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Plate IV.496 · Publications

Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems

Article in Bioinformatics, 3 July 2015.

fMRI Data, Network

  1. A. Raue
  2. B. Steiert
  3. M. Schelker
  4. C. Kreutz
  5. T. Maiwald
  6. H. Hass
  7. J. Vanlier
  8. C. Tönsing
  9. L. Adlung
  10. R. Engesser
  11. W. Mader
  12. T. Heinemann
  13. J. Hasenauer
  14. M. Schilling
  15. T. Höfer
  16. E. Klipp
  17. F. Theis
  18. U. Klingmüller
  19. B. Schöberl
  20. J. Timmer

Abstract

Unlabelled 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. Availability and implementation The Data2Dynamics modeling environment is MATLAB based, open source and freely available at http://www.data2dynamics.org. Supplementary information Supplementary data are available at Bioinformatics online.

Cite

@article{raue2015data2dynamics,
  title = {{Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems}},
  author = {Raue, A. and Steiert, B. and Schelker, M. and Kreutz, C. and Maiwald, T. and Hass, H. and Vanlier, J. and Tönsing, C. and Adlung, L. and Engesser, R. and Mader, W. and Heinemann, T. and Hasenauer, J. and Schilling, M. and Höfer, T. and Klipp, E. and Theis, F. and Klingmüller, U. and Schöberl, B. and Timmer, J.},
  journal = {Bioinformatics},
  publisher = {Oxford University Press (OUP)},
  year = {2015},
  month = jul,
  doi = {10.1093/bioinformatics/btv405},
  url = {https://doi.org/10.1093/bioinformatics/btv405},
  pmid = {26142188}
}
.bib file