"Antelope": a hybrid-logic model checker for branching-time Boolean GRN analysis

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Authors	ARELLANO Gustavo ARGIL Julián AZPEITIA Eugenio BENITEZ Mariana CARRILLO Miguel GONGORA Pedro ROSENBLUETH David A. ALVAREZ-BUYLLA Elena R.
Year of publication	2011
Type	Article in Periodical
Magazine / Source	BMC BIOINFORMATICS
MU Faculty or unit	Central European Institute of Technology
Citation
Web	Article freely available
Doi	http://dx.doi.org/10.1186/1471-2105-12-490
Field	Genetics and molecular biology
Keywords	boolean network; model checking; root apical meristem
Description	We have developed Antelope ("Analysis of Networks through TEmporal-LOgic sPEcifications", http://turing.iimas.unam.mx:8080/AntelopeWEB/), a model checker for analyzing and constructing Boolean GRNs. Currently, software systems for Boolean GRNs use branching time almost exclusively for asynchrony. Antelope, by contrast, also uses branching time for incompletely specified behavior and environment interaction. We show the usefulness of modeling these two phenomena in the development of a Boolean GRN of the Arabidopsis thaliana root stem cell niche. There are two obstacles to a direct approach when applying model checking to Boolean GRN analysis. First, ordinary model checkers normally only verify whether or not a given set of model states has a given property. In comparison, a model checker for Boolean GRNs is preferable if it reports the set of states having a desired property. Second, for efficiency, the expressiveness of many model checkers is limited, resulting in the inability to express some interesting properties of Boolean GRNs. Antelope tries to overcome these two drawbacks: Apart from reporting the set of all states having a given property, our model checker can express, at the expense of efficiency, some properties that ordinary model checkers (e.g., NuSMV) cannot. This additional expressiveness is achieved by employing a logic extending the standard Computation-Tree Logic (CTL) with hybrid-logic operators. We illustrate the advantages of Antelope when (a) modeling incomplete networks and environment interaction, (b) exhibiting the set of all states having a given property, and (c) representing Boolean GRN properties with hybrid CTL.
Related projects:	Regulation of morphogenesis of plant cells and organs