Calit2 Director Larry Smarr delivers an invited talk to the Pre-Biotechnology Industry Organization International Convention Symposium in San Diego, Calif., on June 22, 2014.
Linking Phenotype Changes to Internal/External Longitudinal Time Series in a ...Larry Smarr
This document summarizes Dr. Larry Smarr's presentation on quantifying physiological data from his own body over the past decade. Some key points:
- Smarr has gathered longitudinal time series data on over 200 biomarkers and microbiome samples to study phenotype changes from his autoimmune disease.
- Sensors have tracked daily metrics like weight, activity levels, and symptoms, revealing oscillations and episodes of inflammation.
- Imaging and biomarker analysis identified the specific location and nature of his Crohn's disease.
- Analysis of his microbiome samples over time uncovered a shift in microbial ecology that correlated with changes in drugs and symptoms.
- Expanding this type of personalized, quantitative approach could transform medicine by deeply characterizing individuals
The Quantified Self: From Idiosyncratic Hobby to an Emerging Growth IndustryLarry Smarr
Larry Smarr discusses his decade-long journey of self-quantification by tracking over 100 biomarkers in his blood and stool using various sensors and devices. This led to insights into his health and formed the basis for an emerging personalized wellness industry. The cost of sequencing has fallen dramatically, enabling analysis of one's genome and microbiome to gain health insights. This represents a disruption of the current healthcare system with citizens generating their own health data to partner with doctors.
Machine Learning Opportunities in the Explosion of Personalized Precision Med...Larry Smarr
This document summarizes a presentation given by Dr. Larry Smarr on machine learning opportunities in personalized precision medicine using massive datasets from individuals. Some key points:
- Smarr has tracked over 100 of his own blood biomarkers and microbiome over time, revealing health issues like chronic inflammation.
- Analysis of Smarr's microbiome alongside others revealed major shifts between healthy and disease states that can be classified using machine learning.
- Further analysis of microbial proteins identified which were over or under abundant in disease, helping characterize Smarr's own condition.
- Smarr's microbiome appeared to undergo an abrupt shift between two stable states correlated with a change in symptoms and drug therapy.
Discovering the 100 Trillion Bacteria Living Within Each of UsLarry Smarr
This document provides a summary of a lecture on the human microbiome given by Dr. Larry Smarr. Some key points:
- The human microbiome refers to the trillions of bacteria that live within the human body. Each person contains 100 trillion bacteria, outnumbering human cells.
- Research into the microbiome is a rapidly growing field that provides insights into health and disease. The microbiome plays a role in processes like drug metabolism and immunity.
- The microbiome is established early in life and influenced by factors like birth method and antibiotic use in the first years. This early development can impact future health.
- Microbiome imbalances are linked to diseases like inflammatory bowel disease. New treatments are
Stability in Health vs. Abrupt Changes in Disease in the Human Gut Microbiome...Larry Smarr
The document summarizes research on analyzing changes in human gut microbiome composition over time using 16S rRNA gene sequencing and the UniFrac metric. It presents findings that:
1) A healthy person's gut microbiome composition generally remains stable over periods of 60 days based on samples from multiple body sites.
2) In contrast, for people with C. difficile infections, their gut microbiome composition can abruptly shift to a healthy state within days after a fecal microbiota transplant from a healthy donor.
3) Analysis of one individual's gut microbiome samples over 3.5 years found the composition abruptly shifted between two distinct stable states that correlated with changes in symptoms and weight, before and after a
Linking Phenotype Changes to Internal/External Longitudinal Time Series in a ...Larry Smarr
This document summarizes Dr. Larry Smarr's presentation on quantifying physiological data from his own body over the past decade. Some key points:
- Smarr has gathered longitudinal time series data on over 200 biomarkers and microbiome samples to study phenotype changes from his autoimmune disease.
- Sensors have tracked daily metrics like weight, activity levels, and symptoms, revealing oscillations and episodes of inflammation.
- Imaging and biomarker analysis identified the specific location and nature of his Crohn's disease.
- Analysis of his microbiome samples over time uncovered a shift in microbial ecology that correlated with changes in drugs and symptoms.
- Expanding this type of personalized, quantitative approach could transform medicine by deeply characterizing individuals
The Quantified Self: From Idiosyncratic Hobby to an Emerging Growth IndustryLarry Smarr
Larry Smarr discusses his decade-long journey of self-quantification by tracking over 100 biomarkers in his blood and stool using various sensors and devices. This led to insights into his health and formed the basis for an emerging personalized wellness industry. The cost of sequencing has fallen dramatically, enabling analysis of one's genome and microbiome to gain health insights. This represents a disruption of the current healthcare system with citizens generating their own health data to partner with doctors.
Machine Learning Opportunities in the Explosion of Personalized Precision Med...Larry Smarr
This document summarizes a presentation given by Dr. Larry Smarr on machine learning opportunities in personalized precision medicine using massive datasets from individuals. Some key points:
- Smarr has tracked over 100 of his own blood biomarkers and microbiome over time, revealing health issues like chronic inflammation.
- Analysis of Smarr's microbiome alongside others revealed major shifts between healthy and disease states that can be classified using machine learning.
- Further analysis of microbial proteins identified which were over or under abundant in disease, helping characterize Smarr's own condition.
- Smarr's microbiome appeared to undergo an abrupt shift between two stable states correlated with a change in symptoms and drug therapy.
Discovering the 100 Trillion Bacteria Living Within Each of UsLarry Smarr
This document provides a summary of a lecture on the human microbiome given by Dr. Larry Smarr. Some key points:
- The human microbiome refers to the trillions of bacteria that live within the human body. Each person contains 100 trillion bacteria, outnumbering human cells.
- Research into the microbiome is a rapidly growing field that provides insights into health and disease. The microbiome plays a role in processes like drug metabolism and immunity.
- The microbiome is established early in life and influenced by factors like birth method and antibiotic use in the first years. This early development can impact future health.
- Microbiome imbalances are linked to diseases like inflammatory bowel disease. New treatments are
Stability in Health vs. Abrupt Changes in Disease in the Human Gut Microbiome...Larry Smarr
The document summarizes research on analyzing changes in human gut microbiome composition over time using 16S rRNA gene sequencing and the UniFrac metric. It presents findings that:
1) A healthy person's gut microbiome composition generally remains stable over periods of 60 days based on samples from multiple body sites.
2) In contrast, for people with C. difficile infections, their gut microbiome composition can abruptly shift to a healthy state within days after a fecal microbiota transplant from a healthy donor.
3) Analysis of one individual's gut microbiome samples over 3.5 years found the composition abruptly shifted between two distinct stable states that correlated with changes in symptoms and weight, before and after a
Quantifying Your Dynamic Human Body (Including Its Microbiome), Will Move Us ...Larry Smarr
Invited Presentation Microbiology and the Microbiome and the Implications for Human Health Analytic, Life Science & Diagnostic Association (ALDA) 2016 Senior Management Conference
Half Moon Bay, CA
October 3, 2016
This document discusses how advances in genetic sequencing and computing are enabling humans to read and understand the "software of life" encoded in their human and microbiome DNA. It notes that the human microbiome contains millions of microbial genes compared to the 23,000 genes in human cells. The author details how the cost of DNA sequencing has fallen over 100,000-fold, allowing sequencing of both human and microbial genomes. Machine learning will be needed to understand differences between healthy and diseased states by analyzing enormous genomic and microbiome datasets. The author provides an example of analyzing their own gut microbiome over time and comparing to healthy/IBD populations.
Finding the Patterns in the Big Data From Human Microbiome EcologyLarry Smarr
This document summarizes a talk on analyzing human microbiome data to better understand health and disease. It discusses how sequencing and supercomputing is used to map microbial ecology in hundreds of people. Advanced analytics tools like Ayasdi are helping discover patterns separating healthy from disease states like inflammatory bowel disease. Future goals include applying these techniques to larger datasets and using molecular networks to better understand disease development at the genetic and protein level.
Quantfying Your Gut: A Personal JourneyLarry Smarr
Larry Smarr presented on his personal journey quantifying his gut health issues using advanced technology. He discovered through blood, stool, and MRI tests that he had severe colonic inflammation and Crohn's disease localized to his sigmoid colon. With the help of 3D organ segmentation and virtual reality, he was able to co-plan his successful sigmoid colon resection surgery. Longitudinal analysis of biomarkers and stool microbiome sequencing revealed shifts associated with his autoimmune condition and ties to mental health. Modulating the vagus nerve and microbiome offers possibilities for treating inflammation-related diseases.
Fifty Years of Supercomputing: From Colliding Black Holes to Dynamic Microbio...Larry Smarr
This document provides a summary of a lecture given by Dr. Larry Smarr on the past, present, and future of supercomputing over the last 50 years. The summary discusses:
- How Smarr solved equations for colliding black holes in the 1970s using a megaFLOPs computer, whereas today collisions are detected using petaFLOPs supercomputers - a billion fold increase in speed.
- How Smarr's research has evolved from modeling astrophysical phenomena to mapping the human gut microbiome using terabytes of sequencing data and hundreds of thousands of core-hours of supercomputing.
- Emerging trends in brain-inspired computing architectures and non-von Neumann systems that are better suited to tasks
Assay Lab Within Your Body: Biometrics and BiomesLarry Smarr
This document summarizes a lecture about analyzing the human microbiome and its relationship to human health. It discusses how the human body contains 100 trillion microbial cells that contain 100 times as many genes as human DNA. Analysis of the speaker's own gut microbiome over time revealed changes in bacterial phyla between healthy and inflammatory bowel disease states. Collecting biomarkers from the speaker's body over years showed oscillations linked to gut microbes and immune response. Ongoing research aims to better understand dynamics of the human immune system and gut microbiome.
Dynamics of the Microbiome-Driven by Medical Interventions and Dietary ChangeLarry Smarr
This document summarizes Dr. Larry Smarr's presentation on how his gut microbiome was dramatically impacted by medical interventions and dietary changes. It discusses how his microbiome diversity sharply declined after sigmoid colon resection surgery but stabilized into a new healthy state. Dr. Smarr collaborated with UCSD scientists to analyze stool samples before and after the surgery, finding his microbiome changed more than average differences between individuals. Medical procedures like surgery can induce major gut microbiome shifts. Dr. Smarr then experimented with dietary changes like vegetable fiber and time-restricted eating, finding these interventions improved biomarkers like blood glucose levels and microbiome diversity.
Connecting Body Time Series to Macro Body ChangesLarry Smarr
1) The document summarizes research on how medical interventions like drugs, colonoscopies, and surgery can significantly disrupt and alter an individual's gut microbiome ecology over time.
2) It presents longitudinal data on one individual where their gut microbiome shifted between two relatively stable states that correlated with changes in weight and symptoms. This shift occurred following a course of new drugs.
3) Surgical procedures, antibiotics, and colon cleanses had massive impacts in disrupting the individual's gut microbiome according to data from microbiome samples analyzed. The microbiome composition took weeks or months to stabilize again after such interventions.
Using Advanced Technology to Better Diagnose Somatic DysfunctionLarry Smarr
Joint Presentation
The American Academy of Osteopathy 2017 Convocation
The Balance Point: Bringing the Science and Art of Osteopathic Medicine Together
Colorado Springs, CO
March 24, 2017
Know Thyself: Quantifying Your Human Body and Its One Hundred Trillion MicrobesLarry Smarr
Understanding Cultures and Addressing Disparities in Society: Degrees of Health and Well-Being Public Lecture Series
University of California, San Diego
January 20, 2016
The document discusses supercomputing analysis of the human microbiome. It describes how the human body hosts 100 trillion microorganisms containing 300 times as many genes as human DNA. Dr. Smarr has been collecting extensive personal health data over 7 years, including microbiome samples, to study the coupled immune-microbial system. Analyzing this data requires elaborate software running on high performance computers. The analysis can compare individuals with diseases to healthy populations and track disease progression over time.
Toward Personalized Wellness: An Ounce of Prevention is Worth a Pound of CureLarry Smarr
This document summarizes a talk given by Dr. Larry Smarr on personalized wellness and preventative medicine. The key points are:
1) Dr. Smarr began closely monitoring his own biomarkers and microbiome to better understand his body's systems and health.
2) He realized that to truly personalize wellness, he needed to consider the role of microbes in the body, as microbes make up the vast majority of cells in the human body and play an important role in health.
3) Changes to the Western diet and lifestyle may be contributing to increases in obesity, autoimmune diseases, and other non-communicable diseases by reducing gut microbiome diversity.
4) Dr.
Using Supercomputers to Discover the 100 Trillion Bacteria Living Within Each...Larry Smarr
This document summarizes a talk given by Dr. Larry Smarr on using supercomputers to analyze the human microbiome. It discusses how next-generation sequencing and analysis of microbial DNA reveals major differences between healthy and diseased gut microbiomes. Computational analysis of Smarr's own microbiome time series, in addition to data from hundreds of individuals, provides insights into inflammatory bowel disease. Large supercomputers and visualization resources were crucial for processing and comparing petabytes of sequencing data to advance understanding of microbiome dynamics and their links to human health and disease.
The ITIC will examine NASA's IT infrastructure, software, and data environments to identify opportunities for improvement. This includes investigating collaborative tools, high performance computing, data storage, and aerospace communications. The committee will also review the OCIO's strategic plans and IT governance across NASA to recommend best practices for managing IT infrastructure. The goal is to help NASA utilize leading edge capabilities and disruptive technologies to enhance distributed teams and mission activities.
High Performance Cyberinfrastructure Enabling Data-Driven Science in the Biom...Larry Smarr
11.04.06
Joint Presentation
UCSD School of Medicine Research Council
Larry Smarr, Calit2 & Phil Papadopoulos, SDSC/Calit2
Title: High Performance Cyberinfrastructure Enabling Data-Driven Science in the Biomedical Sciences
A Campus-Scale High Performance Cyberinfrastructure is Required for Data-Int...Larry Smarr
11.12.12
Seminar Presentation
Princeton Institute for Computational Science and Engineering (PICSciE)
Princeton University
Title: A Campus-Scale High Performance Cyberinfrastructure is Required for Data-Intensive Research
Princeton, NJ
Quantifying Your Dynamic Human Body (Including Its Microbiome), Will Move Us ...Larry Smarr
Invited Presentation Microbiology and the Microbiome and the Implications for Human Health Analytic, Life Science & Diagnostic Association (ALDA) 2016 Senior Management Conference
Half Moon Bay, CA
October 3, 2016
This document discusses how advances in genetic sequencing and computing are enabling humans to read and understand the "software of life" encoded in their human and microbiome DNA. It notes that the human microbiome contains millions of microbial genes compared to the 23,000 genes in human cells. The author details how the cost of DNA sequencing has fallen over 100,000-fold, allowing sequencing of both human and microbial genomes. Machine learning will be needed to understand differences between healthy and diseased states by analyzing enormous genomic and microbiome datasets. The author provides an example of analyzing their own gut microbiome over time and comparing to healthy/IBD populations.
Finding the Patterns in the Big Data From Human Microbiome EcologyLarry Smarr
This document summarizes a talk on analyzing human microbiome data to better understand health and disease. It discusses how sequencing and supercomputing is used to map microbial ecology in hundreds of people. Advanced analytics tools like Ayasdi are helping discover patterns separating healthy from disease states like inflammatory bowel disease. Future goals include applying these techniques to larger datasets and using molecular networks to better understand disease development at the genetic and protein level.
Quantfying Your Gut: A Personal JourneyLarry Smarr
Larry Smarr presented on his personal journey quantifying his gut health issues using advanced technology. He discovered through blood, stool, and MRI tests that he had severe colonic inflammation and Crohn's disease localized to his sigmoid colon. With the help of 3D organ segmentation and virtual reality, he was able to co-plan his successful sigmoid colon resection surgery. Longitudinal analysis of biomarkers and stool microbiome sequencing revealed shifts associated with his autoimmune condition and ties to mental health. Modulating the vagus nerve and microbiome offers possibilities for treating inflammation-related diseases.
Fifty Years of Supercomputing: From Colliding Black Holes to Dynamic Microbio...Larry Smarr
This document provides a summary of a lecture given by Dr. Larry Smarr on the past, present, and future of supercomputing over the last 50 years. The summary discusses:
- How Smarr solved equations for colliding black holes in the 1970s using a megaFLOPs computer, whereas today collisions are detected using petaFLOPs supercomputers - a billion fold increase in speed.
- How Smarr's research has evolved from modeling astrophysical phenomena to mapping the human gut microbiome using terabytes of sequencing data and hundreds of thousands of core-hours of supercomputing.
- Emerging trends in brain-inspired computing architectures and non-von Neumann systems that are better suited to tasks
Assay Lab Within Your Body: Biometrics and BiomesLarry Smarr
This document summarizes a lecture about analyzing the human microbiome and its relationship to human health. It discusses how the human body contains 100 trillion microbial cells that contain 100 times as many genes as human DNA. Analysis of the speaker's own gut microbiome over time revealed changes in bacterial phyla between healthy and inflammatory bowel disease states. Collecting biomarkers from the speaker's body over years showed oscillations linked to gut microbes and immune response. Ongoing research aims to better understand dynamics of the human immune system and gut microbiome.
Dynamics of the Microbiome-Driven by Medical Interventions and Dietary ChangeLarry Smarr
This document summarizes Dr. Larry Smarr's presentation on how his gut microbiome was dramatically impacted by medical interventions and dietary changes. It discusses how his microbiome diversity sharply declined after sigmoid colon resection surgery but stabilized into a new healthy state. Dr. Smarr collaborated with UCSD scientists to analyze stool samples before and after the surgery, finding his microbiome changed more than average differences between individuals. Medical procedures like surgery can induce major gut microbiome shifts. Dr. Smarr then experimented with dietary changes like vegetable fiber and time-restricted eating, finding these interventions improved biomarkers like blood glucose levels and microbiome diversity.
Connecting Body Time Series to Macro Body ChangesLarry Smarr
1) The document summarizes research on how medical interventions like drugs, colonoscopies, and surgery can significantly disrupt and alter an individual's gut microbiome ecology over time.
2) It presents longitudinal data on one individual where their gut microbiome shifted between two relatively stable states that correlated with changes in weight and symptoms. This shift occurred following a course of new drugs.
3) Surgical procedures, antibiotics, and colon cleanses had massive impacts in disrupting the individual's gut microbiome according to data from microbiome samples analyzed. The microbiome composition took weeks or months to stabilize again after such interventions.
Using Advanced Technology to Better Diagnose Somatic DysfunctionLarry Smarr
Joint Presentation
The American Academy of Osteopathy 2017 Convocation
The Balance Point: Bringing the Science and Art of Osteopathic Medicine Together
Colorado Springs, CO
March 24, 2017
Know Thyself: Quantifying Your Human Body and Its One Hundred Trillion MicrobesLarry Smarr
Understanding Cultures and Addressing Disparities in Society: Degrees of Health and Well-Being Public Lecture Series
University of California, San Diego
January 20, 2016
The document discusses supercomputing analysis of the human microbiome. It describes how the human body hosts 100 trillion microorganisms containing 300 times as many genes as human DNA. Dr. Smarr has been collecting extensive personal health data over 7 years, including microbiome samples, to study the coupled immune-microbial system. Analyzing this data requires elaborate software running on high performance computers. The analysis can compare individuals with diseases to healthy populations and track disease progression over time.
Toward Personalized Wellness: An Ounce of Prevention is Worth a Pound of CureLarry Smarr
This document summarizes a talk given by Dr. Larry Smarr on personalized wellness and preventative medicine. The key points are:
1) Dr. Smarr began closely monitoring his own biomarkers and microbiome to better understand his body's systems and health.
2) He realized that to truly personalize wellness, he needed to consider the role of microbes in the body, as microbes make up the vast majority of cells in the human body and play an important role in health.
3) Changes to the Western diet and lifestyle may be contributing to increases in obesity, autoimmune diseases, and other non-communicable diseases by reducing gut microbiome diversity.
4) Dr.
Using Supercomputers to Discover the 100 Trillion Bacteria Living Within Each...Larry Smarr
This document summarizes a talk given by Dr. Larry Smarr on using supercomputers to analyze the human microbiome. It discusses how next-generation sequencing and analysis of microbial DNA reveals major differences between healthy and diseased gut microbiomes. Computational analysis of Smarr's own microbiome time series, in addition to data from hundreds of individuals, provides insights into inflammatory bowel disease. Large supercomputers and visualization resources were crucial for processing and comparing petabytes of sequencing data to advance understanding of microbiome dynamics and their links to human health and disease.
The ITIC will examine NASA's IT infrastructure, software, and data environments to identify opportunities for improvement. This includes investigating collaborative tools, high performance computing, data storage, and aerospace communications. The committee will also review the OCIO's strategic plans and IT governance across NASA to recommend best practices for managing IT infrastructure. The goal is to help NASA utilize leading edge capabilities and disruptive technologies to enhance distributed teams and mission activities.
High Performance Cyberinfrastructure Enabling Data-Driven Science in the Biom...Larry Smarr
11.04.06
Joint Presentation
UCSD School of Medicine Research Council
Larry Smarr, Calit2 & Phil Papadopoulos, SDSC/Calit2
Title: High Performance Cyberinfrastructure Enabling Data-Driven Science in the Biomedical Sciences
A Campus-Scale High Performance Cyberinfrastructure is Required for Data-Int...Larry Smarr
11.12.12
Seminar Presentation
Princeton Institute for Computational Science and Engineering (PICSciE)
Princeton University
Title: A Campus-Scale High Performance Cyberinfrastructure is Required for Data-Intensive Research
Princeton, NJ
The UC California Institutes for Science and InnovationLarry Smarr
06.04.25
Invited Talk to
Seminar on Creating a Regional Innovation Cluster: From Discovery to Application
Title: The UC California Institutes for Science and Innovation
La Jolla, CA
How Global-Scale Personal Lighwaves are Transforming Scientific ResearchLarry Smarr
The document discusses how global-scale optical networks called "lambdas" are enabling new forms of data-intensive scientific collaboration. Lambdas provide dedicated high-bandwidth connections between research institutions for applications like streaming high-definition video, interactive visualization of large datasets, and remote access to scientific instruments and supercomputers. Examples are given of how lambdas are used for projects in fields like oceanography, climate science, and microbial genomics. The OptIPuter project aims to further develop lambda-enabled cyberinfrastructure through dedicated optical connections between partner institutions.
Restructuring Campus CI -- UCSD-A LambdaCampus Research CI and the Quest for ...Larry Smarr
09.02.03
Invited Presentation to the
Net@EDU Campus Cyberinfrastructure Working Group
Title: Restructuring Campus CI -- UCSD-A LambdaCampus Research CI and the Quest for Zero Carbon ICT
Tempe, AZ
Calit2: Experiments in Living in the Virtual/Physical WorldLarry Smarr
10.12.15
Invited Talk
"Cultivating Networked Centers of Excellence" CineGrid International Workshop 2010
Title: Calit2: Experiments in Living in the Virtual/Physical World
Project StarGate An End-to-End 10Gbps HPC to User Cyberinfrastructure ANL * C...Larry Smarr
09.11.03
Report to the
Dept. of Energy Advanced Scientific Computing Advisory Committee
Title: Project StarGate An End-to-End 10Gbps HPC to User Cyberinfrastructure ANL * Calit2 * LBNL * NICS * ORNL * SDSC
Oak Ridge, TN
Digital Infrastructure in a Carbon-Constrained WorldLarry Smarr
- The document discusses how digital infrastructure and information and communication technologies (ICT) can help reduce greenhouse gas emissions and combat climate change by enabling efficiencies in other sectors. ICT has the potential to deliver carbon savings five times larger than its own emissions footprint by 2020.
- The University of California San Diego (UCSD) is working to develop green ICT applications and smart grid technologies through its California Institute for Telecommunications and Information Technology (Calit2). Examples mentioned include smart transportation systems, virtual meetings to reduce travel, and instrumenting buildings and campuses as "living labs" of green technologies.
- UCSD is also working to establish a zero carbon emission campus through fuel cell and solar power installations,
Riding the Light: How Dedicated Optical Circuits are Enabling New ScienceLarry Smarr
The document discusses how dedicated optical circuits are enabling new science through high-bandwidth networks. It provides examples of several projects using dedicated optical networks, such as the OptIPuter project, to enable interactive analysis of large datasets through terabit network connections between supercomputing centers. The document concludes by discussing future ocean observatory networks that will use undersea fiber optics to enable remote interactive imaging and sensing.
OptIPuter-A High Performance SOA LambdaGrid Enabling Scientific ApplicationsLarry Smarr
07.03.21
IEEE Computer Society Tsutomu Kanai Award Keynote
At the Joint Meeting of the: 8th International Symposium on Autonomous Decentralized Systems
2nd International Workshop on Ad Hoc, Sensor and P2P Networks
11th IEEE International Workshop on Future Trends of Distributed Computing Systems
Title: OptIPuter-A High Performance SOA LambdaGrid Enabling Scientific Applications
Sedona, AZ
Creating a Community Cyberinfrastructure for Advanced Marine Microbial Ecolog...Larry Smarr
09.03.18
Invited Talk
Honoring David Kingsbury
Gordon and Betty Moore Foundation
Title: Creating a Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (a.k.a. CAMERA)
Palo Alto, CA
The document discusses the history and future of telepresence technology. It describes early visions of telepresence from the 1960s, prototypes in the 1980s, and partnerships in the 1990s that helped advance the technology. It outlines current infrastructure like National LambdaRail that enables remote collaboration and explores future possibilities like connecting very large displays and bringing gigabit internet to homes.
21st Century e-Knowledge Requires a High Performance e-InfrastructureLarry Smarr
11.12.09
Keynote Presentation
40-year anniversary Celebration of SARA
Title: 21st Century e-Knowledge Requires a High Performance e-Infrastructure
Amsterdam, Netherlands
The quantified self movement has grown from a niche hobby to an emerging industry as self-tracking of health metrics has become mainstream. Consumer use of fitness trackers, sleep monitors, and calorie counters has exploded, with leading companies attracting significant funding. The presenter used personal sensors to track various biomarkers and drive health behavior changes. New integrated dashboards combine data from devices, medical records, and genetics to provide personalized health coaching. The self-monitoring business is undergoing consolidation as large companies acquire startups. Healthcare systems will need to integrate high volumes of personal health data from consumers. The presenter's own data revealed previously undiagnosed chronic inflammation, and analysis of microbiome time series provided new insights into inflammatory bowel disease
2014.02.06
Calit2 Director Larry Smarr lecture to the Osher Lifelong Learning Institute as part of the Winter 2014 Qualcomm Institute lecture series for Osher.
Individual, Consumer-Driven Care of the Future: Taking Wellness One Step FurtherLarry Smarr
Calit2 Director Larry Smarr gives the closing keynote address to the 2nd annual Learning Conference on Integrated Delivery Systems in San Diego on May 7, 2014.
The Human Microbiome and the Revolution in Digital HealthLarry Smarr
2014.01.22
Calit2 Director Larry Smarr speaks as part of the Pensacola Evening Lecture Series, organized by the Florida Institute for Human and Machine Cognition, in Pensacola, FL.
From Digitally Enabled Genomic Medicineto Personalized HealthcareLarry Smarr
The document discusses the future of personalized healthcare through digital health technologies and genomic medicine. It describes how continuous monitoring of various biological sensors can capture temporal data on factors like physical activity, diet, sleep, environmental exposures and more. This comprehensive data combined with clinical records, genetic information, and microbial metagenomic analysis can enable true preventative medicine through early detection, feedback loops, and tuning of lifestyle and medical factors.
Assay Lab Within Your Body: Biometrics and BiomesLarry Smarr
This document summarizes a lecture about analyzing the human microbiome and its relationship to human health. It discusses how the human body contains 100 trillion microbial cells that contain 100 times as many genes as human DNA. Recent advances now allow sequencing these microbial genomes and analyzing massive datasets to map the dynamics of the immune-microbial system and its connection to disease states. A key focus is generating high-resolution time series data of the gut microbiome and immune variables from large cohorts to understand how they influence conditions like inflammatory bowel disease. There is potential to design gut microbes as sensors of disease states by programming them to detect specific conditions.
The Emerging Personalized Medicine Paradigm of Time-Series Tracking of Mind, ...Larry Smarr
Invited Zoom Remote Lecture
For Sara Gottfried, MD Personalized Medicine for Mental Health Course
Integrative Psychiatry Institute
Recorded June 28, 2022
Mapping the Human Gut Microbiome in Health and Disease Using Sequencing, Supe...Larry Smarr
Invited Talk Delivered by Mehrdad Yazdani, Calit2 Ayasdi Sponsored Lunch & Learn American Society of Human Genetics (ASHG) San Diego Convention Center October 19, 2014
Towards Digitally Enabled Genomic Medicine: the Patient of TomorrowLarry Smarr
The document summarizes a keynote speech by Dr. Larry Smarr on his vision of digitally enabled genomic medicine and how he has been quantifying his own health metrics over 10 years to serve as a model patient of the future. Some of the metrics he tracks include weight, blood pressure, caloric intake/burn, over 100 blood variables, his gut microbiome, and 1 million SNPs in his human DNA. Through this self-quantification, he discovered he has a genetic predisposition and symptoms of Crohn's disease.
Tracking Large Variations in My Immune Biomarkers and My Gut Microbiome: Infl...Larry Smarr
This document provides a 3-sentence summary of a presentation by Dr. Larry Smarr on tracking changes in his immune biomarkers and gut microbiome in relation to inflammation, Crohn's disease, and colon cancer:
Over the past decade, Dr. Smarr has quantified over a billion data points on his body through measures like blood tests, MRI/CT scans, and analysis of his gut microbiome, discovering through this data that he has episodic chronic inflammation and Crohn's disease affecting his colon. By comparing his biomarkers and symptoms over time and visualizing his microbiome ecology, Dr. Smarr has gained insights into the dynamics and invasiveness of species in his gut microbiome as it relates to his autoimmune
This document summarizes a lecture given by Dr. Larry Smarr on exploring the human microbiome. In 3 sentences:
Dr. Smarr discussed how recent advances in sequencing have revealed that the human body hosts trillions of microbes containing many times more genes than human cells. Longitudinal studies of his own biomarkers and microbiome provided insights into the dynamics of his autoimmune disease. New research is exploring the complex relationships between the gut microbiome and various health conditions.
Exploring Our Inner Universe Using Supercomputers and Gene SequencersLarry Smarr
This document summarizes a talk given by Dr. Larry Smarr on his research exploring the human microbiome using supercomputers and gene sequencers. He began by researching astrophysics but has recently applied those methods to study the microbes within the human body. Through deep genome sequencing of his own stool samples over time and large-scale computational analysis, he was able to map changes in his gut microbiome that provided insights into an undiagnosed autoimmune disease. His research demonstrates how quantitative analysis of the microbiome using advanced technologies can lead to new understandings of health and disease.
Using Supercomputers and Gene Sequencers to Discover Your Inner MicrobiomeLarry Smarr
This keynote talk discusses research using supercomputers and gene sequencing to study the human microbiome. The human microbiome contains 100 trillion microorganisms and their genes outnumber human genes 300 to 1. The speaker has been collecting data from his own body over 7 years to study his microbiome and immune system interactions. Collaborating researchers have sequenced his gut microbiome over time as well as samples from autoimmune disease patients. Supercomputers are needed to analyze the massive amount of sequencing data and reveal details of microbial ecology and genetics in health and disease. Studying the human microbiome will revolutionize medicine in the next decade.
From Me To We: Discovering the Trillions of Microorganisms That are a Part of UsLarry Smarr
The document summarizes a lecture about the human microbiome and its importance in health and disease. It discusses how sequencing DNA has revealed that the human body hosts trillions of microorganisms and that 99% of our genes are microbial. Understanding the microbiome is crucial for medicine as shifts in the microbial ecology can be linked to various diseases. The lecturer discusses his own efforts to track biomarkers and microbiome data over time, revealing how perturbations correlated with disease symptoms and weight changes. Precision approaches analyzing large cohorts will be needed to unravel microbiome dynamics in health and illness.
How Quantified Self Enables Precision MedicineLarry Smarr
This document summarizes Dr. Larry Smarr's talk on how self-quantification has enabled precision medicine for him. It discusses how he has tracked over a trillion data points about himself over 15 years, including biomarkers, genomes, and microbiomes. Analysis of his chronic inflammation led to discovery of inflammatory bowel disease. Pre-surgical planning using his MRI and virtual reality helped guide his successful colon resection surgery. Post-surgery, his inflammation and microbiome returned to normal ranges. His data emphasizes the potential for precision medicine through long-term self-tracking.
Similar to Will the Quantified Self Movement Disrupt Healthcare? (20)
My Remembrances of Mike Norman Over The Last 45 YearsLarry Smarr
Mike Norman has been a leader in computational astrophysics for over 45 years. Some of his influential work includes:
- Cosmic jet simulations in the early 1980s which helped explain phenomena from galactic centers.
- Pioneering the use of adaptive mesh refinement in the 1990s to achieve dynamic load balancing on supercomputers.
- Massive cosmology simulations in the late 2000s with over 100 trillion particles using thousands of processors across multiple supercomputing sites, producing petabytes of data.
- Developing end-to-end workflows in the 2000s to couple supercomputers, high-speed networks, and large visualization systems to enable real-time analysis of extremely large astrophysics simulations.
Metagenics How Do I Quantify My Body and Try to Improve its Health? June 18 2019Larry Smarr
Larry Smarr discusses quantifying his body and health over time through extensive self-tracking. He measures various biomarkers through regular blood tests and analyzes his gut microbiome by sequencing stool samples. This revealed issues like chronic inflammation and an unhealthy microbiome. Smarr then took steps like a restricted eating window and increasing plant diversity in his diet, which reversed metabolic syndrome issues and correlated with shifts in his microbiome ecology. His goal is to continue precisely measuring factors like toxins, hormones, gut permeability and food/supplement impacts to further optimize his health.
Panel: Reaching More Minority Serving InstitutionsLarry Smarr
This document discusses engaging more minority serving institutions (MSIs) in cyberinfrastructure development through regional networks. It provides data showing the importance of MSIs like historically black colleges and universities (HBCUs) in educating underrepresented minority students in STEM fields. Regional networks can help equalize opportunities by assisting MSIs in overcoming barriers to resources through training, networking infrastructure support, and helping institutions obtain necessary staffing and funding. Strategies mentioned include collaborating with MSIs on grants and addressing issues identified in surveys like lack of vision for data use beyond compliance. The goal is to broaden participation in STEAM fields by leveraging the success MSIs have shown in supporting underrepresented students.
Global Network Advancement Group - Next Generation Network-Integrated SystemsLarry Smarr
This document summarizes a presentation on global petascale to exascale workflows for data intensive sciences. It discusses a partnership convened by the GNA-G Data Intensive Sciences Working Group with the mission of meeting challenges faced by data-intensive science programs. Cornerstone concepts that will be demonstrated include integrated network and site resource management, model-driven frameworks for resource orchestration, end-to-end monitoring with machine learning-optimized data transfers, and integrating Qualcomm's GradientGraph with network services to optimize applications and science workflows.
Wireless FasterData and Distributed Open Compute Opportunities and (some) Us...Larry Smarr
This document discusses opportunities for ESnet to support wireless edge computing through developing a strategy around self-guided field laboratories (SGFL). It outlines several potential science use cases that could benefit from wireless and distributed computing capabilities, both in the short term through technologies like 5G, LoRa and Starlink, and longer term through the vision of automated SGFL. The document proposes some initial ideas for deploying and testing wireless edge computing technologies through existing projects to help enable the SGFL vision and further scientific opportunities. It emphasizes that exploring these emerging areas could help drive new science possibilities if done at a reasonable scale.
The Asia Pacific and Korea Research Platforms: An Overview Jeonghoon MoonLarry Smarr
This document provides an overview of Asia Pacific and Korea research platforms. It discusses the Asia Pacific Research Platform working group in APAN, including its objectives to promote HPC ecosystems and engage members. It describes the Asi@Connect project which provides high-capacity internet connectivity for research across Asia-Pacific. It also discusses the Korea Research Platform and efforts to expand it to 25 national research institutes in Korea. New related projects on smart hospitals, agriculture, and environment are mentioned. The conclusion discusses enhancing APAN and the Korea Research Platform and expanding into new areas like disaster and AI education.
Panel: Reaching More Minority Serving InstitutionsLarry Smarr
This document discusses engaging more minority serving institutions (MSIs) in the National Research Platform (NRP). It provides data showing that MSIs serve a disproportionate number of underrepresented minority students and are important producers of STEM graduates from these groups. The NRP can help broaden participation in STEAM fields by providing MSIs access to advanced cyberinfrastructure resources, new learning modalities, and opportunities for collaborative research between MSIs and other institutions. Regional networks also have a role to play in helping MSIs overcome barriers and attracting them to collaborative grants. The goal is to tear down walls between research and teaching and reinvent the university experience for more inclusive learning and innovation.
Panel: The Global Research Platform: An OverviewLarry Smarr
The document provides an overview of the Global Research Platform (GRP), an international collaborative partnership creating a distributed environment for data-intensive global science. The GRP facilitates high-performance data gathering, analytics, transport up to terabits per second, computing, and storage to support large-scale global science cyberinfrastructure ecosystems. It aims to orchestrate research across multiple domains using international testbeds for investigating new technologies related to data-intensive science. Examples of instruments generating exabytes of data that would benefit include the Korea Superconducting Tokamak, the High Luminosity LHC, genomics, the SKA radio telescope, and the Vera Rubin Observatory.
Panel: Future Wireless Extensions of Regional Optical NetworksLarry Smarr
CENIC is a non-profit organization that operates an 8,000+ mile fiber optic network connecting over 12,000 sites across California, including K-12 schools, universities, libraries, and research organizations. It has over 750 private sector partners and contributes over $100 million annually to the California economy. CENIC's network enables research and education collaborations, innovation, and economic growth statewide. It also operates a wireless research network called PRP that connects wireless sensors to supercomputers, supporting applications like wildfire modeling.
Global Research Platform Workshops - Maxine BrownLarry Smarr
The document announces a workshop on global research platforms that will be held virtually in 2021 and in Salt Lake City in 2022, with topics including large-scale science, next-generation platforms, data transport, and international testbeds. It also announces the 4th Global Research Platform Workshop to be held in October 2023 in Limassol, Cyprus co-located with the IEEE eScience 2023 conference.
EPOC and NetSage provide engagement and network monitoring services to support research and education. NetSage collects anonymized network flow data to help understand traffic patterns and troubleshoot performance issues. It provides dashboards and analysis to answer common questions from network engineers and end users. Examples of NetSage deployments and use cases were shown for the CENIC network, including top sources and destinations of traffic, debugging slow flows, and analyzing international traffic patterns by country over time.
The document discusses accelerating science discovery with AI inference-as-a-service. It describes showcases using this approach for high energy physics and gravitational wave experiments. It outlines the vision of the A3D3 institute to unite domain scientists, computer scientists, and engineers to achieve real-time AI and transform science. Examples are provided of using AI inference-as-a-service to accelerate workflows for CMS, ProtoDUNE, LIGO, and other experiments.
Democratizing Science through Cyberinfrastructure - Manish ParasharLarry Smarr
This document summarizes a presentation by Manish Parashar on democratizing science through cyberinfrastructure. The key points are:
1) Broad, fair, and equitable access to advanced cyberinfrastructure is essential for democratizing 21st century science, but there are significant barriers related to knowledge, technical issues, social factors, and balancing capabilities.
2) An advanced cyberinfrastructure ecosystem for all requires integrated portals, access to local and national resources through high-speed networks, diverse allocation modes, embedded expertise networks, and broad training.
3) Realizing this vision will require a scalable federated ecosystem with diverse capabilities and incentives for partnerships to meet growing needs for cyberinfrastructure and
Panel: Building the NRP Ecosystem with the Regional Networks on their Campuses;Larry Smarr
This document summarizes a panel discussion on building the National Research Platform ecosystem with regional networks. The panelists discussed how their regional networks are connecting to and using the Nautilus nodes of the NRP. Examples included using NRP for deep learning and computer vision research at the University of Missouri, challenges of adoption in Nevada and potential solutions, and Georgia Tech's new involvement through the Southern Crossroads regional network. The regional networks see opportunities to expand NRP access and training to enable more researchers in their regions to take advantage of the platform.
Open Force Field: Scavenging pre-emptible CPU hours* in the age of COVID - Je...Larry Smarr
The document discusses Open Force Field (OpenFF), an open-source project that enables rapid development of molecular force fields through automated infrastructure, open data and software, and an open science approach. OpenFF provides access to large quantum chemical datasets, runs quantum chemistry calculations on pre-emptible cloud resources with minimal human intervention, and facilitates easy iteration and testing of new force field hypotheses through an open development model.
Panel: Open Infrastructure for an Open Society: OSG, Commercial Clouds, and B...Larry Smarr
The document discusses open infrastructure for an open society and the role of commercial clouds. It describes how the National Research Platform (NRP), Open Science Grid (OSG), and Open Science Data Federation (OSDF) provide open infrastructure through open source components that anyone can contribute to and use. It then discusses how Southwestern Oklahoma State University leveraged NRP resources on their campus and engaged students and local teachers. Finally, it outlines the pros and cons of commercial clouds, when they may be suitable to use, and how tools like CloudBank and Kubernetes can help facilitate science users' access to cloud resources.
Panel: Open Infrastructure for an Open Society: OSG, Commercial Clouds, and B...Larry Smarr
The document discusses open infrastructure for an open society and the role of commercial clouds. It describes how the National Research Platform (NRP), Open Science Grid (OSG), and Open Science Data Federation (OSDF) provide open infrastructure through open source components that anyone can contribute to and use. It then discusses how Southwestern Oklahoma State University leveraged NRP resources on their campus and engaged students and local teachers. Finally, it outlines the pros and cons of commercial clouds, noting they provide huge capacity and variety but are very expensive for regular use. Facilitating science users on clouds requires services like CloudBank and Kubernetes federation.
Panel: Open Infrastructure for an Open Society: OSG, Commercial Clouds, and B...Larry Smarr
The document discusses open infrastructure for an open society and the role of commercial clouds. It describes how the National Research Platform (NRP), Open Science Grid (OSG), and Open Science Data Federation (OSDF) provide open infrastructure through open source components that anyone can contribute to and use. It then discusses how Southwestern Oklahoma State University leveraged NRP resources on their campus and engaged students and local teachers. Finally, it outlines the pros and cons of commercial clouds, noting they provide huge capacity and variety but are very expensive for regular use. Facilitating science users on clouds requires tools for account management, documentation, and integrating cloud resources through HTCondor and Kubernetes.
Frank Würthwein - NRP and the Path forwardLarry Smarr
NRP will replace PRP and aims to democratize access to national research cyberinfrastructure. The long term vision is to create an open national cyberinfrastructure by federating resources across research institutions. Key innovations include an innovative network fabric, application libraries for FPGAs, a "bring your own resource" model, and innovative scheduling and data infrastructure. The NSF has funded the Prototype National Research Platform project to support NRP for the next 5 years. NRP aims to grow resources, introduce new capabilities, and be driven by the research community.
Health Tech Market Intelligence Prelim Questions -Gokul Rangarajan
The Ultimate Guide to Setting up Market Research in Health Tech part -1
How to effectively start market research in the health tech industry by defining objectives, crafting problem statements, selecting methods, identifying data collection sources, and setting clear timelines. This guide covers all the preliminary steps needed to lay a strong foundation for your research.
This lays foundation of scoping research project what are the
Before embarking on a research project, especially one aimed at scoping and defining parameters like the one described for health tech IT, several crucial considerations should be addressed. Here’s a comprehensive guide covering key aspects to ensure a well-structured and successful research initiative:
1. Define Research Objectives and Scope
Clear Objectives: Define specific goals such as understanding market needs, identifying new opportunities, assessing risks, or refining pricing strategies.
Scope Definition: Clearly outline the boundaries of the research in terms of geographical focus, target demographics (e.g., age, socio-economic status), and industry sectors (e.g., healthcare IT).
3. Review Existing Literature and Resources
Literature Review: Conduct a thorough review of existing research, market reports, and relevant literature to build foundational knowledge.
Gap Analysis: Identify gaps in existing knowledge or areas where further exploration is needed.
4. Select Research Methodology and Tools
Methodological Approach: Choose appropriate research methods such as surveys, interviews, focus groups, or data analytics.
Tools and Resources: Select tools like Google Forms for surveys, analytics platforms (e.g., SimilarWeb, Statista), and expert consultations.
5. Ethical Considerations and Compliance
Ethical Approval: Ensure compliance with ethical guidelines for research involving human subjects.
Data Privacy: Implement measures to protect participant confidentiality and adhere to data protection regulations (e.g., GDPR, HIPAA).
6. Budget and Resource Allocation
Resource Planning: Allocate resources including time, budget, and personnel required for each phase of the research.
Contingency Planning: Anticipate and plan for unforeseen challenges or adjustments to the research plan.
7. Develop Research Instruments
Survey Design: Create well-structured surveys using tools like Google Forms to gather quantitative data.
Interview and Focus Group Guides: Prepare detailed scripts and discussion points for qualitative data collection.
8. Sampling Strategy
Sampling Design: Define the sampling frame, size, and method (e.g., random sampling, stratified sampling) to ensure representation of target demographics.
Participant Recruitment: Plan recruitment strategies to reach and engage the intended participant groups effectively.
9. Data Collection and Analysis Plan
Data Collection: Implement methods for data gathering, ensuring consistency and validity.
Analysis Techniques: Decide on analytical approaches (e.g., statistical
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Mental Health and well-being Presentation. Exploring innovative approaches and strategies for enhancing mental well-being. Discover cutting-edge research, effective strategies, and practical methods for fostering mental well-being.
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TEST BANK FOR Health Assessment in Nursing 7th Edition by Weber Chapters 1 - 34.
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NURSING MANAGEMENT OF PATIENT WITH EMPHYSEMA .PPTblessyjannu21
Prepared by Prof. BLESSY THOMAS, VICE PRINCIPAL, FNCON, SPN.
Emphysema is a disease condition of respiratory system.
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CHAPTER 1 SEMESTER V COMMUNICATION TECHNIQUES FOR CHILDREN.pdfSachin Sharma
Here are some key objectives of communication with children:
Build Trust and Security:
Establish a safe and supportive environment where children feel comfortable expressing themselves.
Encourage Expression:
Enable children to articulate their thoughts, feelings, and experiences.
Promote Emotional Understanding:
Help children identify and understand their own emotions and the emotions of others.
Enhance Listening Skills:
Develop children’s ability to listen attentively and respond appropriately.
Foster Positive Relationships:
Strengthen the bond between children and caregivers, peers, and other adults.
Support Learning and Development:
Aid cognitive and language development through engaging and meaningful conversations.
Teach Social Skills:
Encourage polite, respectful, and empathetic interactions with others.
Resolve Conflicts:
Provide tools and guidance for children to handle disagreements constructively.
Encourage Independence:
Support children in making decisions and solving problems on their own.
Provide Reassurance and Comfort:
Offer comfort and understanding during times of distress or uncertainty.
Reinforce Positive Behavior:
Acknowledge and encourage positive actions and behaviors.
Guide and Educate:
Offer clear instructions and explanations to help children understand expectations and learn new concepts.
By focusing on these objectives, communication with children can be both effective and nurturing, supporting their overall growth and well-being.
2024 Media Preferences of Older Adults: Consumer Survey and Marketing Implica...Media Logic
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Will the Quantified Self Movement Disrupt Healthcare?
1. “Will the Quantified-Self Movement
Disrupt Healthcare?”
Invited Talk
Pre-Biotechnology Industry Organization International Convention Symposium
San Diego, CA
June 22, 2014
Dr. Larry Smarr
Director, California Institute for Telecommunications and Information
Technology
Harry E. Gruber Professor,
Dept. of Computer Science and Engineering
Jacobs School of Engineering, UCSD
1
2. Consumer Self Measurement is Exploding
Totally Outside of the Medical Complex
From the First San Francisco QS Meetup in 2008
To 116 Cities in 37 Countries in Four Years
Quantified Self Public Health Symposium Held
In Calit2’s Qualcomm Institute April 2014
3. I Used a Variety of Emerging Personal Sensors
To Quantify My Body & Drive Behavioral Change
Withings/iPhone-
Blood Pressure
Zeo-Sleep
Azumio-Heart Rate
MyFitnessPal-
Calories Ingested
FitBit -
Daily Steps &
Calories Burned
Withings WiFi Scale -
Daily Weight
4. The Self-Monitoring Business
Has Reached Market Takeoff
• MyFitnessPal
– 40 Million Users
– Aug 2013 Raised $18M Series A, Led by Kleiner Perkins
• Fitbit
– Has Raised ~$70M
• BodyMedia Was Bought by Jawbone
– For ~$100M
• Zeo Sleep Monitor
– Closed Down in 2013
More Mergers Likely as the Shakeout Continues
5. Calit2 is Creating a Network of Innovators
in Personal Health Data
$1.9M Grant From the RWJF
6. The Emergence of P4 Medicine --
Predictive, Preventive, Personalized, Participatory
Systems Biology &
Systems Medicine
Consumer-Driven
Social Networks
P4
MEDICINE
Digital Revolution
Big Data
Source: Lee Hood, ISB
How Will the Quantified Consumer
Be Integrated into Healthcare Systems?
7. Early Adopting MDs Are Creating Partnerships
with Their Quantified Patients
• “The 100 participants will be guided on this 9-month
journey by a coach and when necessary,
be referred to their own health care practitioners.”
• The data sets that will be evaluated include:
– Self-Tracking Devices
– Medical History, Traits, Lifestyle
– Blood, Urine, Saliva
– Gut Microbiome
– Whole Genome Sequencing
There are 8760 Hours in a Year
One of These Hours You Are With a Doctor…
The Other 8759 Hours Are Up to You!
https://pioneer100.systemsbiology.net/
Will Grow to 1000, then 10,000
8. From One to One Billion Data Points Defining Me:
Big Data Coming to the Electronic Medical Record (EMR)
Billion: My Full DNA,
MRI/CT Images
Million: My DNA SNPs,
Zeo, FitBit
Hundred: My Blood VariablesOne:
My WeightWeight
Blood
Variables
SNPs
Human & Microbial Genome
Today’s EMR
Tomorrow’s EMR
9. Visualizing 5-10 Year Time Series of 150 Blood & Stool
Variables Led Me to Discover a Chronic Disease
Calit2 64 megapixel VROOM
11. Healthcare Must Include a Vast Amount
of Microbial Information That is Not in Today’s Medicine
Inclusion of the Microbiome
Will Radically Change Medicine
99% of Your
DNA Genes
Are in Microbe Cells
Not Human Cells
Your Body Has 10 Times
As Many Microbe Cells As Human Cells
12. We Compared Human Gut Microbiomes
With My Time Series
5 Ileal Crohn’s Patients,
3 Points in Time
2 Ulcerative Colitis Patients,
6 Points in Time
“Healthy” Individuals
From Sequences to Bacterial Species Relative Abundance
Required 25 CPU-Years at San Diego Supercomputer Center
Source: Jerry Sheehan, Calit2
Weizhong Li, Sitao Wu, CRBS, UCSD
Total of 27 Billion Reads
Or 2.7 Trillion Bases
IBD Patients
250 Subjects
1 Point in Time
Larry Smarr
6 Points in Time
13. Using Supercomputing Allows Comparison of
the Relative Abundance of 200 Gut Microbe Species
Calit2 VROOM-FuturePatient Expedition
Comparing 3 LS Time Snapshots (Left)
with Healthy, Crohn’s, UC (Right Top to Bottom)
14. We Found Major Shifts in Microbial Ecology
Between Healthy & Two Forms of Inflammatory Bowel Disease
Collapse of
Bacteroidetes
Explosion of
Proteobacteria On the IBD Spectrum
15. Inexpensive Consumer Time Series of Microbiome
Now Possible Through Ubiome
Data source: LS (Yellow Lines Stool Samples);
Sequencing and Analysis Ubiome
16. From a War Metaphor
to Gardening
“I would like to lose the language of warfare,”
said Julie Segre, a senior investigator at
the National Human Genome Research Institute.
”It does a disservice to all the bacteria
that have co-evolved with us
and are maintaining the health of our bodies.”
Will Medicinal Foods Provide New Tools
for Altering Gut Microbiome?
17. The Disruption of Consumer Health Data Gathering
Is Growing Rapidly
Blood Variable Time Series Stool Variable Time Series
MicrobiomeTime SeriesHuman Genetic Variations
18. Deep Learning Will Provide
Personalized Assistants to Coach Us to Wellness
Where Medicine Coaching is Now
Where Wellness Coaching is Going
IBM is Spending
$1 Billion on Watson
19. The Looming Disruption
In Healthcare
• Citizens Create Vast Datasets Outside of EMRs
• Post-“Watson” Personalized Coaches
• Doctors Must Partner with Super-Informed Patients
• From Pharmaceuticals to Medicinal Foods
• From Treating Sickness to Maintaining Wellness
20. Thanks to Our Great Team!
UCSD Metagenomics Team
Weizhong Li
Sitao Wu
Calit2@UCSD
Future Patient Team
Jerry Sheehan
Tom DeFanti
Kevin Patrick
Jurgen Schulze
Andrew Prudhomme
Philip Weber
Fred Raab
Joe Keefe
Ernesto Ramirez
JCVI Team
Karen Nelson
Shibu Yooseph
Manolito Torralba
SDSC Team
Michael Norman
Mahidhar Tatineni
Robert Sinkovits
UCSD Health Sciences Team
William J. Sandborn
Elisabeth Evans
John Chang
Brigid Boland
David Brenner