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Hass, H.* ; Loos, C. ; Raimundez-Alvarez, E. ; Timmer, J.* ; Hasenauer, J. ; Kreutz, C.*

Benchmark problems for dynamic modeling of intracellular processes.

Bioinformatics 35, 3073-3082 (2019)
Publ. Version/Full Text Research data DOI
Open Access Gold (Paid Option)
Creative Commons Lizenzvertrag
Motivation: Dynamic models are used in systems biology to study and understand cellular processes like gene regulation or signal transduction. Frequently, ordinary differential equation (ODE) models are used to model the time and dose dependency of the abundances of molecular compounds as well as interactions and translocations. A multitude of computational approaches, e.g. for parameter estimation or uncertainty analysis have been developed within recent years. However, many of these approaches lack proper testing in application settings because a comprehensive set of benchmark problems is yet missing.Results: We present a collection of 20 benchmark problems in order to evaluate new and existing methodologies, where an ODE model with corresponding experimental data is referred to as problem. In addition to the equations of the dynamical system, the benchmark collection provides observation functions as well as assumptions about measurement noise distributions and parameters. The presented benchmark models comprise problems of different size, complexity and numerical demands. Important characteristics of the models and methodological requirements are summarized, estimated parameters are provided, and some example studies were performed for illustrating the capabilities of the presented benchmark collection.
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Publication type Article: Journal article
Document type Scientific Article
Keywords Parameter-estimation; Identification; Optimization; Mass
ISSN (print) / ISBN 1367-4803
Journal Bioinformatics
Quellenangaben Volume: 35, Issue: 17, Pages: 3073-3082 Article Number: , Supplement: ,
Publisher Oxford University Press
Publishing Place Oxford
Reviewing status Peer reviewed