Novel approaches to the visualization and quantification of biological simulations by emulating experimental techniques

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

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference Proceeding (Non-Journal item)

4 Citations (SciVal)

Abstract

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.

Original languageEnglish
Title of host publicationArtificial Life 14 - Proceedings of the 14th International Conference on the Synthesis and Simulation of Living Systems, ALIFE 2014
EditorsHiroki Sayama, John Rieffel, Sebastian Risi, Rene Doursat, Hod Lipson
PublisherMIT Press Journals
Pages614-621
Number of pages8
ISBN (Electronic)9780262326216
Publication statusPublished - 2014
Event14th International Conference on the Synthesis and Simulation of Living Systems, ALIFE 2014 - Manhattan, United States of America
Duration: 30 Jul 201402 Aug 2014

Publication series

NameArtificial Life 14 - Proceedings of the 14th International Conference on the Synthesis and Simulation of Living Systems, ALIFE 2014

Conference

Conference14th International Conference on the Synthesis and Simulation of Living Systems, ALIFE 2014
Country/TerritoryUnited States of America
CityManhattan
Period30 Jul 201402 Aug 2014

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