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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 2017: 0.77

SCImago Journal Rank (SJR) 2017: 0.336

Open Access
Online
ISSN
1613-4516
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Volume 4, Issue 3

Issues

From MIN model to ordinary differential equations

A. Yartseva
  • Corresponding author
  • IBISC – CNRS, Université d’Evry, 523 place des Terrasses de l’Agora, 91000, Evry, France
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  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ R. Devillers
  • Département d’Informatique, Université Libre de Bruxelles, CP212, B-1050, Bruxelles, Belgium
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ H. Klaudel
  • IBISC – CNRS, Université d’Evry, 523 place des Terrasses de l’Agora, 91000, Evry, France
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ F. Képès
  • Epigenomics Project, Genopole, CNRS & Université d’Evry, 523 place des Terrasses de l’Agora, 91000 Evry, France
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  • De Gruyter OnlineGoogle Scholar
Published Online: 2016-10-18 | DOI: https://doi.org/10.1515/jib-2007-61

Summary

Biological interaction networks can be modeled using the Modular Interaction Network (MIN) formalism, which provides an intermediary modeling level between the biological and mathematical ones. MIN focuses on a simple but structured and versatile representation of biological knowledge, without targeting a particular analysis or simulation technique. In this paper, we propose a translation procedure which, starting from a MIN specification of a biological system, generates its representation in ordinary differential equations (ODEs) allowing to study the dynamics of the system. The translation is illustrated on a classical benchmark: the λ phage genetic switch.

Keywords: Abstract biological models; regulatory interaction networks; ODE

About the article

Published Online: 2016-10-18

Published in Print: 2007-12-01


Citation Information: Journal of Integrative Bioinformatics, Volume 4, Issue 3, Pages 15–26, ISSN (Online) 1613-4516, DOI: https://doi.org/10.1515/jib-2007-61.

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© 2007 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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