AgentCell

University of Chicago
posted on 06/25/2009

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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. 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. AgentCell is free software distributed under the GPL License. It includes other software such as ( Repast , StochSim , ...). Licenses for each package can be found in the licenses directory within the distribution package. Repast is licensed under a BSD license. StochSim 1.4.1 (the modified 1.4 version) is included with AgentCell and is distributed under the LGPL license. AgentCell includes Xerces XML software developed by the Apache Software Foundation ( http://www.apache.org/ ).