Probabilistic model checking of the PDGF signaling pathway

Authors:
Qixia Yuan;Panuwat Trairatphisan;Jun Pang;Sjouke Mauw;Monique Wiesinger;Thomas Sauter
Affiliations:
Computer Science and Communications, University of Luxembourg, Luxembourg, School of Computer Science and Technology, Shandong University, China;Life Sciences Research Unit, University of Luxembourg, Luxembourg;Computer Science and Communications, University of Luxembourg, Luxembourg;Computer Science and Communications, University of Luxembourg, Luxembourg;Life Sciences Research Unit, University of Luxembourg, Luxembourg;Life Sciences Research Unit, University of Luxembourg, Luxembourg
Venue:
Transactions on Computational Systems Biology XIV
Year:
2012

Citing 18
Cited 0

A quantitative model-independent method for global sensitivity analysis of model output

Technometrics
Model-checking continuous-time Markov chains

ACM Transactions on Computational Logic (TOCL)
Termination of Probabilistic Concurrent Program

ACM Transactions on Programming Languages and Systems (TOPLAS)
Model-Checking Algorithms for Continuous-Time Markov Chains

IEEE Transactions on Software Engineering
Systems Biology Toolbox for MATLAB: a computational platform for research in systems biology

Bioinformatics
Simulation and verification for computational modelling of signalling pathways

Proceedings of the 38th conference on Winter simulation
Probabilistic model checking of complex biological pathways

Theoretical Computer Science
Using probabilistic model checking in systems biology

ACM SIGMETRICS Performance Evaluation Review
Toward Verified Biological Models

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Modelling the Tunability of Early T Cell Signalling Events

ICARIS '08 Proceedings of the 7th international conference on Artificial Immune Systems
Approximate Parameter Synthesis for Probabilistic Time-Bounded Reachability

RTSS '08 Proceedings of the 2008 Real-Time Systems Symposium
Probabilistic Reachability for Parametric Markov Models

Proceedings of the 16th International SPIN Workshop on Model Checking Software
A Bayesian Approach to Model Checking Biological Systems

CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
In Silico Modelling and Analysis of Ribosome Kinetics and aa-tRNA Competition

Transactions on Computational Systems Biology XI
What Can Formal Methods Bring to Systems Biology?

FM '09 Proceedings of the 2nd World Congress on Formal Methods
Stochastic model checking

SFM'07 Proceedings of the 7th international conference on Formal methods for performance evaluation
Parameter identification for Markov models of biochemical reactions

CAV'11 Proceedings of the 23rd international conference on Computer aided verification
Analysis of signalling pathways using continuous time markov chains

Transactions on Computational Systems Biology VI

Quantified Score

Hi-index	0.00

Visualization

Abstract

In this paper, we apply the probabilistic symbolic model checker PRISM to the analysis of a biological system --- the Platelet-Derived Growth Factor (PDGF) signaling pathway, demonstrating in detail how this pathway can be analyzed in PRISM. Moreover, we compare the results from verification and ODE simulation on the PDGF pathway and demonstrate by examples the influence of model structure, parameter values and pathway length on the two analysis methods.