[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
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