Welcome to CDC stacks | The Future of Whole-Cell Modeling - 30048 | CDC Public Access
Stacks Logo
Advanced Search
Select up to three search categories and corresponding keywords using the fields to the right. Refer to the Help section for more detailed instructions.
 
 
Help
Clear All Simple Search
Advanced Search
The Future of Whole-Cell Modeling
Filetype[PDF-333.93 KB]


Details:
  • Personal Authors:
  • Keywords:
  • Pubmed ID:
    24556244
  • Pubmed Central ID:
    PMC4111988
  • Description:
    Integrated whole-cell modeling is poised to make a dramatic impact on molecular and systems biology, bioengineering, and medicine--once certain obstacles are overcome. From our group's experience building a whole-cell model of Mycoplasma genitalium, we identified several significant challenges to building models of more complex cells. Here we review and discuss these challenges in seven areas: first, experimental interrogation; second, data curation; third, model building and integration; fourth, accelerated computation; fifth, analysis and visualization; sixth, model validation; and seventh, collaboration and community development. Surmounting these challenges will require the cooperation of an interdisciplinary group of researchers to create increasingly sophisticated whole-cell models and make data, models, and simulations more accessible to the wider community.

  • Document Type:
    Journal Article
  • Collection(s):
    CDC Public Access
  • Funding:
    5DP1LM011510-05/DP/NCCDPHP CDC HHS/United States
    DP1 LM011510/LM/NLM NIH HHS/United States
    DP1 OD006413/OD/NIH HHS/United States
    P50 GM107615/GM/NIGMS NIH HHS/United States
No Related Documents.
You May Also Like:
  1. Why build whole-cell models?
    Personal Author:
    Carrera, Javier; Covert, Markus W.;
    Published:
    Oct 21 2015
    Source:
    Trends Cell Biol. 25(12):719-722.
    Description:
    Our ability to build computational models that account for all known gene functions in a cell has increased dramatically. But why build whole-cell models, and how can they best be used? In this forum, we enumerate several areas in which whole-cell mo...
    File Type:
    Filetype[PDF - 103.52 KB]
  2. WholeCellKB: model organism databases for comprehensive whole-cell models
    Personal Author:
    Karr, Jonathan R.; Sanghvi, Jayodita C.; Macklin, Derek N.; Arora, Abhishek; Covert, Markus W.;
    Published:
    Nov 21 2012
    Source:
    Nucleic Acids Res. 2012; 41(Database issue):D787-D792.
    Description:
    Whole-cell models promise to greatly facilitate the analysis of complex biological behaviors. Whole-cell model development requires comprehensive model organism databases. WholeCellKB (http://wholecellkb.stanford.edu) is an open-source web-based soft...
    File Type:
    Filetype[PDF - 2.49 MB]
  3. Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models
    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 Author:
    DREAM8 Parameter Estimation Challenge Consortium
    Published:
    May 28 2015
    Source:
    PLoS Comput Biol. 2015; 11(5).
    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...
    File Type:
    Filetype[PDF - 1.02 MB]
  4. Accelerated discovery via a whole-cell model
    Personal Author:
    Sanghvi, Jayodita C.; Regot, Sergi; Carrasco, Silvia; Karr, Jonathan R.; Gutschow, Miriam V.; Bolival, Benjamin; Covert, Markus W.;
    Published:
    Nov 03 2013
    Source:
    Nat Methods. 10(12):1192-1195.
    Description:
    To test the promise of whole-cell modeling to facilitate scientific inquiry, we compared growth rates simulated in a whole-cell model with experimental measurements for all viable single-gene disruption Mycoplasma genitalium strains. Discrepancies be...
    File Type:
    Filetype[PDF - 1014.87 KB]
  5. Mixed exposures research agenda; a report by the NORA Mixed Exposures Team
    Corporate Author:
    National Institute for Occupational Safety and Health; NORA Mixed Exposures Team;
    Published:
    December 2004
    Series:
    DHHS publication ; no. (NIOSH) 2005-106
    Description:
    "Workers are continuously exposed to a wide variety of chemical substances, biological agents, physical agents, and other stressors encountered both in and out of the workplace. Each stressor has the potential to cause a physiological effect, whether...
    File Type:
    Filetype[PDF - 31.85 MB]