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PDF 1.01MB
Pages 614-621
First published 30 July 2014

Novel Approaches to the Visualization and Quantification of Biological Simulations by Emulating Experimental Techniques

James A. Butler, Kieran Alden, Henrique Veiga Fernandes, Jon Timmis, and Mark Coles

Abstract (Excerpt)

The use of modeling and simulation as a predictive tool for research in biology is becoming increasingly popular. However, outputs from such simulations are often abstract and presented in a very different manner to equivalent data from the biological domain. Therefore, we have developed a flexible tool-chain for emulating various biological laboratory techniques to produce biologically homomorphic outputs in computer simulations. This includes virtual immunohistochemistry, microscopy, flow cytometry, and gene expression heatmaps. We present a case study in the use of this tool-chain applied to a simulation of pre-natal lymphoid organ development. We find that application of the tool-chain provides additional, biologically relevant data, that is inaccessible with pre-existing methodologies for analysis of simulation results. We argue that biological experimental techniques borrowed from the wet-lab are an important additional approach to the analysis of simulations in computational biology, and might furthermore inspire confidence in simulation results from the perspective of experimental biologists.