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Raue, A.* ; Steiert, B.* ; Schelker, M.* ; Kreutz, C.* ; Maiwald, T.* ; Hass, H.* ; Vanlier, J.* ; Tönsing, C.* ; Adlung, L.* ; Engesser, R.* ; Mader, W.* ; Heinemann, T.* ; Hasenauer, J. ; Schilling, M.* ; Höfer, T.* ; Klipp, E.* ; Theis, F.J. ; Klingmüller, U.* ; Schöberl, B.* ; Timmer, J.*

Data2Dynamics: A modeling environment tailored to parameter estimation in dynamical systems.

Bioinformatics 31, 3558-3560 (2015)
Verlagsversion DOI PMC
Open Access Gold
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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Publikationstyp Artikel: Journalartikel
Dokumenttyp Wissenschaftlicher Artikel
Sprache englisch
Veröffentlichungsjahr 2015
HGF-Berichtsjahr 2015
e-ISSN 1367-4811
Zeitschrift Bioinformatics
Quellenangaben Band: 31, Heft: 21, Seiten: 3558-3560 Artikelnummer: , Supplement: ,
Verlag Oxford University Press
Verlagsort Oxford
Begutachtungsstatus Peer reviewed
Institut(e) Institute of Computational Biology (ICB)
POF Topic(s) 30205 - Bioengineering and Digital Health
Forschungsfeld(er) Enabling and Novel Technologies
PSP-Element(e) G-503800-001
PubMed ID 26142188
DOI 10.1093/bioinformatics/btv405
WOS ID WOS:000365134400025
Scopus ID 84947575588
Erfassungsdatum 2015-07-06
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