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  An approach for dividing models of biological reaction networks into functional units

Ederer, M., Sauter, T., Bullinger, E., Gilles, E. D., & Allgöwer, F. (2003). An approach for dividing models of biological reaction networks into functional units. Simulation: Transactions of the Society for Modeling and Simulation, 79(12), 703-716. doi:10.1177/0037549703040940.

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 Creators:
Ederer, M. 1, Author
Sauter, T.1, Author           
Bullinger, E.1, Author
Gilles, E. D.2, Author           
Allgöwer, F.1, Author
Affiliations:
1Universität Stuttgart, ou_persistent22              
2Systems Biology, Max Planck Institute for Dynamics of Complex Technical Systems, Max Planck Society, ou_1738155              

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 Abstract: Biological reaction networks consist of many substances and reactions between them. Like many other biological systems, they have a modular structure. Therefore, a division of a biological reaction network into smaller units highly facilitates its investigation. The authors propose an algorithm to divide an ordinary differential equation (ODE) model of a biological reaction network hierarchically into functional units. For every compound, an activity function dependent on concentration or concentration change rate is defined. After performing suitable simulations, distances between the compounds are computed by comparing the activities along the trajectories of the simulation. The distance information is used to generate a dendrogram revealing the internal structure of the reaction network. The algorithm identifies functional units in two models of different networks: catabolite repression in Escherichia coli and epidermal growth factor (EGF) signal transduction in mammalian cells. Copyright © 2014 by Simulation Councils Inc. [accessed 2014 October 16]

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Language(s): eng - English
 Dates: 2003
 Publication Status: Issued
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 Rev. Type: -
 Identifiers: eDoc: 123724
DOI: 10.1177/0037549703040940
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Title: Simulation : Transactions of the Society for Modeling and Simulation
Source Genre: Journal
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Pages: - Volume / Issue: 79 (12) Sequence Number: - Start / End Page: 703 - 716 Identifier: -