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Primeur weekly 2020-10-12

Focus

Future of European HPC and TOP500 in the picture at Russian Supercomputing Days ...

Two European approaches for modelling and mapping the COVID-19 pandemic ...

European-Brazilian consortium joins forces in advanced HPC wind turbine simulations for use in on- and offshore wind energy farms ...

Exascale supercomputing

PerMedCoE: Exascale-ready cell-level simulations for European Personalised Medicine ...

Quantum computing

New algorithm could unleash the power of quantum computers ...

Light Rider unveils quantum LiFi technology to create next-generation network security ...

Research and Markets to issue report on Quantum Networking: A Ten-year Forecast and Opportunity Analysis ...

Focus on Europe

Linköping University chooses Atos to build Sweden's largest supercomputer for AI ...

Atos inaugurates BullSequana XH2000 at CSC - the fastest supercomputer in the Nordics ...

Making supercomputers carbon neutral - CSC's data centre will be powered with hydro-electricity supplied by Vattenfall ...

Middleware

Verne Global achieves Dell Technologies Platinum Partner status ...

Altair acquires M-Base Engineering + Software GmbH, leader in plastics material data and technology ...

Hardware

CoolIT Systems launches rack DLC CHx200 CDU ...

NVIDIA introduces new family of BlueField DPUs to bring breakthrough networking, storage and security performance to every data centre ...

CoolIT prevails against Asetek, PTAB determines no challenged claims unpatentable ...

CMKL University implementing DDN and NVIDIA solution for AI-centric supercomputing and research ...

OpenFive and AnalogX to provide optimized Chip-to-Chip interface IP solutions ...

Defense and intelligence executive Melvin Cordova joined Tachyum Government Corp. ...

TrendForce announces tech industry trends for 2021 ...

Cerebras Systems appoints Tony Maslowski as Chief Financial Officer ...

DoD deploys three Liqid composable supercomputing facilities powered by NVIDIA A100 GPU computing and NVIDIA Mellanox HDR 200Gb/s InfiniBand smart networking ...

Panasas ActiveStor data storage supports materials research for dozens of scientists conducting intensive 4D modelling studies at MINES ParisTech University ...

Pavilion expands a US federal deployment, bringing the multi-year relationship to an eight-figure investment, to safeguard American lives ...

C-DAC to commission India's fastest HPC-AI supercomputer PARAM Siddhi - AI with NVIDIA ...

NVIDIA announces partnership with GSK's AI-powered Lab for Discovery of Medicines and Vaccines ...

NVIDIA announces ready-made NVIDIA DGX SuperPODs, offered by global network of certified partners ...

Supermicro expands its portfolio bringing highest density 4U server with NVIDIA HGX A100s 8-GPU and 8U SuperBlade supporting 20 A100 PCI-E GPUs ...

Supermicro to support NVIDIA Bluefield-2 DPU on industry's broadest portfolio of servers optimized for accelerated computational workloads in AI, AR/DR, and data analytics ...

Applications

NVIDIA building large computing system, dedicated to AI research in health care ...

An electrical trigger fires single, identical photons ...

Could megatesla magnetic fields be realized on Earth? ...

Top computer scientists and statisticians launch Foundations of Data Science conference ...

Comet supercomputer calculations boost understanding of immune system ...

Corona supercomputer gets funding for COVID-19 work ...

Steady progress in the battle against COVID-19 at Brookhaven National Laboratory ...

Texascale Days at TACC: Eight research teams test their codes at the largest scale on Frontera ...

Supercomputing helps advance predictive science, exascale computing ...

The Cloud

Inspur unveils Cloud SmartNIC solution based on NVIDIA DPU at GTC 2020 ...

Comet supercomputer calculations boost understanding of immune system


Overview of T cell receptor clonotype sharing between three healthy Caucasian subjects. Comparison to simulated data shows that the degree of overlap is more than two orders of magnitude greater than what would be expected by chance. Credit: San Diego Supercomputer Center at UC San Diego, Vanderbilt University.
7 Oct 2020 San Diego - While researchers around the world race to develop an effective and safe COVID-19 vaccine, a team from the San Diego Supercomputer Center (SDSC) at UC San Diego contributed to a study led by Vanderbilt Vaccine Center of Vanderbilt University Medical Center (VUMC) on T cell receptors, which play a vital role in alerting the adaptive immune system to mount an attack on invading foreign pathogens including the Coronavirus SARS-CoV-2.

SDSC's Comet supercomputer was recently used to perform complex calculations on the receptor sequence data from sorted human T cells to allow scientists to better understand the size and diversity receptor repertoire in healthy individuals. The team's findings were published last month in Cell Reports as a follow-up study to earlier findings about B cells published in the journal Nature last year.

Both B cells and T cells are constituents of the adaptive immune system and form the second line of defense against viruses, bacteria, cancer, and other toxic pathogens that slip past the innate immune response. The adaptive immune system remembers the invading pathogen after first encounter and forms the basis of effective vaccines. To advance our understanding, the researchers sequenced receptors from the transcriptome of billions of cells to assess the somatic recombination of different gene segments that comprise the circulating B and T cell receptors from healthy Caucasian individuals. They found that T cell receptors, like B cell receptors, exhibit significantly higher overlap in different individuals than expected by chance.

In addition, the unprecedented scale of this sequencing project revealed that the size and diversity of immune repertoire are at least an order of magnitude larger than the estimation made from previous studies. This work is part of a broader effort supported by the Human Vaccines Project to decipher the components of the immune system, with the ultimate goal of understanding how to generate life-long protective immunity.

"Our most recent study puts us one step closer to truly understanding the extreme and beneficial diversity in the immune system, and identifying features of immunity that are shared by most people", stated James E. Crowe, Jr., director of the Vanderbilt Vaccine Center of Vanderbilt University Medical Center. "Now we continue to identify T cell receptors and antibodies that can be targets for vaccines and treatments that work more universally across populations."

A primary aspect of the team's ongoing research is focused on integrating the findings of these two studies toward the development of an effective vaccine against emerging and evolving threats. James E. Crowe explained: "We are getting closer to being able to use these large databases of human immune molecules to rapidly discover natural molecules that can be used as biological drugs."

Madhusudan Gujral, a senior bioinformatician at SDSC; Robert Sinkovits, SDSC's director of scientific computing applications; and Cinque Soto, a Vanderbilt computational biologist and lead author of the study, share James E. Crowe's enthusiasm over the implications of this research and recognize the importance of access to high-performance computing resources, such as Comet, to make it possible.

This work was supported by a grant from the Human Vaccines Project and institutional funding from Vanderbilt University Medical Center. The authors acknowledge support from TN-CFAR grant (P30 AI110527). This work also used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by NSF grant (ACI-1548562), and Comet supercomputer at SDSC, supported by NSF grant (ACI-1341698).
Source: San Diego Supercomputer Center - SDSC

Back to Table of contents

Primeur weekly 2020-10-12

Focus

Future of European HPC and TOP500 in the picture at Russian Supercomputing Days ...

Two European approaches for modelling and mapping the COVID-19 pandemic ...

European-Brazilian consortium joins forces in advanced HPC wind turbine simulations for use in on- and offshore wind energy farms ...

Exascale supercomputing

PerMedCoE: Exascale-ready cell-level simulations for European Personalised Medicine ...

Quantum computing

New algorithm could unleash the power of quantum computers ...

Light Rider unveils quantum LiFi technology to create next-generation network security ...

Research and Markets to issue report on Quantum Networking: A Ten-year Forecast and Opportunity Analysis ...

Focus on Europe

Linköping University chooses Atos to build Sweden's largest supercomputer for AI ...

Atos inaugurates BullSequana XH2000 at CSC - the fastest supercomputer in the Nordics ...

Making supercomputers carbon neutral - CSC's data centre will be powered with hydro-electricity supplied by Vattenfall ...

Middleware

Verne Global achieves Dell Technologies Platinum Partner status ...

Altair acquires M-Base Engineering + Software GmbH, leader in plastics material data and technology ...

Hardware

CoolIT Systems launches rack DLC CHx200 CDU ...

NVIDIA introduces new family of BlueField DPUs to bring breakthrough networking, storage and security performance to every data centre ...

CoolIT prevails against Asetek, PTAB determines no challenged claims unpatentable ...

CMKL University implementing DDN and NVIDIA solution for AI-centric supercomputing and research ...

OpenFive and AnalogX to provide optimized Chip-to-Chip interface IP solutions ...

Defense and intelligence executive Melvin Cordova joined Tachyum Government Corp. ...

TrendForce announces tech industry trends for 2021 ...

Cerebras Systems appoints Tony Maslowski as Chief Financial Officer ...

DoD deploys three Liqid composable supercomputing facilities powered by NVIDIA A100 GPU computing and NVIDIA Mellanox HDR 200Gb/s InfiniBand smart networking ...

Panasas ActiveStor data storage supports materials research for dozens of scientists conducting intensive 4D modelling studies at MINES ParisTech University ...

Pavilion expands a US federal deployment, bringing the multi-year relationship to an eight-figure investment, to safeguard American lives ...

C-DAC to commission India's fastest HPC-AI supercomputer PARAM Siddhi - AI with NVIDIA ...

NVIDIA announces partnership with GSK's AI-powered Lab for Discovery of Medicines and Vaccines ...

NVIDIA announces ready-made NVIDIA DGX SuperPODs, offered by global network of certified partners ...

Supermicro expands its portfolio bringing highest density 4U server with NVIDIA HGX A100s 8-GPU and 8U SuperBlade supporting 20 A100 PCI-E GPUs ...

Supermicro to support NVIDIA Bluefield-2 DPU on industry's broadest portfolio of servers optimized for accelerated computational workloads in AI, AR/DR, and data analytics ...

Applications

NVIDIA building large computing system, dedicated to AI research in health care ...

An electrical trigger fires single, identical photons ...

Could megatesla magnetic fields be realized on Earth? ...

Top computer scientists and statisticians launch Foundations of Data Science conference ...

Comet supercomputer calculations boost understanding of immune system ...

Corona supercomputer gets funding for COVID-19 work ...

Steady progress in the battle against COVID-19 at Brookhaven National Laboratory ...

Texascale Days at TACC: Eight research teams test their codes at the largest scale on Frontera ...

Supercomputing helps advance predictive science, exascale computing ...

The Cloud

Inspur unveils Cloud SmartNIC solution based on NVIDIA DPU at GTC 2020 ...