title: Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems.
abstract: 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 datasets 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.
  
  
  METHODS
  The Data2Dynamics modeling environment is MATLAB based, open source and freely available at http://www.data2dynamics.org.
  
  
  BACKGROUND
  andreas.raue@fdm.uni-freiburg.de
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Merrimack Pharmaceuticals Inc., Discovery Devision, Cambridge, MA 02139, USA.
authors.forename: A
authors.initials: A
authors.lastname: Raue
authors.affiliation: University of Freiburg, Institute for Physics, 79104 Freiburg, Germany.
authors.forename: B
authors.initials: B
authors.lastname: Steiert
authors.affiliation: Humboldt-Universität zu Berlin, Theoretical Biophysics, 10115 Berlin, Germany.
authors.forename: M
authors.initials: M
authors.lastname: Schelker
authors.affiliation: University of Freiburg, Institute for Physics, 79104 Freiburg, Germany.
authors.forename: C
authors.initials: C
authors.lastname: Kreutz
authors.affiliation: University of Freiburg, Institute for Physics, 79104 Freiburg, Germany.
authors.forename: T
authors.initials: T
authors.lastname: Maiwald
authors.affiliation: University of Freiburg, Institute for Physics, 79104 Freiburg, Germany.
authors.forename: H
authors.initials: H
authors.lastname: Hass
authors.affiliation: University of Freiburg, Institute for Physics, 79104 Freiburg, Germany.
authors.forename: J
authors.initials: J
authors.lastname: Vanlier
authors.affiliation: University of Freiburg, Institute for Physics, 79104 Freiburg, Germany.
authors.forename: C
authors.initials: C
authors.lastname: Tönsing
authors.affiliation: Systems Biology of Signal Transduction and.
authors.forename: L
authors.initials: L
authors.lastname: Adlung
authors.affiliation: University of Freiburg, Institute for Physics, 79104 Freiburg, Germany.
authors.forename: R
authors.initials: R
authors.lastname: Engesser
authors.affiliation: University of Freiburg, Institute for Physics, 79104 Freiburg, Germany.
authors.forename: W
authors.initials: W
authors.lastname: Mader
authors.affiliation: Divison of Theoretical Systems Biology, German Cancer Research Center, 69120 Heidelberg, Germany, BioQuant, University of Heidelberg, 69120 Heidelberg, Germany.
authors.forename: T
authors.initials: T
authors.lastname: Heinemann
authors.affiliation: Helmholtz Center Munich, Institute of Computational Biology, 85764 Neuherberg, Germany, Technische Universität München, Department of Mathematics, 85748 Garching, Germany and.
authors.forename: J
authors.initials: J
authors.lastname: Hasenauer
authors.affiliation: Systems Biology of Signal Transduction and.
authors.forename: M
authors.initials: M
authors.lastname: Schilling
authors.affiliation: Divison of Theoretical Systems Biology, German Cancer Research Center, 69120 Heidelberg, Germany, BioQuant, University of Heidelberg, 69120 Heidelberg, Germany.
authors.forename: T
authors.initials: T
authors.lastname: Höfer
authors.affiliation: Humboldt-Universität zu Berlin, Theoretical Biophysics, 10115 Berlin, Germany.
authors.forename: E
authors.initials: E
authors.lastname: Klipp
authors.affiliation: Helmholtz Center Munich, Institute of Computational Biology, 85764 Neuherberg, Germany, Technische Universität München, Department of Mathematics, 85748 Garching, Germany and.
authors.forename: F
authors.initials: F
authors.lastname: Theis
authors.affiliation: Systems Biology of Signal Transduction and.
authors.forename: U
authors.initials: U
authors.lastname: Klingmüller
authors.affiliation: Merrimack Pharmaceuticals Inc., Discovery Devision, Cambridge, MA 02139, USA.
authors.forename: B
authors.initials: B
authors.lastname: Schöberl
authors.affiliation: University of Freiburg, Institute for Physics, 79104 Freiburg, Germany, BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
authors.forename: J
authors.initials: J
authors.lastname: Timmer
mesh_terms: D000465:Algorithms; D001499:Bayes Theorem; D008954:Models, Biological; D012984:Software; D049490:Systems Biology / Q000379:methods*