Performance Computing
Performance Computing
February 2021
Copyright © 2021, Oracle and/or its affiliates
Public
1 White Paper / Bringing the power of high-performance computing to drug discovery and healthcare
Copyright © 2021, Oracle and/or its affiliates / Public
“We processed the
large data sets
obtained by the
microscope on the
cloud in a fraction of
the time and at much
lower cost than
previously possible.
We took a 90-day
Summary process and
completed it in
While the underlying drivers of the pharmaceutical (pharma) industry, such as
an aging population, prevalence of chronic conditions, demand for treatments under five days with
of rare conditions, and emerging novel viruses, remain Oracle Cloud HPC."
strong, the industry is under pressure to change. A core focus for industry
Christopher Woods
transformation is addressing drug development cost structures and EPSRC Research Software
improving development effectiveness. Not only are current processes lengthy Engineer Fellowship
and costly (typically 10 years at a cost of US$2.5 billion to bring one therapy
to market1 ), but the ability to produce “blockbuster” therapies that
compensate organisations sufficiently to cover these massive efforts is now a
top priority. A blockbuster therapy generates annual sales of at least US$1
billion for the company that sells it.
Improving research and development (R&D) productivity is contingent—to a
large extent—on the ability of organisations to collect, organise, analyse, and
interpret data from a wide array of sources beyond traditional clinical studies.
While the value, variety, volume, and veracity of such data is increasing
rapidly, organisations are still struggling to keep pace using conventional
data-management approaches. However, the speed at which organisations
can discover and develop more-ambitious therapies is increasingly important
in achieving competitive advantage, as being first to the market is key.
The time is takes to get a therapy to market can be shortened—even by
several years—by leveraging innovative, cloud-based technologies to
accelerate drug discovery and therapeutic development. Cloud technology is
changing what is possible, especially in data-driven, computationally intensive
R&D processes. Moreover, research projects need secure, robust, reliable, and
scalable infrastructure that can be provisioned quickly. Oracle’s technologies
in high-performance computing (HPC), advanced analytics, artificial
intelligence (AI), and machine learning are core components in transforming
the economics of pharmaceutical R&D productivity.
As unlike first generation cloud vendors, Oracle Gen 2 Cloud has been
architected for security, performance/price and comprehensive end-to-end
SLAs covering performance, availability, manageability of services.
1 European Federation of Pharmaceutical Industries (2013): Estimated full cost of bringing a new chemical or biological entity to market
2 White Paper / Bringing the power of high-performance computing to drug discovery and healthcare
Copyright © 2021, Oracle and/or its affiliates / Public
have designed a novel COVID-19 vaccine candidate. The research team
analysed computer models of the SARS-CoV-2 spike protein and its human
receptor ACE2 to identify how the COVID-19 virus infects human cells at a
pace that was dramatically increased2. In another example, the University of
Bristol recently discovered a synthetic vaccine to the mosquito-borne
chikungunya virus in a fraction of the time and at a much lower cost than
previously thought possible, leveraging on-demand access to a large number
of Oracle Cloud Infrastructure processors3 to perform large scale simulation.
On the cost side, there is the manifestation of Eroom’s law. Eroom's law is the
observation that drug discovery is becoming slower and more expensive over
time, despite advances in science and technology. If this trend continues, the
expenses for a newly approved drug will reach unprecedented values over the
next few years.
3 White Paper / Bringing the power of high-performance computing to drug discovery and healthcare
Copyright © 2021, Oracle and/or its affiliates / Public
exploiting data more effectively, helping pharma companies remain
competitive in this quickly changing industry.
These complex projects need to ensure that the data is secure, safe, and
handled with a robust, reliable, and scalable infrastructure. Moreover, they
need the ability to easily provision technology, analyse complex information,
and output results in a desirable format for downstream applications.
4 White Paper / Bringing the power of high-performance computing to drug discovery and healthcare
Copyright © 2021, Oracle and/or its affiliates / Public
CORE PHARMA
CLOUD HPC VALUE EXAMPLE OUTCOMES
CHALLENGES
• Accelerate drug • Enable analysis of larger • Drive faster time to value, and
discovery and the quantities of data from clinical reduce time needed to conduct
treatment development studies, DNA, genetic testing, complex network analysis from
process and EMRs, facilitating months to weeks
• Rapidly analyse and discoveries not previously • Conceive more-ambitious projects
possible
interpret data streams not conceivable before cloud-based
derived from clinical • Reverse engineer data-driven HPC, and ask 'bigger' questions
studies models of human disease • Support effective and productive
• Identify new therapies progression and drug
partner collaborations to facilitate
for disease sufferers not responses
quicker outcomes
served by standard • Simulate models to discover
treatments novel drug targets • Put control directly in the hands of
• Match the right • Automate components of the the research teams that consume
treatment(s) to the right end-to-end R&D process HPC infrastructure
patients more effectively • Gain the ability to increase • Focus on strategic priorities and
capacity to meet spikes in HPC outcomes, rather than
activity and reduce waiting managing infrastructure or fighting
times for capital budget on new hardware
• Pay for resources consumed
• Save on cost, which can contribute
only as they are consumed
to more-competitive pricing
5 White Paper / Bringing the power of high-performance computing to drug discovery and healthcare
Copyright © 2021, Oracle and/or its affiliates / Public
Bioinformatics
Bioinformatics involves application of computational theories and algorithms
for analysis of biological data. This is a multidisciplinary field, which requires
knowledge of biological sciences, mathematics, information science,
computer science, and statistics.
Genomic sequencing is one of the most-important HPC use cases under the
bioinformatics umbrella. During the past few decades, significant growth in
available computing power has made challenging sequencing problems, such
as whole genome sequencing (WGS), computationally feasible and financially
viable. HPC plays an important role in making WGS feasible, and fuels
advances in high-through-put or next-generation sequencing (NGS).
With NGS it becomes possible to analyse millions of genomic sequences in a
single run. Cloud HPC provides the flexibility to scale up resources and
drastically reduce the time taken to analyse genomic sequence data. Oracle
Cloud Infrastructure supports genomic sequencing libraries, such as, NVIDIA
Clara Parabricks, which take advantage of NVIDIA’s latest-generation graphics
processors to reduce time to results.
Virtual screening
Computational chemistry is a discipline that utilises molecular-level
information from the biological target sites related to a disease, such as
proteins or enzymes, to find the chemical compounds with the potential for
treating the health condition. Computer-aided identification of potential drug
molecules involves a process called virtual screening. A combination of virtual
screening and a computational technique called molecular dynamics
simulation helps in narrowing down the number of candidate drugs from tens
of thousands to hundreds. The computer-aided drug discovery process can
be significantly accelerated by using Oracle Cloud Infrastructure HPC.
Personalised medicine
Personalised medicine identifies the most suitable treatment plan for a patient
based upon genetic information. An example of precision medicine is seen in
cancer treatment where the genomic sequence of tumour cells is used in
identifying the mutation that was responsible for the disease. Identification of
a particular mutation in genomic sequence helps in pinpointing the most-
effective therapeutic regime for treating the disease. The flexibility to scale up
sequencing analysis on Oracle Cloud Infrastructure HPC can help identify the
best treatment plan in less time and improve clinical outcomes through wider
adoption of precision medicine.
Virtual human
Designing medical devices, such as heart valves, stents, and pacemakers,
requires careful consideration of the human body’s interior structure. When it
comes to implanting a device inside a vital organ, there is no room for error.
Imaging modalities, such as, X-rays, MRIs, and CT scans, provide two-
dimensional images of internal organs.
A composite model can be created using these images, which provides a
three-dimensional, virtual representation of the human body. This virtual
6 White Paper / Bringing the power of high-performance computing to drug discovery and healthcare
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human provides the flexibility to conduct infinite trials of a medical device
before implanting it inside the body. Measuring the effectiveness of devices is
accelerated by running simulations on the thousands of CPUs that reside in a
cloud HPC cluster.
AI-enabled diagnostics
AI algorithms for computer vision can process images to identify diseases
with high precision, making the work of clinicians easier. It is possible to
implement these AI systems on a large scale by leveraging Oracle Cloud
Infrastructure HPC. Beyond the diagnostic applications, AI algorithms can also
be used in drug discovery where generative algorithms help in designing new
drug molecules that have potential to provide a cure for hard-to-treat
diseases.
University of Bristol
Challenge:
Stop the spread of the infectious, mosquito-borne disease chikungunya that
was spreading throughout the world at an alarming pace. Traditional vaccine
design and production technology resources imped ed innovative vaccine
discoveries.
Approach:
Design a novel vaccine delivery system that is easy to produce in high
volumes.
Output:
Developed a novel, computational approach using Oracle Cloud Infrastructure
HPC to create an accurate, high-resolution digital model of their synthetic
vaccine in a fraction of the time and at a much lower cost than previously
thought possible.
Envisaged a vaccine delivery system from a lab-produced, thermostable,
protein molecule that could be readily manufactured at low cost and does not
require refrigeration to retain viability.
7 White Paper / Bringing the power of high-performance computing to drug discovery and healthcare
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Case study 2—High-throughput screening of potential
candidate molecules
Oracle Gen 2 Cloud offers the latest, high-end components, support for third-
party and open-source technologies, unique support for hybrid and multi-
cloud strategies, and an unwavering commitment to protect sensitive data. It's
8 White Paper / Bringing the power of high-performance computing to drug discovery and healthcare
Copyright © 2021, Oracle and/or its affiliates / Public
a security-first architecture with workload isolation at all levels of networking,
storage, and compute, with no over-provisioning of services at any point,
giving customers uniformly high and predictable performance with service-
level agreements for all workloads at any given time. This also gives Oracle a
highly advantageous cloud cost model, where, simply put, faster is cheaper.
9 White Paper / Bringing the power of high-performance computing to drug discovery and healthcare
Copyright © 2021, Oracle and/or its affiliates / Public
• Get better price-performance than with Our growing
other cloud vendors. (E.g. Oracle is typically collaboration with
44 percent less expensive than Amazon Oracle is fuelling
Web Services for Computational Fluid
incredible
Dynamics (CFD) workloads for Ansys Fluent
CFD workloads)
innovations across a
wide range of
Scalable, independent • Get 6.4 TB of local NVMe flash storage. industries and uses.
instances, more than • Get extreme, low-latency storage for By integrating
any storage
shared-nothing architectures or fast, local NVIDIA’s new A100
scratch storage. Tensor Core GPUs
• Leverage elastic block storage volumes for into its cloud service
additional storage that can provide up to 32 offerings, Oracle is
TB each and up to 35,000 IOPS per volume, giving innovators
backed by performance service-level everywhere access to
agreements. breakthrough
• Choose from wide set of parallel file computing
systems that can be deployed in performance to
three clicks. accelerate their most
critical work in AI,
Specialised network • Achieve 100 Gbps network throughput with machine learning,
latency under 1.5 microseconds with
data analytics and
secure, dedicated RDMA over converged
high-performance
Ethernet (RoCE) v2.
• Scale up to 20,000 cores in a single RDMA computing.”
cluster with latency as low as 1.5 microsec. Ian Buck
• Access compute clusters fast with non- Vice President and General
Conclusion
The pharmaceutical industry is facing unprecedented pressures. A core focus
for organisations is to address R&D cost structures and improve discovery and
development efficiency and effectiveness. At the heart of achieving this is the
acquisition and analysis of data and its subsequent transformation into
actionable insight. Oracle Cloud Infrastructure HPC is a key enabler to
improving the economics of pharmaceutical R&D. It requires fewer
prototypes, accelerates testing, and decreases time to market. The technology
is callable on demand, suitable for any HPC workload, based on the most
advanced compute, storage, networking, and software technologies, and
allows pharma companies to pay for only what they use.
10 White Paper / Bringing the power of high-performance computing to drug discovery and healthcare
Copyright © 2021, Oracle and/or its affiliates / Public
Moreover, Oracle Cloud Infrastructure HPC fits within a wider set of
cloud-based digital platforms and can integrate any data sources into a
comprehensive data platform that supports AI and machine learning to
deliver business value. Data that had previously been locked in silos can now
be released and given a voice to help drive better outcomes across the R&D
value chain—from discovering data sources and analysing, transforming, and
reining them to getting the analysis and insight to empower decision-making.
As unlike first generation cloud vendors, Oracle Gen 2 Cloud has been
architected for security, performance/price and comprehensive SLAs
throughout, which is why organisations are now turning to Oracle.
The pharma industry now has the opportunity to add tremendous value and
be at the heart of the simulated, digital patient journey. However, as with
many other disrupted industries, the success of individual players will hinge
on the speed at which they can transform themselves to meet the new market
reality.
Scale infrastructure up and down quickly, and pay only for the
resources that you use
11 White Paper / Bringing the power of high-performance computing to drug discovery and healthcare
Copyright © 2021, Oracle and/or its affiliates / Public
Appendix: Examples of successful HPC projects with Oracle
"The team has exploited the very latest technologies, including AI,
advanced manufacturing, and Cloud computing to accelerate vaccine
design, shaving years off normal development timeframes."4
Professor Petrovsky, Flinders University Professor and Research Director at Vaxine
Bristol, French National Centre for Scientific Research (CNRS) and Oracle join forces against
tropical disease
Scientists from University of Bristol and the French National Centre for Scientific Research (CNRS) have
identified a candidate synthetic vaccine against the tropical disease Chikungunya.
"We processed the large data sets obtained by the microscope on the
cloud in a fraction of the time and at much lower cost than previously
possible. We took a 90-day process and completed it in under five days
with Oracle Cloud HPC."
Christopher Woods, EPSRC Research Software Engineer Fellowship
"We went looking for the best price-performance, and we found that in
Oracle Cloud Infrastructure."
Sam Mahalingam, Chief Technical Officer for Enterprise Solutions, Altair Engineering
4
https://news.flinders.edu.au/blog/2020/04/03/flinders-targets-covid-19-vaccine/
12 White Paper / Bringing the power of high-performance computing to drug discovery and healthcare
Copyright © 2021, Oracle and/or its affiliates / Public
Gridmarkets run molecular simulations with Brigham Young University, Texas A&M University
Researchers use X-ray diffraction and 3D molecular-modelling software to build a crystal structure of the virus
that causes COVID-19. Using Oracle HPC, the animation rendering platform can render complex molecular
models in less than 24 hours.
"We don't own or maintain any hardware, and we're paying 70 percent
less to spin up an instance on Oracle Cloud infrastructure than we did
running workloads on Amazon Web Services or Google Cloud,"
said GridMarkets Cofounder Mark Ross.
Manchester Metropolitan University and NHS use AI to identify diabetic foot wounds
Manchester-based app Footsnaps AI, supported by Oracle for Research, can identify diabetic foot ulcers and
associated pathologies and provide feedback within 20 seconds using Oracle Cloud Infrastructure. With an
amputation rate 36 percent above the UK national average, Footsnaps AI used deep learning to provide near
real-time medical feedback as well as reduce foot-ulcer-related visits by an expected 50 percent.
"Our virtual humans, which reduce animal and human testing, as well as
product cost and time to market, are created in the Oracle Cloud
infrastructure, where medical device manufacturers, pharmaceutical
companies, and researchers can analyze their products and optimize
treatments to better meet patient needs,"
said Christopher Morton, CEO of ELEM Biotech.
13 White Paper / Bringing the power of high-performance computing to drug discovery and healthcare
Copyright © 2021, Oracle and/or its affiliates / Public
Gromacs simulates the movements of atoms in biomolecules
Gromacs is a molecular dynamics software that simulates the movements of atoms in
biomolecules under a predefined set of conditions. It is used to identify the behaviour of
these biomolecules when exposed to changes in temperature, pressure, and other inputs
that mimic the actual conditions encountered in a living organism. Gromacs can be used to
establish patterns in protein folding, protein-ligand binding, and cell-membrane transport,
making it a very useful application for drug research and discovery.
RIKEN is the owner of the world’s fastest HPC supercomputer known as Fugaku. RIKEN
has chosen Oracle Cloud Infrastructure as the public cloud provider for its elastic HPC
storage and to enable universities and research organizations to connect securely and
cost-effectively through the Science Information Network (SINET). Oracle was chosen
because of its superior performance, enterprise-grade security, and elastic storage
resources as part of the ongoing initiative to promote wider use of the supercomputer.
Using this big data at different geographical levels, the team can predict capacity
pressures on hospitals based on population movement in the local communities that they serve, predict
where it may be possible to ease social distancing measures at the regional and local levels, and monitor
which areas of the country are re-opening for business and which are not.
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