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Computation 2015, 3(2), 197-221; doi:10.3390/computation3020197

Simulation Frameworks for Morphogenetic Problems

1
Department for Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland
2
Swiss Institute of Bioinformatics (SIB), Basel 4058, Switzerland 
Academic Editor: Rainer Breitling
Received: 24 October 2014 / Revised: 4 April 2015 / Accepted: 14 April 2015 / Published: 24 April 2015
(This article belongs to the Special Issue Multiscale Modeling and Simulation in Computational Biology)
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Abstract

Morphogenetic modelling and simulation help to understand the processes by which the form and shapes of organs (organogenesis) and organisms (embryogenesis) emerge. This requires two mutually coupled entities: the biomolecular signalling network and the tissue. Whereas the modelling of the signalling has been discussed and used in a multitude of works, the realistic modelling of the tissue has only started on a larger scale in the last decade. Here, common tissue modelling techniques are reviewed. Besides the continuum approach, the principles and main applications of the spheroid, vertex, Cellular Potts, Immersed Boundary and Subcellular Element models are discussed in detail. In recent years, many software frameworks, implementing the aforementioned methods, have been developed. The most widely used frameworks and modelling markup languages and standards are presented. View Full-Text
Keywords: cell-based modelling; computational morphogenesis; computational biology cell-based modelling; computational morphogenesis; computational biology
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Tanaka, S. Simulation Frameworks for Morphogenetic Problems. Computation 2015, 3, 197-221.

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