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Journal of Integrative Bioinformatics

Editor-in-Chief: Schreiber, Falk / Hofestädt, Ralf

Managing Editor: Sommer, Björn

Ed. by Baumbach, Jan / Chen, Ming / Orlov, Yuriy / Allmer, Jens

Editorial Board: Giorgetti, Alejandro / Harrison, Andrew / Kochetov, Aleksey / Krüger, Jens / Ma, Qi / Matsuno, Hiroshi / Mitra, Chanchal K. / Pauling, Josch K. / Rawlings, Chris / Fdez-Riverola, Florentino / Romano, Paolo / Röttger, Richard / Shoshi, Alban / Soares, Siomar de Castro / Taubert, Jan / Tauch, Andreas / Yousef, Malik / Weise, Stephan / Hassani-Pak, Keywan


CiteScore 2018: 0.90

SCImago Journal Rank (SJR) 2018: 0.315

Open Access
Online
ISSN
1613-4516
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Volume 7, Issue 1

Issues

From Binary to Multivalued to Continuous Models: The lac Operon as a Case Study

Raimo Franke
  • Corresponding author
  • Department of Chemical Biology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
  • Email
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Fabian J. Theis
  • Institute for Bioinformatics and Systems Biology, Helmholtz Centre Munich - German Research Center for Environmental Health, 85764 Neuherberg, Germany
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Steffen Klamt
Published Online: 2016-10-18 | DOI: https://doi.org/10.1515/jib-2010-151

Summary

Using the lac operon as a paradigmatic example for a gene regulatory system in prokaryotes, we demonstrate how qualitative knowledge can be initially captured using simple discrete (Boolean) models and then stepwise refined to multivalued logical models and finally to continuous (ODE) models. At all stages, signal transduction and transcriptional regulation is integrated in the model description. We first show the potential benefit of a discrete binary approach and discuss then problems and limitations due to indeterminacy arising in cyclic networks. These limitations can be partially circumvented by using multilevel logic as generalization of the Boolean framework enabling one to formulate a more realistic model of the lac operon. Ultimately a dynamic description is needed to fully appreciate the potential dynamic behavior that can be induced by regulatory feedback loops. As a very promising method we show how the use of multivariate polynomial interpolation allows transformation of the logical network into a system of ordinary differential equations (ODEs), which then enables the analysis of key features of the dynamic behavior.

About the article

Published Online: 2016-10-18

Published in Print: 2010-03-01


Citation Information: Journal of Integrative Bioinformatics, Volume 7, Issue 1, Pages 172–190, ISSN (Online) 1613-4516, DOI: https://doi.org/10.1515/jib-2010-151.

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© 2010 The Author(s). Published by Journal of Integrative Bioinformatics.. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License. BY-NC-ND 4.0

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