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WholeCellViz: data visualization for whole-cell models

Ruby Lee1, Jonathan R Karr2 and Markus W Covert1*

Author Affiliations

1 Department of Bioengineering, Stanford University, Stanford, CA 94025, USA

2 Graduate Program in Biophysics, Stanford University, Stanford, CA 94025, USA

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BMC Bioinformatics 2013, 14:253  doi:10.1186/1471-2105-14-253

Published: 21 August 2013



Whole-cell models promise to accelerate biomedical science and engineering. However, discovering new biology from whole-cell models and other high-throughput technologies requires novel tools for exploring and analyzing complex, high-dimensional data.


We developed WholeCellViz, a web-based software program for visually exploring and analyzing whole-cell simulations. WholeCellViz provides 14 animated visualizations, including metabolic and chromosome maps. These visualizations help researchers analyze model predictions by displaying predictions in their biological context. Furthermore, WholeCellViz enables researchers to compare predictions within and across simulations by allowing users to simultaneously display multiple visualizations.


WholeCellViz was designed to facilitate exploration, analysis, and communication of whole-cell model data. Taken together, WholeCellViz helps researchers use whole-cell model simulations to drive advances in biology and bioengineering.

Whole-cell modeling; Data visualization; Cell physiology; Computational biology; Mycoplasma; Bacteria; Systems biology