The Era of Personalized Medicine: An Interview with Peter Coveney

By Wolfgang Gentzsch and Sverre Jarp

September 3, 2015

What opportunities and challenges come with personalized medicine? What amount of computing is necessary to get meaningful results? Are we able to handle substantial quantities of patient data and to use them to perform predictive, mechanistic modelling and simulation? Based on this, will we be able to deliver therapies and to enhance clinical decision making. Can we guaranty secure access to personal data, as well as to powerful computational resources? Answers to these and other critical questions are discussed in this interview with Professor Peter Coveney who holds a Chair in Physical Chemistry and is Director of the Centre for Computational Science (CCS), an Honorary Professor in Computer Science and a member of CoMPLEX at University College London (UCL). He is also Professor Adjunct within the Medical School at Yale University. Prof. Coveney led the Network of Excellence within the EU FP7 Virtual Physiological Human initiative, which will form part of his keynote lecture on “The Virtual Human: In Silico Methods for Personalized Medicine” at the ISC Cloud & Big Data Conference September 28 – 30 in Frankfurt, Germany.

Peter, thanks for making time for this interview. Please tell us a bit more about one of your major research projects, the Virtual Physiological Human.

Peter Coveney: The Virtual Physiological Human (VPH) is a methodological and technological framework that enables the collaborative investigation of the human body as a single complex system. The collective framework makes it possible to share resources and observations formed by institutions and organisations creating disparate but integrated computer models of the mechanical, physical and biochemical functions of a living human body. As an EU funded initiative, VPH was at its height during Framework Programme 7 (2007-2014), but the agenda is so wide ranging and ambitious that it is something that needs to be pursued throughout the entirety of the twenty-first century.

Can you highlight the great opportunities this research will present over time for us humans?

Coveney: It enables collaborative investigation of the human body across all relevant scales and introduces multiscale methodologies into medical and clinical research, in order to allow greater personalisation of medical treatments. Best summarised by John C. Lechleiter, Ph.D., President and Chief Executive Officer, Eli Lilly and Company: “The power in tailored therapeutics is for us to say more clearly to payers, providers, and patients, — ‘this drug is not for everyone, but it is for you’ — that is exceedingly powerful.”

And what are the major challenges you and your team are currently facing, and which additional challenges do you see arising in a few years?

Coveney: There is the need for rapid development of computational science and informatics capabilities to deal with management and analysis of data. Major challenges relate to the acquisition and storage of personal medical data, and accessing security HPC facilities to process the data.

Where do you anticipate resistance from the general public and the politicians?

Peter Coveney: The sharing and use of personal medical data and the potential efficacy of treatments selected by computer.

Can you give us an example of the amount of computing and data analysis necessary to make this project a success?

Coveney: For an instance of patient specific drug treatment, as applied to a single individual, we would require of the order of 200,000 core hours with 5 terabytes of data being generated and analysed in the process of ranking the drugs concerned. This is of course in addition to all the data and processing needed to obtain the genomic data originally (again this would amount to terabytes of data and many tens of thousands core hours with current so-called “next generation sequencing” technologies). Needless to say, the answer is a moving target inasmuch as both compute and sequencing technologies are perpetually evolving and are likely to reduce dramatically over the next 5-10 year period.

This interview with Professor Peter Coveney has been conducted by Wolfgang Gentzsch and Sverre Jarp, the co-chairs of the ISC Cloud & Big Data Conference, taking place this year in Frankfurt, September 28 – 30. Prof. Coveney will explore these topics in greater detail during his keynote presentation.

Subscribe to HPCwire's Weekly Update!

Be the most informed person in the room! Stay ahead of the tech trends with industy updates delivered to you every week!

With New Owner and New Roadmap, an Independent Omni-Path Is Staging a Comeback

July 23, 2021

Put on a shelf by Intel in 2019, Omni-Path faced a uncertain future, but under new custodian Cornelis Networks, OmniPath is looking to make a comeback as an independent high-performance interconnect solution. A "significant refresh" – called Omni-Path Express – is coming later this year according to the company. Cornelis Networks formed last September as a spinout of Intel's Omni-Path division. Read more…

PEARC21 Panel Reviews Eight New NSF-Funded HPC Systems Debuting in 2021

July 23, 2021

Over the past few years, the NSF has funded a number of HPC systems to further supply the open research community with computational resources to meet that community’s changing and expanding needs. A review of these systems at the PEARC21 conference (July 19-22) highlighted... Read more…

Chameleon’s HPC Testbed Sharpens Its Edge, Presses ‘Replay’

July 22, 2021

“One way of saying what I do for a living is to say that I develop scientific instruments,” said Kate Keahey, a senior fellow at the University of Chicago and a computer scientist at Argonne National Laboratory, as s Read more…

PEARC21 Plenary Session: AI for Innovative Social Work

July 21, 2021

AI analysis of social media poses a double-edged sword for social work and addressing the needs of at-risk youths, said Desmond Upton Patton, senior associate dean, Innovation and Academic Affairs, Columbia University. S Read more…

Summer Reading: “High-Performance Computing Is at an Inflection Point”

July 21, 2021

At last month’s 11th International Symposium on Highly Efficient Accelerators and Reconfigurable Technologies (HEART), a group of researchers led by Martin Schulz of the Leibniz Supercomputing Center (Munich) presented a “position paper” in which they argue HPC architectural landscape... Read more…

AWS Solution Channel

Accelerate innovation in healthcare and life sciences with AWS HPC

With Amazon Web Services, researchers can access purpose-built HPC tools and services along with scientific and technical expertise to accelerate the pace of discovery. Whether you are sequencing the human genome, using AI/ML for disease detection or running molecular dynamics simulations to develop lifesaving drugs, AWS has the infrastructure you need to run your HPC workloads. Read more…

PEARC21 Panel: Wafer-Scale-Engine Technology Accelerates Machine Learning, HPC

July 21, 2021

Early use of Cerebras’ CS-1 server and wafer-scale engine (WSE) has demonstrated promising acceleration of machine-learning algorithms, according to participants in the Scientific Research Enabled by CS-1 Systems panel Read more…

With New Owner and New Roadmap, an Independent Omni-Path Is Staging a Comeback

July 23, 2021

Put on a shelf by Intel in 2019, Omni-Path faced a uncertain future, but under new custodian Cornelis Networks, OmniPath is looking to make a comeback as an independent high-performance interconnect solution. A "significant refresh" – called Omni-Path Express – is coming later this year according to the company. Cornelis Networks formed last September as a spinout of Intel's Omni-Path division. Read more…

Chameleon’s HPC Testbed Sharpens Its Edge, Presses ‘Replay’

July 22, 2021

“One way of saying what I do for a living is to say that I develop scientific instruments,” said Kate Keahey, a senior fellow at the University of Chicago a Read more…

Summer Reading: “High-Performance Computing Is at an Inflection Point”

July 21, 2021

At last month’s 11th International Symposium on Highly Efficient Accelerators and Reconfigurable Technologies (HEART), a group of researchers led by Martin Schulz of the Leibniz Supercomputing Center (Munich) presented a “position paper” in which they argue HPC architectural landscape... Read more…

PEARC21 Panel: Wafer-Scale-Engine Technology Accelerates Machine Learning, HPC

July 21, 2021

Early use of Cerebras’ CS-1 server and wafer-scale engine (WSE) has demonstrated promising acceleration of machine-learning algorithms, according to participa Read more…

15 Years Later, the Green500 Continues Its Push for Energy Efficiency as a First-Order Concern in HPC

July 15, 2021

The Green500 list, which ranks the most energy-efficient supercomputers in the world, has virtually always faced an uphill battle. As Wu Feng – custodian of the Green500 list and an associate professor at Virginia Tech – tells it, “noone" cared about energy efficiency in the early 2000s, when the seeds... Read more…

Frontier to Meet 20MW Exascale Power Target Set by DARPA in 2008

July 14, 2021

After more than a decade of planning, the United States’ first exascale computer, Frontier, is set to arrive at Oak Ridge National Laboratory (ORNL) later this year. Crossing this “1,000x” horizon required overcoming four major challenges: power demand, reliability, extreme parallelism and data movement. Read more…

Quantum Roundup: IBM, Rigetti, Phasecraft, Oxford QC, China, and More

July 13, 2021

IBM yesterday announced a proof for a quantum ML algorithm. A week ago, it unveiled a new topology for its quantum processors. Last Friday, the Technical Univer Read more…

ExaWind Prepares for New Architectures, Bigger Simulations

July 10, 2021

The ExaWind project describes itself in terms of terms like wake formation, turbine-turbine interaction and blade-boundary-layer dynamics, but the pitch to the Read more…

AMD Chipmaker TSMC to Use AMD Chips for Chipmaking

May 8, 2021

TSMC has tapped AMD to support its major manufacturing and R&D workloads. AMD will provide its Epyc Rome 7702P CPUs – with 64 cores operating at a base cl Read more…

Intel Launches 10nm ‘Ice Lake’ Datacenter CPU with Up to 40 Cores

April 6, 2021

The wait is over. Today Intel officially launched its 10nm datacenter CPU, the third-generation Intel Xeon Scalable processor, codenamed Ice Lake. With up to 40 Read more…

Berkeley Lab Debuts Perlmutter, World’s Fastest AI Supercomputer

May 27, 2021

A ribbon-cutting ceremony held virtually at Berkeley Lab's National Energy Research Scientific Computing Center (NERSC) today marked the official launch of Perlmutter – aka NERSC-9 – the GPU-accelerated supercomputer built by HPE in partnership with Nvidia and AMD. Read more…

Ahead of ‘Dojo,’ Tesla Reveals Its Massive Precursor Supercomputer

June 22, 2021

In spring 2019, Tesla made cryptic reference to a project called Dojo, a “super-powerful training computer” for video data processing. Then, in summer 2020, Tesla CEO Elon Musk tweeted: “Tesla is developing a [neural network] training computer called Dojo to process truly vast amounts of video data. It’s a beast! … A truly useful exaflop at de facto FP32.” Read more…

Google Launches TPU v4 AI Chips

May 20, 2021

Google CEO Sundar Pichai spoke for only one minute and 42 seconds about the company’s latest TPU v4 Tensor Processing Units during his keynote at the Google I Read more…

CentOS Replacement Rocky Linux Is Now in GA and Under Independent Control

June 21, 2021

The Rocky Enterprise Software Foundation (RESF) is announcing the general availability of Rocky Linux, release 8.4, designed as a drop-in replacement for the soon-to-be discontinued CentOS. The GA release is launching six-and-a-half months after Red Hat deprecated its support for the widely popular, free CentOS server operating system. The Rocky Linux development effort... Read more…

CERN Is Betting Big on Exascale

April 1, 2021

The European Organization for Nuclear Research (CERN) involves 23 countries, 15,000 researchers, billions of dollars a year, and the biggest machine in the worl Read more…

Iran Gains HPC Capabilities with Launch of ‘Simorgh’ Supercomputer

May 18, 2021

Iran is said to be developing domestic supercomputing technology to advance the processing of scientific, economic, political and military data, and to strengthen the nation’s position in the age of AI and big data. On Sunday, Iran unveiled the Simorgh supercomputer, which will deliver.... Read more…

Leading Solution Providers

Contributors

HPE Launches Storage Line Loaded with IBM’s Spectrum Scale File System

April 6, 2021

HPE today launched a new family of storage solutions bundled with IBM’s Spectrum Scale Erasure Code Edition parallel file system (description below) and featu Read more…

Julia Update: Adoption Keeps Climbing; Is It a Python Challenger?

January 13, 2021

The rapid adoption of Julia, the open source, high level programing language with roots at MIT, shows no sign of slowing according to data from Julialang.org. I Read more…

10nm, 7nm, 5nm…. Should the Chip Nanometer Metric Be Replaced?

June 1, 2020

The biggest cool factor in server chips is the nanometer. AMD beating Intel to a CPU built on a 7nm process node* – with 5nm and 3nm on the way – has been i Read more…

GTC21: Nvidia Launches cuQuantum; Dips a Toe in Quantum Computing

April 13, 2021

Yesterday Nvidia officially dipped a toe into quantum computing with the launch of cuQuantum SDK, a development platform for simulating quantum circuits on GPU-accelerated systems. As Nvidia CEO Jensen Huang emphasized in his keynote, Nvidia doesn’t plan to build... Read more…

Microsoft to Provide World’s Most Powerful Weather & Climate Supercomputer for UK’s Met Office

April 22, 2021

More than 14 months ago, the UK government announced plans to invest £1.2 billion ($1.56 billion) into weather and climate supercomputing, including procuremen Read more…

Q&A with Jim Keller, CTO of Tenstorrent, and an HPCwire Person to Watch in 2021

April 22, 2021

As part of our HPCwire Person to Watch series, we are happy to present our interview with Jim Keller, president and chief technology officer of Tenstorrent. One of the top chip architects of our time, Keller has had an impactful career. Read more…

Quantum Roundup: IBM, Rigetti, Phasecraft, Oxford QC, China, and More

July 13, 2021

IBM yesterday announced a proof for a quantum ML algorithm. A week ago, it unveiled a new topology for its quantum processors. Last Friday, the Technical Univer Read more…

Senate Debate on Bill to Remake NSF – the Endless Frontier Act – Begins

May 18, 2021

The U.S. Senate today opened floor debate on the Endless Frontier Act which seeks to remake and expand the National Science Foundation by creating a technology Read more…

  • arrow
  • Click Here for More Headlines
  • arrow
HPCwire