Types as abstract interpretations
Proceedings of the 24th ACM SIGPLAN-SIGACT symposium on Principles of programming languages
Model checking
POPL '77 Proceedings of the 4th ACM SIGACT-SIGPLAN symposium on Principles of programming languages
Constructive design of a hierarchy of semantics of a transition system by abstract interpretation
Theoretical Computer Science
Petri Net Representations in Metabolic Pathways
Proceedings of the 1st International Conference on Intelligent Systems for Molecular Biology
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
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
Abstract interpretation and types for systems biology
Theoretical Computer Science
An Abstract Machine for the Stochastic Bioambient calculus
Electronic Notes in Theoretical Computer Science (ENTCS)
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
Model revision from temporal logic properties in computational systems biology
Probabilistic inductive logic programming
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
Type inference in systems biology
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
CMBSlib: a library for comparing formalisms and models of biological systems
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
From syntax to semantics in systems biology towards automated reasoning tools
Transactions on Computational Systems Biology IV
External Control in Process Algebra for Systems Biology
Electronic Notes in Theoretical Computer Science (ENTCS)
Stochastic Behavior and Explicit Discrete Time in Concurrent Constraint Programming
ICLP '08 Proceedings of the 24th International Conference on Logic Programming
The κ-Lattice: Decidability Boundaries for Qualitative Analysis in Biological Languages
CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
Probabilistic Model Checking of Biological Systems with Uncertain Kinetic Rates
RP '09 Proceedings of the 3rd International Workshop on Reachability Problems
A flexible and extensible architecture for experimental model validation
Proceedings of the 3rd International ICST Conference on Simulation Tools and Techniques
A semantic equivalence for Bio-PEPA based on discretisation of continuous values
Theoretical Computer Science
Design and development of software tools for Bio-PEPA
Winter Simulation Conference
Expressive statistical model checking of genetic networks with delayed stochastic dynamics
CMSB'12 Proceedings of the 10th international conference on Computational Methods in Systems Biology
Complex functional rates in rule-based languages for biochemistry
Transactions on Computational Systems Biology XIV
Complex Functional Rates in the Modeling of Nano Devices (Extended Abstract)
Electronic Notes in Theoretical Computer Science (ENTCS)
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Biologists use diagrams to represent interactions between molecular species, and on the computer, diagrammatic notations are also employed in interactive maps. These diagrams are fundamentally of two types: reaction graphs and activation/inhibition graphs. In this tutorial, we study these graphs with formal methods originating from programming theory. We consider systems of biochemical reactions with kinetic expressions, as written in the Systems Biology Markup Language (SBML), and interpreted in the Biochemical Abstract Machine (Biocham) at different levels of abstraction, by either an asynchronous boolean transition system, a continuous time Markov chain, or a system of Ordinary Differential Equations over molecular concentrations. We show that under general conditions satisfied in practice, the activation/inhibition graph is independent of the precise kinetic expressions, and is computable in linear time in the number of reactions. Then we consider the formalization of the biological properties of systems, as observed in experiments, in temporal logics. We show that these logics are expressive enough to capture semi-qualitative semi-quantitative properties of the boolean and differential semantics of reaction models, and that model-checking techniques can be used to validate a model w.r.t. its temporal specification, complete it, and search for kinetic parameter values. We illustrate this modelling method with examples on the MAPK signalling cascade, and on Kohn's map of the mammalian cell cycle.