Toward Community Standards and Software for Whole-Cell Modeling

IEEE Trans Biomed Eng. 2016 Oct;63(10):2007-14. doi: 10.1109/TBME.2016.2560762. Epub 2016 Jun 10.


Objective: Whole-cell (WC) modeling is a promising tool for biological research, bioengineering, and medicine. However, substantial work remains to create accurate comprehensive models of complex cells.

Methods: We organized the 2015 Whole-Cell Modeling Summer School to teach WC modeling and evaluate the need for new WC modeling standards and software by recoding a recently published WC model in the Systems Biology Markup Language.

Results: Our analysis revealed several challenges to representing WC models using the current standards.

Conclusion: We, therefore, propose several new WC modeling standards, software, and databases.

Significance: We anticipate that these new standards and software will enable more comprehensive models.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology
  • Computer Simulation*
  • Cytological Techniques
  • Female
  • Humans
  • Male
  • Models, Biological*
  • Software*
  • Systems Biology / education
  • Systems Biology / organization & administration
  • Systems Biology / standards*