Quantifying The Dynamics of Your Superorganism Body Using Big Data Supercomputing
Larry Smarr (Harry E. Gruber Professor, Dept. of Computer Science and Engineering, UC San Diego Founding Director, California Institute for Telecommunications and Information Technology (UCSD/UCI))
CSE Distinguished Lecture Series
Thursday, October 9, 2014, 3:30pm
EEB-105
Abstract
As a member of Lee Hood's 100 Person Wellness Project, headquartered in Seattle's Institute for System Biology, I am engaged in experiments to read out the time varying state of a complex dynamical system - my human body. However, the human body is host to 100 trillion microorganisms, ten times the number of cells in the human body, and these microbes contain 100 times the number of DNA genes that our human DNA does. The microbial component of this "superorganism" is comprised of hundreds of species spread over many taxonomic phyla. The human immune system is tightly coupled with this microbial ecology and in cases of autoimmune disease, both the immune system and the microbial ecology can have dynamic excursions far from normal. To provide a deeper context for the microbiome results from the 100 Person Wellness Project, I have been exploring the variation in the microbiome ecology across healthy and chronically ill populations. Our research starts with trillions of DNA bases, produced by Illumina Next Generation sequencers, of the human gut microbial DNA taken from my own body over time, as well as from hundreds of people sequenced under the NIH Human Microbiome Project. To decode the details of the microbial ecology we feed this data into parallel supercomputers, running sophisticated bioinformatics software pipelines. We then use Calit2/SDSC designed Big Data PCs to manage the data and drive innovative scalable visualization systems to examine the complexities of the changing human gut microbial ecology in health and disease. I will show how advanced data analytics tools find patterns in the resulting microbial distribution data that suggest new hypotheses for clinical application.
Bio:
Larry Smarr is the founding Director of the California Institute for Telecommunications and Information Technology (Calit2), a UC San Diego/UC Irvine partnership, and holds the Harry E. Gruber professorship in the Department of Computer Science and Engineering (CSE) of UCSD’s Jacobs School of Engineering. Before that he was the founding director of the National Center for Supercomputing Applications (NCSA) at the University of Illinois at Champaign-Urbana. He is a member of the National Academy of Engineering, as well as a Fellow of the American Physical Society and the American Academy of Arts and Sciences. In 2006 he received the IEEE Computer Society Tsutomu Kanai Award for his lifetime achievements in distributed computing systems. He is a member of the DOE ESnet Policy Board. He served on the NASA Advisory Council to 4 NASA Administrators, was chair of the NSF Advisory Committee on Cyberinfrastructure for the last 3 years, and for 8 years he was a member of the NIH Advisory Committee to the NIH Director, serving 3 directors. He was PI of the NSF OptIPuter project and of the Moore Foundation CAMERA global microbial metagenomics computational repository. His personal interests include growing orchids, snorkeling coral reefs, and quantifying the state of his body. You can follow him on his life-streaming portal at http://lsmarr.calit2.net.