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Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models

Author

Listed:
  • Jonathan R Karr
  • Alex H Williams
  • Jeremy D Zucker
  • Andreas Raue
  • Bernhard Steiert
  • Jens Timmer
  • Clemens Kreutz
  • DREAM8 Parameter Estimation Challenge Consortium
  • Simon Wilkinson
  • Brandon A Allgood
  • Brian M Bot
  • Bruce R Hoff
  • Michael R Kellen
  • Markus W Covert
  • Gustavo A Stolovitzky
  • Pablo Meyer

Abstract

Whole-cell models that explicitly represent all cellular components at the molecular level have the potential to predict phenotype from genotype. However, even for simple bacteria, whole-cell models will contain thousands of parameters, many of which are poorly characterized or unknown. New algorithms are needed to estimate these parameters and enable researchers to build increasingly comprehensive models. We organized the Dialogue for Reverse Engineering Assessments and Methods (DREAM) 8 Whole-Cell Parameter Estimation Challenge to develop new parameter estimation algorithms for whole-cell models. We asked participants to identify a subset of parameters of a whole-cell model given the model’s structure and in silico “experimental” data. Here we describe the challenge, the best performing methods, and new insights into the identifiability of whole-cell models. We also describe several valuable lessons we learned toward improving future challenges. Going forward, we believe that collaborative efforts supported by inexpensive cloud computing have the potential to solve whole-cell model parameter estimation.Author Summary: Whole-cell models promise to enable rational bioengineering by predicting how cells behave. Even for simple bacteria, whole-cell models require thousands of parameters, many of which are poorly characterized or unknown. New approaches are needed to estimate these parameters. We organized the Dialogue for Reverse Engineering Assessments and Methods (DREAM) 8 Whole-Cell Parameter Estimation Challenge to develop new approaches for whole-cell model parameter identification. Here we describe the challenge, the best performing methods, new insights into the identifiability of whole-cell models, and several lessons we learned for improving future challenges. Going forward, we believe that collaborative efforts have the potential to produce powerful tools for identifying whole-cell models.

Suggested Citation

  • Jonathan R Karr & Alex H Williams & Jeremy D Zucker & Andreas Raue & Bernhard Steiert & Jens Timmer & Clemens Kreutz & DREAM8 Parameter Estimation Challenge Consortium & Simon Wilkinson & Brandon A Al, 2015. "Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models," PLOS Computational Biology, Public Library of Science, vol. 11(5), pages 1-21, May.
  • Handle: RePEc:plo:pcbi00:1004096
    DOI: 10.1371/journal.pcbi.1004096
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    References listed on IDEAS

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    2. Seth Cooper & Firas Khatib & Adrien Treuille & Janos Barbero & Jeehyung Lee & Michael Beenen & Andrew Leaver-Fay & David Baker & Zoran Popović & Foldit players, 2010. "Predicting protein structures with a multiplayer online game," Nature, Nature, vol. 466(7307), pages 756-760, August.
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    1. Alejandro F Villaverde & Antonio Barreiro & Antonis Papachristodoulou, 2016. "Structural Identifiability of Dynamic Systems Biology Models," PLOS Computational Biology, Public Library of Science, vol. 12(10), pages 1-22, October.

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