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Bioinformatics Advance Access originally published online on June 17, 2009
Bioinformatics 2009 25(16):2057-2063; doi:10.1093/bioinformatics/btp361
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Modeling multi-cellular behavior in epidermal tissue homeostasis via finite state machines in multi-agent systems

Thomas Sütterlin 1, Simone Huber 2, Hartmut Dickhaus 1 and Niels Grabe 1,*

1 Medical Informatics Department, Institute of Medical Biometry and Informatics, University Hospital Heidelberg, Im Neuenheimer Feld 305 and Hamamatsu Tissue Imaging and Analysis Center (TIGA), BIOQUANT, University Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg and 2 Department of Informatics, Heilbronn University, Max-Planck-Str. 39, 74081 Heilbronn, Germany

*To whom correspondence should be addressed.


  Abstract

Motivation: For the efficient application of multi-agent systems to spatial and functional modeling of tissues flexible and intuitive modeling tools are needed, which allow the graphical specification of cellular behavior in a tissue context without presuming specialized programming skills.

Results: We developed a graphical modeling system for multi-agent based simulation of tissue homeostasis. An editor allows the intuitive and hierarchically structured specification of cellular behavior. The models are then automatically compiled into highly efficient source code and dynamically linked to an interactive graphical simulation environment. The system allows the quantitative analysis of the morphological and functional tissue properties emerging from the cell behavioral model. We demonstrate the relevance of the approach using a recently published model of epidermal homeostasis as well as a series of cell-cycle models.

Availability: The complete software is available in binary executables for MS-Windows and Linux at tiga.uni-hd.de

Contact: niels.grabe{at}bioquant.uni-heidelberg.de

Associate Editor: Trey Ideker

Received on December 2, 2008; revised on May 18, 2009; accepted on June 9, 2009

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