A benchmark for methods in reverse engineering and model discrimination: Problem formulation and solutions

[en] A benchmark problem is described for the reconstruction and analysis of biochemical networks given sampled experimental data. The growth of the organisms is described in a bioreactor in which one substrate is fed into the reactor with a given feed rate and feed concentration. Measurements for some intracellular components are provided representing a small biochemical network. Problems of reverse engineering, parameter estimation, and identifiability are addressed. The contribution mainly focuses oil the problem of model discrimination. If two or more model variants describe the available experimental data, a new experiment must be designed to discriminate between the hypothetical models. For the problem presented, the feed rate and feed concentration of a bioreactor system are available as control inputs. To verify calculated input profiles an interactive Web site (http://www.sysbio.de/projects/benchmark/) is provided. Several solutions based oil linear and nonlinear models are discussed.

Disciplines :

Life sciences: Multidisciplinary, general & others

Author, co-author :

Kremling, Andreas

Fischer, Sophia

Gadkar, Kapil

Doyle, Francis J

Sauter, Thomas

Bullinger, Eric ; Université de Liège - ULiège > Dép. d'électric., électron. et informat. (Inst.Montefiore) > Méthodes computationnelles pour la biologie systémique

Allgöwer, Frank

Gilles, Ernst Dieter

Language :

English

Title :

A benchmark for methods in reverse engineering and model discrimination: Problem formulation and solutions

Publication date :

2004

Journal title :

Genome Research

ISSN :

1088-9051

eISSN :

1549-5469

Publisher :

Cold Spring Harbor Laboratory Press, Cold Spring Harbor, United States - New York

Volume :

Issue :

Pages :

1773-1785

Peer reviewed :

Peer Reviewed verified by ORBi

Available on ORBi :

since 08 May 2009

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Scopus citations^®

104

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127

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