antelope a hybrid-logic model checker for branching-time boolean grn analysis羚羊branching-time布尔入库单分析hybrid-logic模型检查器.pdfVIP

“Antelope”: a hybrid-logic model checker for branching-time Boolean GRN analysis Arellano et al. Arellano et al. BMC Bioinformatics 2011, 12:490 /1471-2105/12/490 (22 December 2011) Arellano et al. BMC Bioinformatics 2011, 12:490 /1471-2105/12/490 SOFTWARE Open Access “Antelope: a hybrid-logic model checker for branching-time Boolean GRN analysis 5 5 1,2 1,3,4 5 5 Gustavo Arellano , Julián Argil , Eugenio Azpeitia , Mariana Benítez , Miguel Carrillo , Pedro Góngora , David A Rosenblueth1,5* and Elena R Alvarez-Buylla1,2 Abstract Background: In Thomas’ formalism for modeling gene regulatory networks (GRNs), branching time, where a state can have more than one possible future, plays a prominent role. By representing a certain degree of unpredictability, branching time can model several important phenomena, such as (a) asynchrony, (b) incompletely specified behavior, and (c) interaction with the environment. Introducing more than one possible future for a state, however, creates a difficulty for ordinary simulators, because infinitely many paths may appear, limiting ordinary simulators to statistical conclusions. Model checkers for branching time, by contrast, are able to prove properties in the presence of infinitely many paths. Results: 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 contras