Statistical Model Checking in BioLab: Applications to the Automated Analysis of T-Cell Receptor Signaling Pathway [chapter]

Edmund M. Clarke, James R. Faeder, Christopher J. Langmead, Leonard A. Harris, Sumit Kumar Jha, Axel Legay
2008 Lecture Notes in Computer Science  
We present an algorithm, called BioLab, for verifying temporal properties of rule-based models of cellular signalling networks. Bi-oLab models are encoded in the BioNetGen language, and properties are expressed as formulae in probabilistic bounded linear temporal logic. Temporal logic is a formalism for representing and reasoning about propositions qualified in terms of time. Properties are then verified using sequential hypothesis testing on executions generated using stochastic simulation.
more » ... Lab is optimal, in the sense that it generates the minimum number of executions necessary to verify the given property. Bio-Lab also provides guarantees on the probability of it generating Type-I (i.e., false-positive) and Type-II (i.e., false-negative) errors. Moreover, these error bounds are pre-specified by the user. We demonstrate Bio-Lab by verifying stochastic effects and bistability in the dynamics of the T-cell receptor signaling network. ⋆
doi:10.1007/978-3-540-88562-7_18 fatcat:vc6ut2at75hb3nlpbgtn6mtmgq