KARDIO: a study in deep and qualitative knowledge for expert systems
KARDIO: a study in deep and qualitative knowledge for expert systems
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
Theoretical Computer Science - Special issue: Computational systems biology
BioAmbients: an abstraction for biological compartments
Theoretical Computer Science - Special issue: Computational systems biology
Type inference in systems biology
CMSB'06 Proceedings of the 2006 international conference on Computational Methods in Systems Biology
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
Probabilistic Model Checking of Biological Systems with Uncertain Kinetic Rates
RP '09 Proceedings of the 3rd International Workshop on Reachability Problems
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
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Systems biologists build models of bio-molecular processes from knowledge acquired both at the gene and protein levels, and at the phenotype level through experiments done in wild-life and mutated organisms. In this chapter, we present qualitative and quantitative logic learning tools, and illustrate how they can be useful to the modeler. We focus on biochemical reaction models written in the Systems Biology Markup Language SBML, and interpreted in the Biochemical Abstract Machine BIOCHAM. We first present a model revision algorithm for inferring reaction rules from biological properties expressed in temporal logic. Then we discuss the representations of kinetic models with ordinary differential equations (ODEs) and with stochastic logic programs (SLPs), and describe a parameter search algorithm for finding parameter values satisfying quantitative temporal properties. These methods are illustrated by a simple model of the cell cycle control, and by an application to the modelling of the conditions of synchronization in period of the cell cycle by the circadian cycle.