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WholeCellViz: data visualization for whole-cell models
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  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. WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions
    Personal Author:
    Karr, Jonathan R.; Phillips, Nolan C.; Covert, Markus W.;
    Published:
    Sep 16 2014
    Source:
    Database (Oxford). 2014; 2014.
    Description:
    Mechanistic 'whole-cell' models are needed to develop a complete understanding of cell physiology. However, extracting biological insights from whole-cell models requires running and analyzing large numbers of simulations. We developed WholeCellSimDB...
    File Type:
    Filetype[PDF - 768.26 KB]
  5. Quadratic variance models for adaptively preprocessing SELDI-TOF mass spectrometry data
    Personal Author:
    Emanuele, Vincent A; Gurbaxani, Brian M;
    Published:
    Oct 13 2010
    Source:
    BMC Bioinformatics. 2010; 11:512.
    Description:
    Background : Surface enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI) is a proteomics tool for biomarker discovery and other high throughput applications. Previous studies have identified various areas for improvement in ...
    File Type:
    Filetype[PDF - 2.49 MB]