Parameter inference for asynchronous logical networks using discrete time series

Authors:
Hannes Klarner;Heike Siebert;Alexander Bockmayr
Affiliations:
Freie Universität Berlin, Berlin, Germany;Freie Universität Berlin, Berlin, Germany;Freie Universität Berlin, Berlin, Germany
Venue:
Proceedings of the 9th International Conference on Computational Methods in Systems Biology
Year:
2011

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Abstract

This paper is concerned with the dynamics of asynchronous logical models of regulatory networks as introduced by R. Thomas. Available knowledge about the dynamics of a regulatory network is often limited to a sequence of snapshots in the form of a discrete time series. Using CTL formulas together with the concept of partially monotone paths, a methodology is elaborated to investigate the compatibility of a given time series and a Thomas model. The approach can be used to revise the model, but also to evaluate the given data. Additionally, suggestions are made to analyze a model pool for common properties regarding component behavior and interaction types, aiming at results exploitable for experimental design.