From Quantified Self to Personalized Medicine

By Tiffany Trader

November 6, 2014

The University of Washington Computer Science and Engineering Distinguished Lecture series recently welcomed Calit2 luminary Larry Smarr to speak on a very interesting topic, bringing wellness into the digital age.

Smarr is the founding Director of the California Institute for Telecommunications and Information Technology (Calit2), a UC San Diego/UC Irvine partnership. Smarr was also the founding Director of the National Center for Supercomputing Applications (NCSA), a position and center he helped create with a 1983 proposal to the National Science Foundation. At Calit2, Smarr has continued to drive major developments in supercomputing, networking, and Web technologies.

During his recent talk, “Quantifying The Dynamics of Your Superorganism Body Using Big Data Supercomputing,” Smarr discusses the development of a new approach to living things, one that he believes is on track to transform medicine and potentially health care. The idea extends back to a 2001 experiment to “put your body online.”

Smarr Putting You Online slide

 

Smarr:

“With the development of the miniaturization of sensors, you would be able to read out in real-time your body just as the whole automobile industry had been transformed in the previous decades from knowing you had a problem when the smoke came out of the hood, to a situation where there were more computers in the 90s sold into the automobile industry than into personal computers.

“These instruments just measure things, for no good reason, that’s the important thing, measure and get the data. Then when you go in preventively they compare the data across national networks, and if you are in the middle of the bell curve, that’s fine. If not, there’s an algorithm that tells you what to do.”

But we don’t do this for our bodies.

Smarr asked, why not take an engineer’s approach to the body so that the subsystems work well?

There is data associated with nutrition, exercise, sleep and stress.

What began as an experiment of one has grown into a much larger wellness project, being conducted by the Institute for Systems Biology. Smarr is one of the “Healthy 100 Pioneers” in a nine-month study focused on P4 Medicine, i.e., predictive, personalized, preventive, and participatory. If successful, the project will expand to 1,000 and eventually 10,000 people.

The data sets that will be evaluated in the Pioneer 100 wellness project include self-tracking devices, medical history and lifestyle, food journals, blood, urine and saliva testing, gut microbiome, and whole genome sequencing.

There is real value in data that can clue you in on disease states, as Smarr knows better than most. By keeping careful watch on his health data, Smarr discovered that he had immune system dysfunction and gut microbes that were associated with Crohn’s disease. In the end, a process that began with tracking his weight turned into a quest to quantify his specific brand of autoimmune disorder.

To add deeper understanding to the Wellness Project, Smarr is also exploring the variation in microbiome ecology across healthy and ill populations. This is where big data meets big compute. Smarr’s team has already used 25 CPU years on SDSC’s Gordon supercomputer and another 35,000 cores on Dell’s Sanger cluster. They’re looking for another 1 or 2 million CPU hours to round out the experiment. The project is now set to move data from R Systems/Dell in Urbana Champaign, Illinois, to Calit2 at UCSD on a dedicated 10 gigabit link.

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