WholeCellViz is a web-based software program for visually analyzing whole-cell simulations of the Gram-positive bacterium Mycoplasma genitalium. WholeCellViz enables users to analyze several aspects of cell physiology including

Getting started

The best ways to get started are to browse or search WholeCellViz using the menu or the search box at the top of this page. See the tutorial for additional help getting started.

Installing WholeCellViz locally

The WholeCellViz source code and simulated data are freely available at SimTK.

Citing WholeCellViz

Please use the following references to cite WholeCellViz:

Development Team

WholeCellViz was developed by a team of three researchers at Stanford University:


WholeCellViz consists of a graphical user interface and storage server. The WholeCellViz user interface was implemented in javascript using jQuery, flot, and three.js. The WholeCellViz server was implemented using PHP and MySQL. Simulations were stored on the server using JSON. The user interface and server communicated using JSON.

Questions & comments

Please contact us at with any questions and/or comments about WholeCellViz.