Epistasis Blog

From the Computational Genetics Laboratory at the University of Pennsylvania (www.epistasis.org)

Monday, September 13, 2010

Human Microbiome Visualization Using 3D Technology

Our paper on visualization of human microbiome data has been accepted for publication as part of the 2011 Pacific Symposium on Biocomputing (PSB). This paper describes our 3D Heatmap application that harnesses the power of 3D video game engines. The 3dheatmap software is freely available from Sourceforge.net. Be sure and buy a 3D mouse!

Moore JH, Cowper Sal.Lari R, Hibberd P, Hill D, Madan JC. Human microbiome visualization using 3D technology. Pacific Symposium on Biocomputing, in press (2011).

Abstract

High-throughput sequencing technology has opened the door to the study of the human microbiome and its relationship with health and disease. This is both an opportunity and a significant biocomputing challenge. We present here a 3D visualization methodology and freely-available software package for facilitating the exploration and analysis of high-dimensional human microbiome data. Our visualization approach harnesses the power of commercial video game development engines to provide an interactive medium in the form of a 3D heat map for exploration of microbial species and their relative abundance in different patients. The advantage of this approach is that the third dimension provides additional layers of information that cannot be visualized using a traditional 2D heat map. We demonstrate the usefulness of this visualization approach using microbiome data collected from a sample of premature babies with and without sepsis.

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