV
Adapting biochemical kripke structures for distributed model checking
Transactions on Computational Systems Biology VII
Biomodel engineering – from structure to behavior
Transactions on Computational Systems Biology XII
Electronic Notes in Theoretical Computer Science (ENTCS)
A Probabilistic Model for Molecular Systems
Fundamenta Informaticae - Concurrency Specification and Programming (CS&P 2004)
Synthesis of biological models from mutation experiments
POPL '13 Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming languages
Uncertainty quantification in hybrid dynamical systems
Journal of Computational Physics
At the interface of biology and computation
Proceedings of the SIGCHI Conference on Human Factors in Computing Systems
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Model checking is an automatic method for deciding if a circuit or a program, expressed as a concurrent transition system, satisfies a set of properties expressed in a temporal logic such as CTL. In this paper we argue that symbolic model checking is feasible in systems biology and that it shows some advantages over simulation for querying and validating formal models of biological processes. We report our experiments on using the symbolic model checker NuSMV and the constraint-based model checker DMC, for the modeling and querying of two biological processes: a qualitative model of the mammalian cell cycle control after Kohn's diagrams, and a quantitative model of gene expression regulation.