There are 100 billion stars in the Andromeda galaxy and 100 billion galaxies in the known universe.
It s a microbial world there are 100 million times as many bacteria on Earth as stars in the universe. Microbiology is the ultimate Big Data science!
Most of Life s Evolutionary Time Was in the Microbial World You Are Here Tree of Life Derived from 16S rrna Sequences Source: Carl Woese, et al
President Obama Announces National Microbiome Initiative May 13, 2016
Your Microbiome is Your Near-Body Environment The Microbiome Contains 300x as Many DNA Genes As Your Human DNA Inclusion of the Dark Matter of the Body Will Radically Alter Medicine
Your Gut Microbiome Contains Hundreds of Microbial Species Note Log Scale Average Over 250 Healthy People From NIH Human Microbiome Project Clostridium difficile Source: Weizhong Li, Andrew Prudomme, Larry Smarr, UCSD
Exploring the Gut Microbiome Time Series by Collaborating with the UCSD Knight Lab My Welcome Present to Rob
Mouth Skin Vagina Stool Source: Knight Lab, UCSD
Source: Knight Lab, UCSD
But Microbiome Time Series Are Very Different in Disease States
Fecal Transplants From Healthy Donor To C. Diff Patients Source: Knight Lab, UCSD
As a Model for the Precision Medicine Initiative, I Have Tracked My Internal Biomarkers To Understand My Body s Dynamics Calit2 64 Megapixel VROOM My Quarterly Blood Draw
By Creating a Time Series of an Immune System Biomarker I Discovered I Had an Autoimmune Disease Lactoferrin is a Protein Shed from Neutrophils - An Antibacterial that Sequesters Iron Typical Lactoferrin Value for Active Inflammatory Bowel Disease (IBD) 124x Upper Limit for Healthy Normal Range <7.3 µg/ml
From a Time Series of My Gut Microbiome I Can Explain Changes in My Body Weekly Weight Frequent IBD Symptoms Weight Loss 7/1/12 to 12/1/14 Few IBD Symptoms Weight Gain 1/1/14 to 8/1/15 Blue Balls on Diagram to the Right 12/1/13-1/1/14 Lialda & Uceris 12/1/13 to 1/1/14 Red Balls on Diagram to the Right Weight Data from Larry Smarr, Calit2, UCSD Principal Coordinate Analysis of Microbiome Ecology PCoA by Justine Debelius and Jose Navas, Knight Lab, UCSD
From N=1 to a Population of People with Disease Drs. William J. Sandborn, John Chang, & Brigid Boland UCSD School of Medicine, Division of Gastroenterology Announced November 7, 2014 Inflammatory Bowel Disease Biobank For Healthy and Disease Patients Over 300 Enrolled
Combining Deep Metagenomics and Supercomputing Time to Map the Differences Between Health and Disease Controls: 100s of Healthy Subjects Smarr Gut Microbiome Time Series ~80 Samples Over 5 Years Hundreds of IBD Patients Phenotyped Patients Drawn from Sandborn BioBank Knight/Smarr Labs Using 100 CPU-Years of Supercomputer Time
Forty Years of Computing Gravitational Waves From Colliding Black Holes LIGO Consortium Spiral Black Hole Collision 2016 L. Smarr and K. Eppley Gravitational Radiation Computed from an Axisymmetric Black Hole Collision 40 Years 1977
Complexity of Computing First Gut Microbiome Dynamics Versus First Dynamics of Colliding Black Holes My 1975 PhD Dissertation Solving Einstein s Equations of General Relativity for Colliding Black Holes and Grav Waves CDC 6600 Megaflop/s Hundreds of Hours Rob Knight and Smarr Gut Microbiome Map Mapping From Illumina Sequencing to Taxonomy and Gene Abundance Dynamics Comet Petaflop/s Comet Core is 40,000x CDC6600 Speed Million Core-Hours 10,000x Supercomputer Time Gut Microbiome Takes ~ ½ Billion Times the Compute Power of Early Solutions of Dynamic General Relativity
The Future Foundation of Medicine is an Exponential Scaling-Up of the Number of Deeply Quantified Humans Source: @EricTopol Twitter 9/27/2014
Next Generation Telescopes Will Track Time Series of the Entire Universe On-Line in Five Years, Tracks Time Series of ~40B Objects, Creates 10M Alerts/Night Within 1 Minute of Observing NCSA Supercomputer 2x40Gbps