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Open Access Green as soon as Postprint is submitted to ZB.
Data2Dynamics: A modeling environment tailored to parameter estimation in dynamical systems.
Bioinformatics 31, 3558-3560 (2015)
Modeling of dynamical systems using ordinary differential equations is a popular approach in the field of Systems Biology. Two of the most critical steps in this approach are to construct dynamical models of biochemical reaction networks for large data sets and complex experimental conditions and to perform efficient and reliable parameter estimation for model fitting. We present a modeling environment for MATLAB that pioneers these challenges. The numerically expensive parts of the calculations such as the solving of the differential equations and of the associated sensitivity system are parallelized and automatically compiled into efficient C code. A variety of parameter estimation algorithms as well as frequentist and Bayesian methods for uncertainty analysis have been implemented and used on a range of applications that lead to publications. AVAILABILITY AND IMPLEMENTATION: The Data2Dynamics modeling environment is MATLAB based, open source and freely available at http://www.data2dynamics.org. CONTACT: andreas.raue@fdm.uni-freiburg.de SUPPLEMENTARY INFORMATION: is provided online and contains detailed description of methodology, a user guide and documentation.
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Publication type
Article: Journal article
Document type
Scientific Article
ISSN (print) / ISBN
1367-4803
Journal
Bioinformatics
Quellenangaben
Volume: 31,
Issue: 21,
Pages: 3558-3560
Publisher
Oxford University Press
Publishing Place
Oxford
Non-patent literature
Publications
Reviewing status
Peer reviewed
Institute(s)
Institute of Computational Biology (ICB)