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Representation, Simulation and Hypothesis Generation in Graph and Logical Models of Biological Networks

Ken Whelan, Oliver Ray, Ross King, Representation, Simulation and Hypothesis Generation in Graph and Logical Models of Biological Networks. Chapter in Yeast Systems Biology. Methods and Protocols, Methods in Molecular Biology, pp. 465–482. July 2011. PDF, 954 Kbytes.

Abstract

This chapter discusses metabolic network modelling from two related perspectives: graph theory and logical modelling. It includes a relatively informal presentation of some of the possible representations in graph theory, propositional and First Order Logic (FOL) and how these representations are related. The chapter focuses on the FOL models used as background theories for two Robot Scientists that, by a combination of laboratory automation and computational hypothesis formulation, can automate some aspects of the scientific discovery process. The discussion will highlight how the various methods used for hypothesis formation have constrained the available representations for the models and how more recent techniques have allowed relaxation of these constraints.

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