Model checking
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
Modeling and querying biomolecular interaction networks
Theoretical Computer Science - Special issue: Computational systems biology
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 '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
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
A Model and Analysis of the AKAP Scaffold
Electronic Notes in Theoretical Computer Science (ENTCS)
Trend-Based analysis of a population model of the AKAP scaffold protein
Transactions on Computational Systems Biology XIV
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Recent progress in Biology and data-production technologies push research toward a new interdisciplinary field, named Systems Biology, where the challenge is to break the complexity walls for reasoning about large biomolecular interaction systems. Pioneered by Regev, Silverman and Shapiro, the application of process calculi to the description of biological processes has been a source of inspiration for many researchers coming from the programming language community. In this presentation, we give an overview of the Biochemical Abstract Machine (BIOCHAM), in which biochemical systems are modeled using a simple language of reaction rules, and the biological properties of the system, known from experiments, are formalized in temporal logic. In this setting, the biological validation of a model can be done by model-checking, both qualitatively and quantitatively. Moreover, the temporal properties can be turned into specifications for learning modifications or refinements of the model, when incorporating new biological knowledge.