Utilizing stochastic model checking to analyze genetic circuits

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Publication Type pre-print
School or College College of Engineering
Department Electrical & Computer Engineering
Creator Myers, Chris J.
Other Author Madsen, Curtis; Roehner, Nicholas; Winstead, Chris; Zhang, Zhen
Title Utilizing stochastic model checking to analyze genetic circuits
Date 2012-01-01
Description When designing and analyzing genetic circuits, researchers are often interested in the probability of the system reaching a given state within a certain amount of time. Usually, this involves simulating the system to produce some time series data and analyzing this data to discern the state probabilities. However, as the complexity of models of genetic circuits grow, it becomes more difficult for researchers to reason about the different states by looking only at time series simulation results of the models. To address this problem, this paper employs the use of stochastic model checking, a method for determining the likelihood that certain events occur in a system, with continuous stochastic logic (CSL) properties to obtain similar results. This goal is accomplished by the introduction of a methodology for converting a genetic circuit model (GCM) into a continuous-time Markov chain (CTMC). This CTMC is analyzed using transient Markov chain analysis to determine the likelihood that the circuit satisfies a given CSL property in a finite amount of time. This paper illustrates a use of this methodology to determine the likelihood of failure in a genetic toggle switch and compares these results to stochastic simulation-based analysis of this same circuit. Our results show that this method results in a substantial speedup as compared with conventional simulation-based approaches.
Type Text
Publisher Institute of Electrical and Electronics Engineers (IEEE)
First Page 379
Last Page 386
Dissertation Institution University of Utah
Language eng
Bibliographic Citation Madsen, C., Myers, C. J., Roehner, N., Winstead, C., & Zhang, Z. (2012). Utilizing stochastic model checking to analyze genetic circuits. 2012 IEEE Symposium on Computational Intelligence and Computational Biology, CIBCB 2012, 379-86.
Rights Management (c) 2012 IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE.
Format Medium application/pdf
Format Extent 1,204,954 bytes
Identifier uspace,17678
ARK ark:/87278/s66407gx
Setname ir_uspace
ID 708080
Reference URL https://collections.lib.utah.edu/ark:/87278/s66407gx
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