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

Details

• Alternative Title:
  PLoS Comput Biol
• Personal Author:
  Karr, Jonathan R. ; Williams, Alex H. ; Zucker, Jeremy D. ; Raue, Andreas ; Steiert, Bernhard ; Timmer, Jens ; Kreutz, Clemens ; Wilkinson, Simon ; Allgood, Brandon A. ; Bot, Brian M. ; Hoff, Bruce R. ; Kellen, Michael R. ; Covert, Markus W. ; Stolovitzky, Gustavo A. ; Meyer, Pablo
• Corporate Authors:
  DREAM8 Parameter Estimation Challenge Consortium
• Description:
  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.
• Subjects:
  Perspective
• Source:
  PLoS Comput Biol. 2015; 11(5).
• Pubmed ID:
  26020786
• Pubmed Central ID:
  PMC4447414
• Document Type:
  Journal Article
• Funding:
  5DP1LM01150-05/DP/NCCDPHP CDC HHS/United States ; DP1 LM011510/LM/NLM NIH HHS/United States ; DP1 OD006413/OD/NIH HHS/United States
• Volume:
  11
• Issue:
  5
• Collection(s):
  CDC Public Access
• Main Document Checksum:
  urn:sha256:10f075cc59d47fe1a77de62d87ef8e1664adba7d987184fc24c267325cceb881
• Download URL:
  https://stacks.cdc.gov/view/cdc/31978/cdc_31978_DS1.pdf
• File Type:
  [PDF - 1.02 MB ]