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A benchmark for methods in reverse engineering and model discrimination: problem formulation and solutions.
Kremling, Andreas; Fischer, Sophia; Gadkar, Kapil et al.
2004In Genome Research, 14 (9), p. 1773-85
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Keywords :
Algorithms; Biochemistry/statistics & numerical data; Biomedical Engineering; Computational Biology; Computer Simulation; Genes; Genetic Engineering/methods; Kinetics; Models, Genetic; Nonlinear Dynamics; Research Design; Software
Abstract :
[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 on 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 ( is provided. Several solutions based on 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 ;  University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Life Science Research Unit
Bullinger, Eric
Allgower, Frank
Gilles, Ernst D.
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Title :
A benchmark for methods in reverse engineering and model discrimination: problem formulation and solutions.
Publication date :
Journal title :
Genome Research
Publisher :
Cold Spring Harbor Laboratory Press, United States - New York
Volume :
Issue :
Pages :
Peer reviewed :
Peer Reviewed verified by ORBi
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