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On Parameter Synthesis by Parallel Model Checking
May-June 2012 (vol. 9 no. 3)
pp. 693-705
A. Streck, Fac. of Inf., Masaryk Univ., Brno, Czech Republic
A. Krejci, Fac. of Inf., Masaryk Univ., Brno, Czech Republic
L. Brim, Fac. of Inf., Masaryk Univ., Brno, Czech Republic
J. Barnat, Fac. of Inf., Masaryk Univ., Brno, Czech Republic
D. Safranek, Fac. of Inf., Masaryk Univ., Brno, Czech Republic
M. Vejnar, Fac. of Inf., Masaryk Univ., Brno, Czech Republic
T. Vejpustek, Fac. of Inf., Masaryk Univ., Brno, Czech Republic
An important problem in current computational systems biology is to analyze models of biological systems dynamics under parameter uncertainty. This paper presents a novel algorithm for parameter synthesis based on parallel model checking. The algorithm is conceptually universal with respect to the modeling approach employed. We introduce the algorithm, show its scalability, and examine its applicability on several biological models.

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Index Terms:
parallel processing,biology computing,formal verification,biological models,parameter synthesis,parallel model checking,computational system biology,biological systems dynamics,parameter uncertainty,Biological system modeling,Computational modeling,Algorithm design and analysis,Cost accounting,Kinetic theory,systems biology.,Biological networks,parallel model checking,dynamical systems,parameter synthesis
Citation:
A. Streck, A. Krejci, L. Brim, J. Barnat, D. Safranek, M. Vejnar, T. Vejpustek, "On Parameter Synthesis by Parallel Model Checking," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 9, no. 3, pp. 693-705, May-June 2012, doi:10.1109/TCBB.2011.110
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