Handbook of theoretical computer science (vol. B)
Model checking
Information Processing Letters
Modeling Dynamic Phenomena in Molecular and Cellular Biology
Modeling Dynamic Phenomena in Molecular and Cellular Biology
Symbolic Model Checking of Biochemical Networks
CMSB '03 Proceedings of the First International Workshop on Computational Methods in Systems Biology
Completely Derandomized Self-Adaptation in Evolution Strategies
Evolutionary Computation
System Modeling in Cellular Biology: From Concepts to Nuts and Bolts
System Modeling in Cellular Biology: From Concepts to Nuts and Bolts
Robustness analysis and tuning of synthetic gene networks
Bioinformatics
Using probabilistic model checking in systems biology
ACM SIGMETRICS Performance Evaluation Review
From Reaction Models to Influence Graphs and Back: A Theorem
FMSB '08 Proceedings of the 1st international workshop on Formal Methods in Systems Biology
On temporal logic constraint solving for analyzing numerical data time series
Theoretical Computer Science
A Model Checking Approach to the Parameter Estimation of Biochemical Pathways
CMSB '08 Proceedings of the 6th International Conference on Computational Methods in Systems Biology
Robust sampling for MITL specifications
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
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
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
Robustness of temporal logic specifications
FATES'06/RV'06 Proceedings of the First combined international conference on Formal Approaches to Software Testing and Runtime Verification
Synthesis of biological models from mutation experiments
POPL '13 Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming languages
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Finding mathematical models satisfying a specification built from the formalization of biological experiments, is a common task of the modeler that techniques like model-checking help solving, in the qualitative but also in the quantitative case. In this article we define a continuous degree of satisfaction of temporal logic formulae with constraints. We show how such a satisfaction measure can be used as a fitness function with state-of-the-art evolutionary optimization methods in order to find biochemical kinetic parameter values satisfying a set of biological properties formalized in temporal logic. We also show how it can be used to define a measure of robustness of a biological model with respect to some temporal specification. These methods are evaluated on models of the cell cycle and of the MAPK signaling cascade.