Model-checking continuous-time Markov chains
ACM Transactions on Computational Logic (TOCL)
Robustness analysis and tuning of synthetic gene networks
Bioinformatics
Using probabilistic model checking in systems biology
ACM SIGMETRICS Performance Evaluation Review
Modelling and simulation of biological processes in BlenX
ACM SIGMETRICS Performance Evaluation Review
The temporal logic of programs
SFCS '77 Proceedings of the 18th Annual Symposium on Foundations of Computer Science
Bio-PEPA: A framework for the modelling and analysis of biological systems
Theoretical Computer Science
Modelling Epigenetic Information Maintenance: A Kappa Tutorial
CAV '09 Proceedings of the 21st International Conference on Computer Aided Verification
MARCO: a reachability algorithm for multi-affine systems with applications to biological systems
HSCC'07 Proceedings of the 10th international conference on Hybrid systems: computation and control
Hybrid dynamics of stochastic programs
Theoretical Computer Science
Proving stabilization of biological systems
VMCAI'11 Proceedings of the 12th international conference on Verification, model checking, and abstract interpretation
Model repair for probabilistic systems
TACAS'11/ETAPS'11 Proceedings of the 17th international conference on Tools and algorithms for the construction and analysis of systems: part of the joint European conferences on theory and practice of software
From cardiac cells to genetic regulatory networks
CAV'11 Proceedings of the 23rd international conference on Computer aided verification
PRISM 4.0: verification of probabilistic real-time systems
CAV'11 Proceedings of the 23rd international conference on Computer aided verification
Osteoporosis: a multiscale modeling viewpoint
Proceedings of the 9th International Conference on Computational Methods in Systems Biology
Analysis of signalling pathways using continuous time markov chains
Transactions on Computational Systems Biology VI
PARAM: a model checker for parametric markov models
CAV'10 Proceedings of the 22nd international conference on Computer Aided Verification
Multilevel Computational Modeling and Quantitative Analysis of Bone Remodeling
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
A Probabilistic Model for Molecular Systems
Fundamenta Informaticae - Concurrency Specification and Programming (CS&P 2004)
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We present a set of formal techniques and a methodology for a composite formal analysis at the tissue and organ level, focusing on the verification of quantitative properties in the process of bone remodelling. Starting from a differential equation model, we derive a stochastic model and a piecewise multi-affine approximation in order to perform model checking of stabilisation properties for the biological tissue, and to assess the differences between a regular remodelling activity and a defective activity typical of pathologies like osteoporosis. The complex nonlinear dynamics of bone remodelling is analysed with a variety of techniques: sensitivity analysis for the differential equation model; quantitative probabilistic model checking for the stochastic model; and classical model checking and parameter synthesis on the piecewise multi-affine model. Such analyses allow us to extract a wealth of information that is not only useful for a deeper understanding of the biological process but also towards medical diagnoses.