Rapidly exploring structural and dynamic properties of signaling networks using PathwayOracle.

BMC Systems Biology
Derek RuthsPrahlad T Ram

Abstract

In systems biology the experimentalist is presented with a selection of software for analyzing dynamic properties of signaling networks. These tools either assume that the network is in steady-state or require highly parameterized models of the network of interest. For biologists interested in assessing how signal propagates through a network under specific conditions, the first class of methods does not provide sufficiently detailed results and the second class requires models which may not be easily and accurately constructed. A tool that is able to characterize the dynamics of a signaling network using an unparameterized model of the network would allow biologists to quickly obtain insights into a signaling network's behavior. We introduce PathwayOracle, an integrated suite of software tools for computationally inferring and analyzing structural and dynamic properties of a signaling network. The feature which differentiates PathwayOracle from other tools is a method that can predict the response of a signaling network to various experimental conditions and stimuli using only the connectivity of the signaling network. Thus signaling models are relatively easy to build. The method allows for tracking signal flow in a network a...Continue Reading

References

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Citations

Jul 25, 2009·Molecular Biology Reports·Péter Poczai, Jaakko Hyvönen
Oct 18, 2011·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Tien-Ho LinRobert F Murphy
May 13, 2010·BMC Bioinformatics·Jan KrumsiekFabian J Theis
Feb 26, 2009·BMC Systems Biology·Jussi Paananen, Garry Wong
Nov 19, 2013·PLoS Computational Biology·Natalie BerestovskyLuay Nakhleh
Jul 21, 2017·NPJ Systems Biology and Applications·Huihai WuAndrzej M Kierzek
Nov 12, 2014·World Journal of Gastroenterology : WJG·Ciarán P FisherJ Bernadette Moore

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Software Mentioned

PathwayOracle
CellDesigner
System Biology Toolkit for Matlab
SBML
CellNetAnalyze
auto
Cytoscape
LKB
CellIllustrator
EGF

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