Data-driven optimizations for model checking of multi-valued regulatory networks.
The model checking method has been long since established as an important tool for modelling and reverse engineering of biological systems. However, due to a high complexity of both the method and the biological systems, this approach often requires a vast amount of computational resources. In this article we show that by reducing the expressivity of the method we can gain performance while still being able to use all biologically relevant data. We utilize this approach to conduct a study of mutations in the EGFR signalling, motivated by a paper from Klinger et al. (2013). Here we aim at constructing approximated models of multiple cell-lines from sizeable sets of experimental data. Due to cancerous mutations in each cell line, there is a high degree of parameter uncertainty and the study would not be practically tractable without the performance optimizations described here.
FB Mathematik und Informatik, Arnimallee 6, 14195 Berlin, Germany. Electronic address: adam.streck@fu-berlin.de.
Adam
A
Streck
FB Mathematik und Informatik, Arnimallee 6, 14195 Berlin, Germany.
Kirsten
K
Thobe
FB Mathematik und Informatik, Arnimallee 6, 14195 Berlin, Germany.
Heike
H
Siebert
D000818:Animals; D019295:Computational Biology / Q000379:methods*; D016208:Databases, Factual; D053263:Gene Regulatory Networks / Q000502:physiology; D018773:Genes, erbB-1 / Q000502:physiology; D006801:Humans; D008962:Models, Theoretical
Büchi automata; Colorectal cancer; Model checking; Regulatory networks