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
Using Cutwidth to Improve Symbolic Simulation and Boolean Satisfiability
HLDVT '01 Proceedings of the Sixth IEEE International High-Level Design Validation and Test Workshop (HLDVT'01)
PRISM 2.0: A Tool for Probabilistic Model Checking
QEST '04 Proceedings of the The Quantitative Evaluation of Systems, First International Conference
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
The biochemical abstract machine BIOCHAM
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
Timed Concurrent Constraint Programming for Analysing Biological Systems
Electronic Notes in Theoretical Computer Science (ENTCS)
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
Bounded Asynchrony: Concurrency for Modeling Cell-Cell Interactions
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
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
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
CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
Model checking genetic regulatory networks with parameter uncertainty
HSCC'07 Proceedings of the 10th international conference on Hybrid systems: computation and control
Model checking liveness properties of genetic regulatory networks
TACAS'07 Proceedings of the 13th international conference on Tools and algorithms for the construction and analysis of systems
AB'07 Proceedings of the 2nd international conference on Algebraic biology
Deducing interactions in partially unspecified biological systems
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
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
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
Modular Verification of Interactive Systems with an Application to Biology
Electronic Notes in Theoretical Computer Science (ENTCS)
How might petri nets enhance your systems biology toolkit
PETRI NETS'11 Proceedings of the 32nd international conference on Applications and theory of Petri Nets
Nondeterministic update of CTL models by preserving satisfaction through protections
ATVA'11 Proceedings of the 9th international conference on Automated technology for verification and analysis
A stochastic semantics for bioambients
PaCT'07 Proceedings of the 9th international conference on Parallel Computing Technologies
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One central issue in systems biology is the definition of formal languages for describing complex biochemical systems and their behavior at different levels. The biochemical abstract machine BIOCHAM is based on two formal languages, one rule-based language used for modeling biochemical networks, at three abstraction levels corresponding to three semantics: boolean, concentration and population; and one temporal logic language used for formalizing the biological properties of the system. In this paper, we show how the temporal logic language can be turned into a specification language. We describe two algorithms for inferring reaction rules and kinetic parameter values from a temporal specification formalizing the biological data. Then, with an example of the cell cycle control, we illustrate how these machine learning techniques may be useful to the modeler.