Welcome to WholeCell.org!

What is whole-cell modeling?

The goal of whole-cell modeling is predict how genotype determines phenotype. Whole-cell models account for the specific function of every gene product and predict the dynamics of every molecule over the entire life cycle. Whole-cell models have the potential to enable engineers to rationally design cells to perform useful functions such as synthesizing drugs, sensing disease, and decontaminating waste. In addition, they have the potential to enable physicians to provide personalized medical care.

Getting started with whole-cell modeling

Please see the following resources to get started in whole-cell modeling:

More information

See the following reviews and primary research articles for more information:

  • Lay articles and news and views
    • Karr JR, Chew YH & Goldberg AP (2015). Whole-cell computational models can predict how genes influence behavior. Atlas of Science.
    • Covert MW (2014). Simulating a living cell. Sci Am 310, 44-51.
    • Freddolino PL & Tavazoie S (2012). The dawn of virtual cell biology. Cell 150, 248-50.
    • Gunawardena J (2012). Silicon dreams of cells into symbols. Nat Biotechnol 30, 838-40.
  • Perspectives
    • Goldberg AP, Szigeti B, Chew YH, Sekar JAP, Roth YD & Karr JR (In review). Emerging whole-cell modeling principles and methods. Curr Opin Syst Biol.
    • Szigeti B, Roth YD, Sekar JAP, Goldberg AP, Pochiraju SC & Karr JR (In review). A blueprint for human whole-cell modeling. Curr Opin Biotechnol.
    • Medley JK, Goldberg AP & Karr JR (2016). Guidelines for reproducibly building and simulating systems biology models. IEEE Trans Biomed Eng 63, 2015–2020.
    • Waltemath D, Karr JR et al (2016). Toward community standards and software for whole-cell modeling. IEEE Trans Biomed Eng 63, 2007-2014.
    • Carrera J & Covert MW (2015). Why Build Whole-Cell Models? Trends in Cell Biology 25, 719-722.
    • Karr JR, Takahasi K & Funahashi A (2015). The principles of whole-cell modeling. Curr Opin Microbiol 27, 18–24.
    • Macklin DN, Ruggero NA & Covert MW (2014). The future of whole-cell modeling. Curr Opin Biotechnol 28, 111-5.
  • Research articles
    • Karr JR, Sanghvi JC, Macklin DN, Gutschow MV, Jacobs JM, Bolival B, Assad-Garcia N, Glass JI & Covert MW (2012). A whole-cell computational model predicts phenotype from genotype. Cell 150, 389–401.
    • Covert MW, Xiao N, Chen TJ, and Karr JR (2008). Integrated flux balance analysis model of Escherichia coli. Bioinformatics 24, 2044–50.
    • Sanghvi JC, Regot S, Carrasco S, Karr JR, Gutschow MV, Bolival B & Covert MW (2013). Accelerated discovery via a whole-cell model. Nat Methods 10, 1192–5.
    • Birch EW, Udell M & Covert MW (2014). Incorporation of flexible objectives and time-linked simulation with flux balance analysis. J Theor Biol 345, 12-21.
    • Purcell O, Jain B, Karr JR, Covert MW & Lu T (2013). Towards a whole-cell modeling approach for synthetic biology. Chaos 23, 025112.
    • Karr JR, Sanghvi JC, Macklin DN, Arora A & Covert MW (2013). WholeCellKB: model organism databases for comprehensive whole-cell models. Nucleic Acids Res 41, D787–92.
    • Lee R, Karr JR & Covert MW (2013). WholeCellViz: data visualization for whole-cell models. BMC Bioinformatics 14, 253.
    • Karr JR, Phillips NC & Covert MW (2014). WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions. Database 2014, bau095.

Getting involved in whole-cell modeling

Need help?

See the following resources

  • Primer: introduction to whole-cell modeling with exercises
  • Forum: for discussion
Last updated Oct 23, 2017. Contact wholecell@lists.stanford.edu.
© 2012-2017 WholeCell.org.