Imagine a world where doctors can diagnose diseases in minutes, researchers can discover new drugs in days, and patients can receive personalized treatments in hours.
This is not a science fiction scenario, but a realistic possibility with the help of high-performance computing (HPC).
HPC refers to the use of powerful and specialized hardware and software to process large amounts of data and perform complex calculations at high speeds.
HPC has many applications in various fields, such as engineering, physics, astronomy, and biology. But one of the most promising and impactful areas where HPC can make a difference is healthcare.
Healthcare generates and requires massive amounts of data and computation. From genomic sequencing to molecular docking, disease prediction to drug discovery, and medical imaging to personalized medicine, healthcare challenges demand computational solutions that are fast, accurate, and scalable. This is where HPC comes in.
HPC can enable faster and more accurate diagnosis, better understanding of biological mechanisms, and more effective and customized treatments. HPC can also reduce the cost and time of medical research and development, and improve the quality and accessibility of healthcare services.
HPC can transform healthcare from a reactive and generic approach to a proactive and personalized one.
However, HPC is not without its challenges and limitations. It requires significant investment in infrastructure, skills, and regulations. Ethical, social, and environmental issues must also be addressed.
HPC is not a magic bullet but a powerful tool that needs to be used wisely and responsibly.
In this post, we will explore the role of HPC in healthcare, including green and renewable HPC solutions, the challenges and opportunities of HPC adoption, case studies of successful HPC implementations, and future trends of HPC in healthcare.
We will show you how HPC can unleash the power of healthcare in a digital odyssey.
HPC can play a vital role in healthcare by accelerating complex simulations, data analysis, and modeling, which are essential for medical research and development.
HPC can handle large and diverse datasets, such as genomic sequences, molecular structures, medical images, and electronic health records. HPC can also perform sophisticated and computationally intensive tasks, such as simulating biological processes, analyzing disease patterns, and modeling drug interactions.
HPC can provide faster and more accurate results, insights, and predictions that can improve healthcare outcomes and quality.
To illustrate HPC's role in healthcare, let's look at some real-world examples of HPC applications in three critical domains: genomics, drug discovery, and personalized medicine.
Genomics is the study of an organism's complete set of genetic information. It can help us understand the causes and mechanisms of diseases, identify potential targets for drugs, and design better treatments.
However, genomics also involves massive amounts of data and computation. For example, sequencing a human genome produces about 200 GB of raw data, and analyzing it requires about 3,000 CPU hours.
HPC can enable faster and cheaper genomic sequencing and analysis using parallel and distributed computing techniques, such as cloud computing, grid computing, and cluster computing.
It can also enable more comprehensive and accurate genomic analysis by using advanced algorithms and tools, such as machine learning, artificial intelligence, and bioinformatics. Thus, HPC can help us unlock the secrets of the genome and advance the field of precision medicine.
One example of HPC in genomics is the 1000 Genomes Project, which aimed to create the most detailed and comprehensive catalog of human genetic variation.
The project involved sequencing and analyzing the genomes of more than 2,500 individuals from 26 different populations around the world.
It used HPC resources from various institutions, such as the National Institutes of Health (NIH), the European Bioinformatics Institute (EBI), and the Beijing Genomics Institute (BGI).
The project generated about 200 TB of data and provided valuable insights into human genetic diversity and disease susceptibility.
Another example of HPC in genomics is the COVID-19 Genomics UK (COG-UK) Consortium, which aims to sequence and analyze the genomes of the SARS-CoV-2 virus that causes COVID-19.
The consortium involves more than 20 academic and public health institutions across the UK and uses HPC resources from the UK Research and Innovation (UKRI) and the Wellcome Trust.
The consortium has sequenced and analyzed more than 500,000 viral genomes, helping to track the virus's spread and evolution, identify new variants, and inform public health responses.
Drug discovery is the process of finding and developing new drugs to treat or cure diseases. It involves multiple steps, such as target identification, lead optimization, preclinical testing, and clinical trials.
Drug discovery is also costly and time-consuming, with an average cost of $2.6 billion and a duration of 10 years per drug.
HPC can accelerate and improve drug discovery by using computational methods and models to simulate and optimize the interactions between drugs and their targets.
It can also use data mining and machine learning techniques to analyze large and complex datasets, such as chemical libraries, biological databases, and clinical records.
HPC can help us discover new drugs faster and cheaper with fewer side effects and failures.
One example of HPC in drug discovery is the OpenEye Scientific Software, which provides software tools for molecular modeling, cheminformatics, and drug design.
The software uses HPC techniques, such as parallel processing, distributed computing, and cloud computing, to perform molecular docking, pharmacophore modeling, virtual screening, and lead optimization tasks.
Many pharmaceutical and biotechnology companies, such as Pfizer, Merck, and GSK, have used the software to discover and develop new drugs for various diseases, such as cancer, diabetes, and Alzheimer’s.
Another example of HPC in drug discovery is the ExaScience Life Lab, a collaboration between Intel, imec, and five Flemish universities in Belgium.
The lab uses HPC systems, such as the ExaNeSt and ExaNoDe supercomputers, to perform tasks such as molecular dynamics simulations, quantum chemistry calculations, and machine learning applications.
It aims to discover new drugs for neurodegenerative diseases, such as Parkinson’s and Alzheimer’s, by using HPC to model the interactions between proteins and potential drugs.
Personalized medicine is the practice of tailoring medical treatments to the individual characteristics and needs of each patient. It can improve the effectiveness and safety of treatments and reduce the risk of adverse reactions and complications.
However, personalized medicine also requires a great deal of data and computation, including genomic, phenotypic, environmental, and behavioral data.
HPC can enable personalized medicine by using data analysis and machine learning techniques to integrate and interpret the data from various sources and generate personalized recommendations and predictions for each patient.
HPC can also use simulation and modeling techniques to test and optimize treatments for each patient and monitor and evaluate the outcomes. Thus, HPC can help us deliver more precise and customized healthcare to each patient.
One example of HPC in personalized medicine is the Cancer Moonshot Initiative, an effort to accelerate cancer research and improve cancer prevention, diagnosis, and treatment.
The initiative involves multiple agencies and organizations, such as the NIH, the National Cancer Institute (NCI), and the Department of Energy (DOE). It uses HPC resources from various facilities, such as the Oak Ridge National Laboratory (ORNL), the Argonne National Laboratory (ANL), and the Lawrence Livermore National Laboratory (LLNL).
The initiative uses HPC to perform tasks such as genomic analysis, molecular modeling, image analysis, and clinical decision support. Its goal is to create a comprehensive and personalized cancer care system for each patient.
Another example of HPC in personalized medicine is the All of Us Research Program, which aims to collect and analyze data from one million or more people living in the United States.
The program involves multiple partners and collaborators, such as the NIH, the Mayo Clinic, and the Scripps Research Institute, and uses HPC resources from the Google Cloud Platform.
It uses HPC to perform tasks such as data integration, data analysis, data visualization, and data sharing. The program aims to create a rich and diverse data resource that can enable researchers and clinicians to advance precision medicine for all.
HPC can offer many benefits to healthcare, but it also comes with a high environmental cost. HPC consumes a lot of energy and generates a lot of heat and carbon emissions.
According to a report by the International Energy Agency (IEA), data centers accounted for about 1% of the global electricity demand and 0.3% of the global carbon dioxide emissions in 2018. HPC systems are estimated to consume about 10% of the total energy in data centers.
Moreover, the energy demand and carbon footprint of HPC are expected to increase as healthcare's data and computation needs grow. Therefore, it’s essential to pursue sustainability in computing and to develop green and renewable HPC solutions that can reduce the energy consumption and environmental impact of HPC.
Green and renewable HPC solutions can also save money, improve performance, and enhance social responsibility. They can be achieved by using energy-efficient architectures and renewable energy sources.
Energy-efficient architectures are hardware and software designs that can optimize the energy efficiency and performance of HPC systems. They can include components such as processors, memory, storage, cooling, and networking.
Energy-efficient architectures can also use power management, load balancing, fault tolerance, and dynamic scaling techniques. These can help HPC systems consume less energy and generate less heat and noise while maintaining or improving computation speed and quality.
One example of energy-efficient architecture is the Green500 List, which ranks the most energy-efficient supercomputers in the world.
The list is based on the performance per watt metric, which measures how many floating-point operations per second (FLOPS) a supercomputer can perform with one watt of power. It’s updated twice a year and showcases the latest innovations and trends in green HPC.
As of November 2020, the top-ranked supercomputer on the Green500 List was the MN-3 system from Preferred Networks in Japan, which achieved 29.70 gigaflops per watt (GFLOPS/W).
Another example of energy-efficient architecture is the SpiNNaker Project, a collaboration between the University of Manchester and other UK and European partners.
The project aims to create a novel computer architecture that mimics the structure and function of the human brain. The project uses a network of low-power ARM processors that can communicate and compute in parallel, similar to how neurons and synapses work.
It can perform tasks such as neural network simulations, machine learning applications, and brain-computer interfaces. The project claims to be 100 times more energy-efficient than conventional computers.
Renewable energy sources are natural and inexhaustible, and they can power HPC systems without emitting greenhouse gases or depleting fossil fuels.
Renewable energy sources include solar, wind, hydro, geothermal, and biomass. These can generate electricity for HPC systems or provide cooling and heating for HPC facilities.
Using renewable energy can help HPC systems reduce their dependence on the grid, lower their energy costs, and mitigate their environmental impact.
One example of a renewable energy source being utilized is the National Renewable Energy Laboratory (NREL), a research center of the US Department of Energy (DOE) that focuses on advancing renewable energy and energy efficiency technologies.
The NREL operates the Energy Systems Integration Facility (ESIF), which is a state-of-the-art HPC facility that supports research and development in various domains, such as smart grids, electric vehicles, and biofuels.
A 10-megawatt solar photovoltaic array powers the ESIF and uses an innovative warm-water liquid cooling system that recycles waste heat for building heating and cooling.
Another example is the Mont-Blanc Project, a European consortium that aims to design and build a new generation of low-power HPC systems based on ARM processors and GPU accelerators.
The project uses the MareNostrum 4 supercomputer at the Barcelona Supercomputing Center (BSC) as a testbed for its prototypes and experiments.
A 9.9-megawatt photovoltaic plant powers the MareNostrum 4 and uses a free cooling system that takes advantage of Barcelona's mild climate.
The project aims to achieve a 15-30% reduction in energy consumption compared to conventional HPC systems.
HPC can offer many opportunities to healthcare institutions but also poses challenges. HPC adoption in healthcare requires significant investment, infrastructure, skills, and regulations. It also raises ethical, social, and legal issues that must be considered.
Some of the challenges faced by healthcare institutions in adopting HPC are:
Some of the opportunities offered by HPC to healthcare institutions are:
We will present three case studies of successful HPC implementations in healthcare organizations to demonstrate the benefits and challenges of adoption in healthcare. These case studies feature collaborations between researchers, clinicians, and technology experts, and showcase the use of HPC in different domains and contexts of healthcare.
The Human Brain Project (HBP) is a large-scale research initiative that aims to create a comprehensive and integrated understanding of the human brain. It also uses this knowledge to develop new treatments for brain disorders and new technologies inspired by the brain.
The HBP involves more than 500 scientists from 131 institutions in 19 countries, and the European Commission funds it with a €1 billion budget over 10 years.
The HBP uses HPC to perform various tasks, such as:
The HBP uses several HPC facilities and platforms, such as:
The HBP has achieved several milestones and impacts, such as:
The Cancer Genome Atlas (TCGA) is a landmark project that aims to map the genomic changes of various types of cancer. The project involves more than 150 institutions and 2,800 researchers across the US, and uses HPC resources from the NIH and the DOE.
The project has collected and analyzed more than 11,000 tumor samples from 33 different cancer types and generated more than 2.5 petabytes of data.
It has used HPC to perform tasks such as genomic sequencing, data integration, data analysis, data visualization, and data sharing and has produced many discoveries and publications that have advanced the understanding and treatment of cancer.
Some of the achievements and impacts of the TCGA project are:
The Virtual Physiological Human (VPH) is a visionary project that aims to digitally represent the human body and its functions. The project involves more than 100 institutions and 1,200 researchers across Europe, and uses HPC resources from various facilities, such as the Partnership for Advanced Computing in Europe (PRACE) and the European Grid Infrastructure (EGI).
The project has developed and validated more than 20 models and simulations of various organs and systems, such as the heart, brain, liver, and musculoskeletal system.
It has used HPC to perform tasks such as data collection, processing, modeling, simulation, and visualization. The project has enabled and supported many applications and innovations in healthcare, such as diagnosis, prognosis, prevention, and intervention.
Some of the achievements and impacts of the VPH project are:
HPC is a dynamic and evolving field that constantly seeks to improve and innovate its methods and technologies. It is also influenced and driven by the emerging and future needs and challenges of healthcare.
In this section, we will predict some of the future trends of HPC in healthcare, including quantum computing, edge computing, and the role of AI and machine learning.
Quantum computing is a new paradigm of computing that uses the principles and phenomena of quantum physics, such as superposition, entanglement, and interference, to manipulate and process information.
It has the potential to achieve exponential speedup and scalability compared to classical computing, and to solve problems that are intractable or impractical for conventional computers.
Quantum computing can have a significant impact on HPC in healthcare by enabling new and improved applications and solutions, such as:
However, quantum computing also faces many challenges and limitations, such as:
Edge computing is a distributed and decentralized approach to computing that moves the computation and storage of data closer to the source and destination of the data, such as sensors, devices, and users, rather than relying on centralized and remote servers or clouds.
Compared to cloud computing, edge computing has the potential to achieve lower latency and higher bandwidth and to enable more responsive and reliable applications and services.
Edge computing can have a significant impact on HPC in healthcare by enabling new and improved applications and solutions, such as:
However, edge computing also faces many challenges and limitations, such as:
AI and machine learning are branches of computer science that use data and algorithms to create and enable systems to perform tasks that normally require human intelligence, such as reasoning, learning, and decision-making.
They are closely related and interdependent with HPC and use and enhance each other’s methods and technologies.
AI and machine learning can play a vital role in enhancing HPC capabilities in healthcare by enabling and improving tasks such as:
HPC is a powerful and promising tool that can transform healthcare in a digital odyssey. HPC can enable faster and more accurate diagnosis, better understanding of biological mechanisms, and more effective and personalized treatments.
HPC can also reduce the cost and time of medical research and development and improve the quality and accessibility of healthcare services. Further, it can enable medical breakthroughs and innovations that can advance the frontiers of medical science and technology.
However, it is not without its challenges and limitations. HPC requires significant investment, infrastructure, skills, and regulations. HPC also poses ethical, social, and environmental issues that must be addressed. HPC is not a magic bullet, but a powerful tool that needs to be used wisely and responsibly.
It’s a dynamic and evolving field that constantly seeks to improve and innovate its methods and technologies. If you want to learn more about green HPC data centers and how they can benefit your healthcare organization, we invite you to contact us here at Sesterce.
Sesterce is a leading provider of HPC solutions that are sustainable, efficient, and reliable. We offer a full range of services related to high-performance computing power, such as design, installation, operation, and maintenance.
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