Model checking
Petri Net Representations in Metabolic Pathways
Proceedings of the 1st International Conference on Intelligent Systems for Molecular Biology
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
Theoretical Computer Science - Special issue: Computational systems biology
BioAmbients: an abstraction for biological compartments
Theoretical Computer Science - Special issue: Computational systems biology
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
AMT: a property-based monitoring tool for analog systems
FORMATS'07 Proceedings of the 5th international conference on Formal modeling and analysis of timed systems
A unifying framework for modelling and analysing biochemical pathways using Petri nets
CMSB'07 Proceedings of the 2007 international conference on Computational methods in systems biology
Temporal logic constraints in the biochemical abstract machine BIOCHAM
LOPSTR'05 Proceedings of the 15th international conference on Logic Based Program Synthesis and Transformation
Probabilistic model checking of complex biological pathways
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
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
CMSB '08 Proceedings of the 6th International Conference on Computational Methods in 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
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Temporal logics and model-checking have proved successful in expressing biological properties of complex biochemical systems, and automatically verify their satisfaction, in both qualitative and quantitative models. In this article, we go beyond model-checking and present a constraint solving algorithm for quantifier-free first-order temporal logic formulae, with constraints over the reals. This algorithm computes the domain of the real valued variables occurring in a formula that makes it true in a model. We illustrate this approach for the automatic generation of a temporal logic specification from biological data time series. We provide a set of biologically relevant patterns of formulae, and apply them to numerical data time series of models of the cell cycle control and MAPK signal transduction. We show in these examples that this approach infers automatically semi-qualitative, semi-quantitative information about concentration thresholds, amplitude of oscillations, stability properties, checkpoints and influences between species.