A Benchmark for Methods in Reverse Engineering and Model Discrimination: Problem Formulation and Solutions

A. Kremling
2004 Genome Research  
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
more » ... 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. 5 Corresponding author. E-MAIL kremling@mpi-magdeburg.mpg.de; FAX 391-6110526. Article and publication are at
doi:10.1101/gr.1226004 pmid:15342560 pmcid:PMC515324 fatcat:ceptheigfvekndnnhyes6lwqeq