HPC in healthcare

Application of HPC in Healthcare Industry

1
Confidential

HPC is being used to quickly diagnose Cancer (1/2)

Pathwork Diagnostics uses cloud-based HPC to diagnose Cancer

•Of the 1.4 million new cancer cases that occur each year in the United States, 90% are
diagnosed rapidly; however, the remaining 10% are difficult to identify using the best
traditional means. This is because cancer tumors may have mutated and/or spread to
Pathwork Diagnostics Genomic Testing For Cancer
multiple regions in the body, making the origin, and thus the type of tumor (e.g., lung,
pancreatic, skin, etc.) unknown

Why does this matter ?

According to recent studies, a patient’s response to treatment is significantly better
when the tumor’s origin is known and patients can receive tumor-specific therapies

•To address this crucial 10% of new cases, Pathwork Diagnostics has created its Tissue
of Origin Laboratory Developed Test (LDT).
•This unique application uses microarray technology to identify the unknown tumor by
genomically comparing it to the DNA profiles of known tumors.
•Once the sample has been analyzed, the physician receives a report with the profile Source: Pathwork Diagnostics

and recommended treatment.

Source: Forrester

HPC is being used to quickly diagnose Cancer (2/2)

Pathwork Diagnostics uses cloud-based HPC to diagnose Cancer

Specifically, it takes large amounts of loosely coupled compute resources to develop a model to analyze the
data and generate a result. The larger the compute capacity, the faster this product can be built; on the
Is a classic high- flipside, the more resources, the higher the cost to achieve the result. If you are a large research university or
performance government agency that can spread this investment across multiple HPC projects or can justify the
investment against one large project with a significant compute demand, you might be able to make the
computing (HPC)
upfront investment necessary to drive fast results. But for Pathwork, a small biotech firm without access to
problem this type of capital, and without a clear picture of the demand or volume of analyses needed by the medical
community, another answer was necessary

…Under the above constraints, Pathwork would have needed years to develop this model with its Would take years to
current resources, preventing cancer patients from getting much-needed answers now. To meet complete with
the market needs that it forecasts, Pathwork would need the compute capacity to develop this
model in two to three months. Once the model has been developed, the company could then
traditional HPC
analyze hundreds of samples per day. models…

With the capital to access compute resources of this magnitude out of reach, Pathwork turned to
…but can be done infrastructure-as-a-service (IaaS) cloud computing, where it could leverage on-demand access to this
on time and volume of resources but keep its operating costs low by not having to pay for these resources (not to
cheaper with the mention the power, data center facility, and ongoing operating costs) when they’re not in use. Pathwork
not only met its time-to-market objective, but the company said that the cost-avoidance of this model has
cloud already saved Pathwork an estimated $160,000.

Source: Forrester

Bringing the power of HPC to Drug Discovery (1/2)

GNS Healthcare is using the power of HPC to accelerate drug discovery and treatment development process

•In medieval times, leeches were used to “cure” arthritis and a number of other ailments. Today, while these rather repulsive little creatures are making a medical
comeback of sorts, most people would rather treat creaky joints with less Draconian methods. Fortunately, there are companies like GNS Healthcare engaged in
research to find new drug therapies to treat arthritis and many other common ailments.

Challenges
The National Institute of Health estimates that 20-30 percent of patients do •Accelerate the drug discovery and treatment development process
not respond sufficiently to a given anti-TNF drug. Developing effective drugs •Find relief for disease sufferers that are not helped by standard
that will benefit this population is a major research opportunity therapies
•Match the right treatment(s) to the right patient
Colin Hill, CEO and president of GNS
•Help meet the increasingly complex health needs of an aging
population.
•Deal with overwhelming amounts of data derived from the clinical
studies, such as the Cancer Genome Atlas Project and DNA testing

Reverse Engineering/Forward Simulation (REFS)
Approach

•Apply the power of in-house and commercially available HPC resources to reverse-engineer data-
driven models of human disease progression and drug response
•Simulate these models to discover novel drug targets that can be used by GNS partners to
develop new drug programs for patients suffering from diseases such as cancer, diabetes and
rheumatoid arthritis.
•Automate aspects of the scientific method from the creation of hypotheses through the stages of
testing and validation

Source: Council on Competitiveness High Performance Computing

Bringing the power of HPC to Drug Discovery (2/2)

GNS Healthcare is using the power of HPC to accelerate drug discovery and treatment development process

•As recently as eight years ago, the application of high performance computing (HPC) techniques to drug discovery efforts was problematic at best. Using the best
artificial intelligence platforms available at the time, even clusters composed of 40 or 50 processors could take up to 12 months to run through the DNA sequence
data and corresponding gene expression and clinical response data needed to identify the important genes in a tumor when compared to normal tissue. Today, due to
advances in supercomputing and software platforms from companies like GNS with its REFS computational environment, Wolfram Research with Mathematica, and
The MathWorks with MATLAB, results of this type can now be achieved in weeks—and, Hill adds, “much more comprehensively.”

REFS (Reverse Engineering/Forward Simulation) Data Driven Process

The REFS process begins with the creation of model building blocks, proceeds through the construction of an ensemble of models from the building
blocks, and results in the simulation of the ensemble of models to extract quantitative outcome predictions accompanied by confidence levels

Improving Healthcare Delivery through HPC (1/6)

Ohio Supercomputer Center (OSC) applies advanced computer technology for pioneering healthcare delivery

1 IMPROVING THE EPIDURAL

• The epidural is a common anesthetic for childbirth, back and hip surgeries. Epidural Anesthesiology
But in inexperienced hands it poses serious risks. Residents traditionally
laern the delicate procedure on live patients. time-consuming and costly,
multiple human trials, always in the presence of a supervising doctor are
required.

• Residents at the Ohio University College of Medicine and three other
university medical centers soon will be learning to administer epidural blocks
through virtual simulation techniques developed at the OSC-honing their skill
on supercomputers before attempting to work on patients.

• Three-dimensional graphics and force-reflecting "Cyberglove", which
realistically simulate appropriate patient anatomy and provide instant
feedback of errors, have been tested and approved for this purpose by
anesthesiology experts. This research is funded by the US Air force Source: Coalition of Academic Supercomputing Centers (CASC)



2 REMOTE MEDICAL TRIAGE

• Being able to provide sophisticated medical services to remote geographic
areas is an unanticipated benefit of high speed computer networking.
University-based supercomputer centers, credited with developing
networking technology, are now pioneers in applying it to health care.

• The Remote Medical Triage project is one example.

• The University of Hawaii, OSC and the Georgetown University Medical
center in Washington, D.C., are testing the feasibility of long distance
radiation treatment planning. Patient data, such as an MRI, is sent by
satellite from a medical site in Hawaii to Ohio for 3-D imaging, then to
Washington for expert consultation and back to Hawaii for treatment. Each
transmission takes only a few seconds.

• The speed of NASA's COMSAT and funds from the Advanced Research
Projects Agency make this project possible

Source: Coalition of Academic Supercomputing Centers (CASC)



3 WHEELCHAIR DESIGN

• Under a grant from the US Department of Education, OSC researchers are
using virtually reality to test the efficiency of various wheelchair designs and
to streamline architectural elements required for compliance with the
Americans With Disabilities Act.

• This research tracks power wheelchair users as they navigate through a
simulated architectural environments. The technique also enables disabled
individuals to gain the dexterity needed to operate power chairs, and allows
health care providers to fine-tune wheelchair operations on the basis of high
accuracy assessment of user proficiency.



University of Colorado School of Medicine Initiative

4 THE VISIBLE HUMAN PROJECT
Cryosection through the head of a human male
• Researchers at the University of Colorado School of Medicine, have been working
with the National Center for Atmospheric Research (NCAR) to create the radiologic
and photographic definition of a male cadaver in three-dimensions, with details as
small as one millimeter resolved clearly

• Funded by the National Library of Medicine, the project provides the most
comprehensive computer image database of human anatomy ever available for
teaching and research.

• It consists of 1,878 full-color CT scans that define the entire human body at every
location in space. But the work is far from done. Funding is being sought to finish
segmenting and classifying this volume data into anatomical objects and to explore
the potential for biomedical research that will open up once this is complete

Discoveries
By studying the data set, researchers at Columbia University found several errors in
anatomy textbooks, related to the shape of a muscle in the pelvic region and the
location of the urinary bladder and prostate



University of Texas Initiative

5 KINESIOLOGY

• Researchers at the University of Texas at Austin Biomechanics Laboratory
are using high performance computing to create full dynamic simulations of
muscle interactions and multi-joint coordination of the human skeleton in
action.

• These simulations, involving complex mathematical models of muscle-joint
dynamics and the forces induced by such everyday tasks as jumping,
running, walking and rising from a chair, are leading to improved diagnosis
and treatment of bone and joint disease.

• This project is funded by NASA's Office of Space Science Applications.



University of Texas Initiative

6 BONE TRANSPLANT BIOENGINEERING

• Researchers with the Department of Mechanical and Aerospace Engineering
at Cornell University are using advanced computers at the Cornell Theory
Center to study the efficacy of various bone-implant systems, with emphasis
on the hip.

• The models they produce of the stresses placed on normal bones and on the
artificial components of hip joints are leading to customized prostheses and
reducing the need for prosthesis replacement surgery


HPC helps create new treatment for Stroke Victims
(1/2)
Medical devices and services provider Medrad uses HPC for advancement of catheter technology

“The patented prototype device seemed
•When someone has a stroke, the faster they can be brought to the hospital, the better. like a good fit with Medrad's growth
objectives, so we purchased the rights to
Doctors have a very small window in which to introduce drugs into the patients' the technology”
circulatory system in order to break up the clot-any delay can lead to paralysis or death. -John Kalafut, Principal research scientist at Medrad

But before commissioning expensive
Go-or-no-go product development activity, Medrad
Development work on Jell-O decision needed to test its feasibility
About 5 years ago, two engineers developed a prototype device that would speed up •Not only did Medrad need to understand
treatment by mechanically breaking up clots in the brain or elsewhere in the body. As
the physics of how the device worked, it
part of their research and development, they used Jell-O to simulate the physical
properties of the brain. also wanted to explore different design and
manufacturing approaches.

•It felt that doing this computationally
would be more efficient and faster than
•This work on interventional catheter technology came to the attention of Medrad, Inc building lots of different physical Business Case for
prototypes” HPC
of Indianola, PA. Medrad is a leader in providing medical devices and services that
enable and enhance diagnostics and therapeutic imaging procedures in the human However, the R&D group's high-end
body. workstations lacked the horsepower to
conduct the complex simulations. They also
did not have the in-house expertise to
•An affiliate of Bayer Schering Pharmaceutical AG, Germany, Medrad's diagnostic develop the detailed CFD (Computational
products have captured 70 to 80% market share. the company wanted to expand its Fluid Dynamics) codes. They needed access
to HPC and software, and the expertise to
business by moving into the interventional applications market Business Case for
help them harness its full potential
HPC


HPC helps create new treatment for Stroke Victims
(2/2)
Busting Blood Clots with High Performance Computing

Simulated flow field from the prototype device as
computed by 3D CFD Software at PSC
•Breaking with a long tradition of building numerous physical prototypes to
research the potential of a new technology, Medrad turned to the NSF-funded
Pittsburgh Supercomputing Center, experts at the Carnegie Mellon University for
use of complex numerical simulations running on high performance computers to
determine if the catheter technology was worth pursuing.

•Medrad used HPC to simulate the process of the catheter destroying the clots,
adjusting the parameters again and again to ensure that the phenomenon was
repeatbale. This validated the science behind the patent's theory was solid and
that the device would do what its inventors claimed.

•Then HPC was used to mathematically refine the prototypes by simulating many
different combinations of cahnges -more than could be done physically in the
Source: Medrad
time frame or budget available - to arrive at the best design

HPC allows us to tackle projects that were otherwise beyond our reach and has streamlined and optimized our production processes
in new ways that translate into lower costs and higher productivity
John Kalafut, Principal research scientist at Medrad

Breakthroughs in Brain Research with HPC (1/2)
•Researchers at the Salt Lake Institute are using supercomputers at the nearby NSF-funded San Diego Supercomputer
Center to investigate how the synapses of the brain work. Their research has the potential to help people suffering from
mental disorders such as Alzheimer's, schizophrenia and manic depressive disorders.
•In addition, the use of supercomputers is helping to change the very nature of biology-from a science that has relied
primarily on observation to a science that relies on high performance computing to achieve previously impossible in-depth
quantitative results

Researchers at the Salk Institute have been studying the ciliary ganglion of chickens with the help of high
performance computing (HPC). The ciliary ganglion is a mass of neurons in the ciliary muscle-the muscle that
opens and closes the iris in a human or animal eye. it acts like a circuit controlling the muscle's functions.
Within the ganglion is a synapse-the communication junction point where nerve cells communicate with target
cells like those in a muscle or gland. By studying the ciliary ganglion of a chicken and how the synapse controls
neural communication, researchers like Sejnowski and Bartol are gaining new insights into the neural
Treatment of Neural Disorder communication pathways of the human brain that could lead to new treatments for serious mental disorders

Compared to the tangled skin of synapses in the brain, the ciliary ganglion of a chicken is highly accessible,
rather large and can be easily removed for study. The synapse within the ganglion has many communication
release sites and every intricate geometry, allowing researchers to conduct experiments that would not be
possible with the brain itself.

Most drugs for neurological disorders are targeted at these synapses and, to some extent, are able to
rebalance these synapses Better Drugs for Better Living
While the synapse that controls the eye's ciliary muscle has been under study for many years, the Salk Institute
became involved when its researchers described the shape of the synapse in three dimensions-and a very
strange shape it was.

The researchers made an initial setting of the parameters, ran the model on in-house workstations and then
looked to see what happened. “In a sense”, Bartol explains "we brought this little piece of tissue back to life
Bringing tissue to Life inside the computer".


Breakthroughs in Brain Research with HPC (2/2)

Looking and Seeing with HPC

Realistic computer simulation of neurotransmission in a
chick ciliary ganglion synapse
•The Salk Institute researchers did what is called a 'parameter sweep'. This
consists of making numerous adjustments to the numerical parameters used to
provide an approximate model of reality.

“So, I have nine different parameters, and now I want to know what will happen
to my model when I vary all nine of these parameters, let's say using five
different values, all independently of each other. That's nine to the fifth power-
and now we are in major supercomputing territory". -Bartol

•The parameter sweeps and simulations executed on the SDSC high performance
computer had some surprises in store for the Salk investigators. The classic view
of how synapses work, derived from laboratory investigation, is that neural
transmissions occur primarily in dense protein rich areas called active zones. But
when the Salk team ran their models on the SDSC system, the results indicated
that neural communication was not confined to just the synaptic active zones,
but took place in peripheral areas as well outside of the synapses. this was highly
unexpected and exploded the traditional thinking of how synapses work.

Source: Salk Institute for Bilogical Studies

The high performance supercomputer gives us a scientific instrument like none other that has ever existed and will lead to discoveries
thatw e can't even contemplate now. It is changing the way we think about the brain and the way we think about the brain, and the
way we think about biology in general. We are entering a whole new era
Terry Sejnowski, Professor and head of the Computational Neurolobilogy Laboratory, Salk Institute for Bilogical Studies

HPC helps create simulation of the Human Heart (1/2)

Lawrence Livermore and IBM creates simulation that aims to realistically mimic a beating human heart

•Developed by Laboratory scientists working with colleagues at the IBM T. J. Watson Research Center in New York, the code accurately simulates the activation of
each heart muscle cell and the cell-to-cell electric coupling . The new simulations are made possible by a highly scalable code, called Cardioid, that replicates the
electrophysiology of the human heart.
Without medical intervention, a serious arrhythmia can lead to sudden death and accounts for about 325,000 deaths every year in the U.S.

•On every heartbeat, electric signals normally traverse the entire heart in an orderly manner, resulting in a coordinated contraction that efficiently pumps blood
throughout the body. However, these signals can become disorganized and cause an arrhythmia, a dysfunctional mechanical response that disrupts the heart’s
pumping process and can reduce blood flow throughout the body.

Cardioid Heart Simulations through HPC

•The Cardioid code
developed by a team of
Livermore and IBM
scientists divides the
heart into a large number
of manageable pieces, or
subdomains.

•The development team
used two approaches,
called Voronoi (left) and
grid (right), to break the
enormous computing
challenge into much
smaller individual tasks

Source: Lawrence Livermore National Laboratory

HPC helps create simulation of the Human Heart (2/2)

Extended cardiac simulations are critical when investigating how specific medications affect heart rate

•Many drugs disrupt heart rhythm. In fact, even those designed to prevent Snapshots from a Cardioid simulation show how a drug
might affect heart function
arrhythmias can be harmful to some patients. In most cases, however,
researchers do not fully understand the exact mechanisms producing these
negative side effects. With Cardioid, scientists can examine heart function as an
anti-arrhythmia medication is absorbed into the bloodstream and its
concentration changes

“So, I have nine different territory". -Bartol

•Operating on Sequoia, the Cardioid code can simulate hundreds of times as
many heartbeats as previous codes. One minute of Sequoia processing time is
required to replicate nine human heartbeats at a nearly cellular spatial
resolution. Simulating an hour of heart activity, or several thousand heartbeats,
can be accomplished in seven hours when using the full Sequoia system. Less
sophisticated codes took up to 45 minutes to compute a single heartbeat,
making it impossible to model the heart’s response to a drug or an
electrocardiogram trace for a particular heart problem.

Source: Lawrence Livermore National Laboratory

The Cardioid simulation has been named as a finalist in the 2012 Gordon Bell Prize competition, which annually recognizes the most
important advances in HPC applications. The Livermore–IBM team hopes the code will grow into a product that is widely adopted by
medical centers, pharmaceutical companies, and medical device firms, helping them better understand the mechanisms that can lead
to heart ailments and the potential drug interactions that may occur during treatment

Improving Microscopy through HPC

Confocal Microscopy uses High Performance Computing for processing and visualizing neuro-anatomical information

• Confocal microscopy is an optical imaging technique
used to increase optical resolution and contrast of a
micrograph by using point illumination and a spatial
pinhole to eliminate out-of-focus light in specimens
•Depth-z-stacks generate 3D data
that are thicker than the focal plane.
•Time-time series of organelle migration
• HPC has enabled better reconstruction of three-
•Colour-differential fluorescence to
dimensional structures from the obtained images. identify location of molecules
• Paras Prasad, SUNY Distinguished Professor in the
departments of Chemistry and Physics, and executive
director of the Institute for Lasers, Photonics and
Biophotonics, has used CCR's visualization resources
Confocal Microscope to create a fully immersive, three-dimensional image
High definition, of a human cell based on two-dimensional slices
Multidimensional image data
obtained using confocal microscopy

Source: Cancer Research UK, University of Cambridge

HPC–assisted diagnosis tools to aid pathologists

Histopathology yields higher throughput; quicker, more-consistent diagnoses

Histopathology • Researchers are leveraging Ohio Supercomputer Center resources to develop

Robotic Image Scanner computer-assisted diagnosis tools that will provide pathologists grading
Follicular Lymphoma samples with quicker, more consistently accurate
diagnoses.
• The advent of digital whole-slide scanners in recent years has spurred a
revolution in imaging technology for histopathology

.

• The large multi-gigapixel images
produced by these scanners
contain a wealth of information
potentially useful for computer-
assisted disease diagnosis, grading
and prognosis

Tissue microarrays – hundreds
. of samples per slide
Source: Cancer Research UK, University of Cambridge

Each sample scanned at high resolution

HPC helps create Nano Machines for Bionic Proteins

Bionic Proteins could play an important role in innovating pharmaceutical research

Self-knotted structure of the bionic protein

•Physicists of the University of Vienna together with researchers from the
University of Natural Resources and Life Sciences Vienna developed nano-
machines which recreate principal activities of proteins. They present the first
versatile and modular example of a fully artificial protein-mimetic model system.

“Imitating the astonishing bio-mechanical properties of proteins and transferring
them to a fully artificial system is our long term objective”- Ivan Coluzza

•Using computer simulations, they reverse engineered proteins by focusing on
the key elements that give them the ability to execute the program written in the
genetic code. The computationally very intensive simulations have been made
possible by access to the powerful Vienna Scientific Cluster (VSC), a high
performance computing infrastructure operated jointly by the University of
Vienna, the Vienna University of Technology and the University of Natural
Resources and Life Sciences Vienna.

Source: University of Vienna

The team now works on realizing such artificial proteins in the laboratory using specially functionalized nano-particles. The particles
will then be connected into chains following the sequence determined by the computer simulations, such that the artificial proteins fold
into the desired shapes. Such knotted nanostructures could be used as new stable drug delivery vehicles and as enzyme-like, but more
stable, catalysts.

Healthcare HPC in Developing Countries

Application/Trends in Developing Countries
Supercomputing Telemedicine Platforms

Live demonstration of endoscopy at the Prince of Wales Hospital in the Chinese Initiatives
University of Hong Kong, connecting Xian and Shanghai in China, and Fukuoka, Japan
•South Africa-India-Tanzania is involved ina tripartite collaboration on
telemedicine initiative for high impact service delivery .
•The Tanzanian HPC facility is a two teraflops machine developed through the
India-Tanzania Centre of Excellence in ICT
•Elsewhere, The Medical Informatics Group (MIG) of Centre for Development of
Advanced Computing (C-DAC), Pune has successfully completed the rollout phase
of Odisha Telemedicine Network (Phase-III) program

Bio-molecular Simulation
Screenshot of a sample Biomolecular simulation being conducted at South
Africa’s CHPC using AMBER Software
Initiatives
•School of Computational & Integrative Sciences at JNU is working on application of
computer simulation to biological phenomena using supercomputers
•South Africa’s CHPC (Centre for High Performance Computing) , in partnership with the
University of KwaZulu Natal (UKZN), is working on Biomolecular Simulations using AMBER
Software

Genome Analysis
Screenshot of a sample research on Denovo assembly of eukaryotic genomes from India’s
CRL Laboratory

Initiatives
•Brazilian Supercomputer epigeal, purchased by Laboratory for Scientific Computing
(LCC) is speeding up research on metabolism and genome analysis.
•India’s own Computational Research Laboratories (CRL), have developed a tool for
parallel Denovo assembly of eukaryotic genomes which makes the assembly process
faster and cheaper. The laboratory provide an automated pipeline in its HPC Cloud for
the analysis of next generation sequencing data covering De Novo assembly,
resequencing, analysis and annotation

Application/Trends in Developing Countries
Advanced Functional Visualization
Sample Screenshots from Cura’s HPC-based Medical Imaging Devices

Initiatives
•Leading Developer of Supercomputing Functional Visualization Ziosoft has
recently partnered with Advanced Medical Systems of APAC to address needs of
rapidly Growing Healthcare Market in India, Malaysia and Singapore. The
company's sophisticated, 3D-5D advanced visualization software provides a wide
array of diagnostic tools at any chosen location.
•Chennai-based Cura Healthcare is also working on high performance medical
imaging equipment for the developing world. The company is currently also
working on a collimator algorithm using HPC platform

Cloud HPC based Hospital Information System
Dr. Devi Shetty, Founder, Narayana Hrudayalaya signing the
agreement on HPC with Harsh Chitale, CEO, HCL Infosystems

Initiatives
•India's Narayana Hrudayalaya is using cloud-based HPC for its Hospital
Information Systems (HIS) application.
•It has tied up with HCL Infosystems for this unique initiative.
•HCL blu Enterprise Cloud's Infrastructure as a Service (IaaS) solution is being
deployed across 22 NH hospitals and has been already rolled out in Bangalore,
Ahmedabad, Jamshedpur and Jaipur.
•The high performance cloud computing services are backed by a strong
infrastructure backbone and HCL's national support network to ensure business
continuity. The HCL IaaS includes components from Cisco, EMC, Net App and
VMware.

The tie up is the result of a rigorous evaluation and a painstaking proof of concept
exercise which took almost a year to come to fruition.

Disruptive Innovation or Trend

Disruptive Innovation/Trend in Healthcare HPC

1 $100 Genome : Personalized Medicine Revolution

DNA is the blue print of life, telling our cells what to become and when to become it. While even 5 years back, it cost roughly $60,000 to sequence a human
genome, with advancement in technology, especially high performance computers, several companies are trying to create an inexpensive sequencing technology.
it is widely believed that affordable and accurate reads of the entire genome will open the door to a whole new level of diagnostic and therapeutic discovery

The Problem
Learning to sequence DNA fast and cheap might be the most important challenge in health technology.
Understanding each patient's full genetic sequencing would give doctors X-Ray vision into their patients'
unique makeup and future diseases. There's one big catch. Gene sequencing costs tens of thousands of
dollars

Two companies, Complete Genomics and BioNanomatrix,
are collaborating to create a novel approach that would
sequence our genome for less than the price of a nice pair of
jeans–and the technology could read the complete genome in
a single workday. IBM is also building a "DNA Transistor"
that would be the world's cheapest genetic reader

The Idea
This would work sort of like a DNA View-Master on the smallest conceivable level. Scientists drill a nano-
sized hole -- 3,000 times slimmer than a human hair -- through a silicon computer chip and thread a DNA
strands through it. As the molecule is passed through the nanopore, it is ratcheted one unit of DNA at a
time. Click, click, click, and the long sequence of DNA would be sequenced.

If doctors could know and use the full genetic sequence of every patient, the potential would be enormous. It would turn doctors into little prophets.
Diseases and disorders could be caught and diagnosed early. Medicine could be radically personalized. Doctors would be working with a kind of super-
X-Ray into the latent and not-so-latent illnesses of their patients.


2 When Medicine and Machine meet Eye to Eye

Recently, the USFDA approved a device that can restore sight to
the blind. the bionic device, made by California-based Second
Sight called Argus II, helps people with retinitis pigmentosa, a
genetic condition that damages light sensitive cells and can lead
to blindness.

The project leveraged Livermore National
Laboratories supercomputing facility to create
simulations for the artificial retinal prosthesis

One day, blind people fitted with artificial retinas will not only get sight, but like a smart phone, a range of apps will emerge that will allow recording,
zooming and augmented reality. Eventually you reach the point where you can start doing things that normal people can't do
-Dr Anders Sandberg, Future of Humanity Institute, University of Oxford


3 Analysis of Human Rhinovirus
St. Vincent's Institute of Medical Research (AUSTRALIA)

A cross-organizational team comprising researchers from St. Vincent’s Institute of Medical Why is it Disruptive ?

Research, Victorian Infectious Disease Research Laboratories, IBM Research Collaboratory for Life Understanding how anti-viral drugs work on
rhinoviruses and related viruses can potentially
Sciences – Melbourne, and Victorian Life Sciences Computation Initiative developed a method to
speed up the development of new treatments,
simulate the 3D atomic motion of the complete human rhinovirus on Australia’s fastest and could produce savings in development costs.
The research has the potential to produce savings
supercomputer, paving the way for new drug development. This research is the first time that the
in drug discovery and pre-clinical development of
atomic motion of a complete human rhinovirus has been simulated on a computer up to $1,000,000 per year

4 Biomechanical Modeling
ALYA RED (Barcelona)
Barcelona Supercomputing Center developed a first of its kind, in-house, end-to-end biomechanical
model including numerical methods, parallel implementation, mesh generation, and visualization.
The Alya System is a computational mechanics code with two main features. First, it is specially Why is it Disruptive ?

designed for running with high efficiency in large-scale supercomputing facilities. Secondly, it is The Alya Red biomechanical model can help bring
drugs to market faster through HPC simulation
capable of solving different physics tasks in a coupled way, each one with its own modeling
driven testing. This could result in tens of millions
characteristics: fluids, solids, electrical activity, species concentration, free surface, etc. The long of dollars in potential savings
term vision of Alya Red Project is to create an IT infrastructure of hardware and software that can
help medical doctors, clinical researchers, and the pharmacological industry to use HPC to
positively impact healthcare

Source: Both of them has been featured in the IDC HPC Innovation Excellence Awards declared on Nov, 2012

HPC in healthcare

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