TY - GEN
T1 - Novel approaches to the visualization and quantification of biological simulations by emulating experimental techniques
AU - Butler, James A.
AU - Alden, Kieran
AU - Fernandes, Henrique Veiga
AU - Timmis, Jon
AU - Coles, Mark
N1 - Funding Information:
This work is supported by the Engineering and Physical Sciences Research Council, United Kingdom.
Funding Information:
This work is supported by the Engineering and Physical Sci-encesResearchCouncil,UnitedKingdom.
Publisher Copyright:
© Artificial Life 14 - Proceedings of the 14th International Conference on the Synthesis and Simulation of Living Systems, ALIFE 2014. All rights reserved.
PY - 2014
Y1 - 2014
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85017155990&partnerID=8YFLogxK
M3 - Conference Proceeding (Non-Journal item)
AN - SCOPUS:85017155990
T3 - Artificial Life 14 - Proceedings of the 14th International Conference on the Synthesis and Simulation of Living Systems, ALIFE 2014
SP - 614
EP - 621
BT - Artificial Life 14 - Proceedings of the 14th International Conference on the Synthesis and Simulation of Living Systems, ALIFE 2014
A2 - Sayama, Hiroki
A2 - Rieffel, John
A2 - Risi, Sebastian
A2 - Doursat, Rene
A2 - Lipson, Hod
PB - MIT Press Journals
T2 - 14th International Conference on the Synthesis and Simulation of Living Systems, ALIFE 2014
Y2 - 30 July 2014 through 2 August 2014
ER -