The University of Auckland
poster-figshare.pdf (1.71 MB)

Computational Tools for the Creation, Simulation and Dissemination of Epithelial Cell Models

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posted on 2015-03-25, 20:10 authored by David NickersonDavid Nickerson, Kirk Hamilton, Daniel BeardDaniel Beard, Peter Hunter

My poster presented at Experimental Biology 2015.


We have developed a software suite for the creation, simulation, and dissemination of epithelial cell models. The suite, known as GET (Generalized Epithelial Transport), is freely available under an open-source license at: GET consists of a model creation tool, a simulation tool, and a server that provides access to some functionality from these tools via web services. The server also provides access to data from the Physiome Model Repository. The GET framework makes use of standard community file formats to store mathematical model and numerical simulation information in order to ensure users are able to reuse, reproduce, and exchange their work with other software tools, repositories, and scientists. The mathematical models are encoded in the CellML format ( and the SED-ML format ( is used to encode descriptions of the computational simulation experiments. The development of the GET suite has led to proposals for extensions to both the CellML and SED-ML specifications in order to meet the requirements of the epithelial cell models.