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Bioinformatics Advance Access originally published online on March 17, 2005
Bioinformatics 2005 21(11):2714-2721; doi:10.1093/bioinformatics/bti391
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

AgentCell: a digital single-cell assay for bacterial chemotaxis

Thierry Emonet 1,*, Charles M. Macal 2, Michael J. North 2, Charles E. Wickersham 1 and Philippe Cluzel 1

1The Institute for Biophysical Dynamics and the James Franck Institute, The University of Chicago 5640 S. Ellis Avenue, Chicago, IL 60637, USA
2Center for Complex Adaptive Agent Systems Simulation, Decision and Information Sciences Division, Argonne National Laboratory 9700 S. Cass Avenue, Argonne IL 60439, USA

*To whom correspondence should be addressed.

Motivation: In recent years, single-cell biology has focused on the relationship between the stochastic nature of molecular interactions and variability of cellular behavior. To describe this relationship, it is necessary to develop new computational approaches at the single-cell level.

Results: We have developed AgentCell, a model using agent-based technology to study the relationship between stochastic intracellular processes and behavior of individual cells. As a test-bed for our approach we use bacterial chemotaxis, one of the best characterized biological systems. In this model, each bacterium is an agent equipped with its own chemotaxis network, motors and flagella. Swimming cells are free to move in a 3D environment. Digital chemotaxis assays reproduce experimental data obtained from both single cells and bacterial populations.

Availability: AgentCell is available on request from the authors.

Contact: emonet{at}uchicago.edu

Supplementary information: Available at http://bioinformatics.oupjournals.org/cgi/data/bti391/DC1/1


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