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

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 i...

Full description

Saved in:
Bibliographic Details
Published in:Genome research 2004-09, Vol.14 (9), p.1773-1785
Main Authors: Kremling, Andreas, Fischer, Sophia, Gadkar, Kapil, Doyle, Francis J, Sauter, Thomas, Bullinger, Eric, Allgöwer, Frank, Gilles, Ernst D
Format: Article
Language:English
Subjects:
Algorithms
Biochemistry - statistics & numerical data
Biomedical Engineering
Computational Biology
Computer Simulation
Genes
Genetic Engineering - methods
Kinetics
Life sciences
Methods
Models, Genetic
Nonlinear Dynamics
Research Design
Sciences du vivant
Software
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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 (http://www.sysbio.de/projects/benchmark/) is provided. Several solutions based on linear and nonlinear models are discussed.
ISSN:1088-9051
1549-5469
DOI:10.1101/gr.1226004