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Scalable HPC and AI Infrastructure for COVID-19 Therapeutics [article]

Hyungro Lee, Andre Merzky, Li Tan, Mikhail Titov, Matteo Turilli, Dario Alfe, Agastya Bhati, Alex Brace, Austin Clyde, Peter Coveney, Heng Ma, Arvind Ramanathan (+6 others)
2020 arXiv   pre-print
COVID-19 has claimed more 1 million lives and resulted in over 40 million infections. There is an urgent need to identify drugs that can inhibit SARS-CoV-2.  ...  In response, the DOE recently established the Medical Therapeutics project as part of the National Virtual Biotechnology Laboratory, and tasked it with creating the computational infrastructure and methods  ...  SCIENTIFIC RESULTS The previous section characterized the performance of the scalable HPC and AI infrastructure developed to support campaigns to advance COVID-19 therapeutics.  ... 
arXiv:2010.10517v1 fatcat:e4b3fafjbbgpzk2znm4ofeivre

Distributed Computing in a Pandemic: A Review of Technologies Available for Tackling COVID-19 [article]

Jamie J Alnasir
2021 arXiv   pre-print
Extremely large-scale COVID-19 research has also utilised some of the world's fastest supercomputers, such as IBM's SUMMIT -- for ensemble docking high-throughput screening against SARS-CoV-2 targets for  ...  Much of this COVID-19 research depends on distributed computing.  ...  Particularly applicable to COVID-19 research are the extremely large scalability grid computing offers and the infrastructure for international collaboration they facilitate, which we will discuss in the  ... 
arXiv:2010.04700v3 fatcat:kxakuqjlyjfilbroj5nl55xgbq

BioExcel Deliverable 2.6 – Integration of BioExcel software framework with standards and international initiatives

Stian Soiland-Reyes, Adam Hospital, Genís Bayarri, Ania Niewelska, Cibin Sadasivan Baby, Douglas Lowe, Pau Andrio, Josep Ll. Gelpi
2022 Zenodo  
An ongoing challenge for users to take advantage of BioExcel tools in workflow management systems and across multiple compute infrastructures is to get the software installed and integrated into their  ...  This is important to reliably apply a workflow through a wide range of scenarios: from training and prototyping, through development and customization towards scalable production runs.  ...  The COVID-19 Molecular Structure and Therapeutics Hub is a community-driven data repository and curation service for molecular structures, models, therapeutics, and simulations related to COVID-19 computational  ... 
doi:10.5281/zenodo.5824544 fatcat:kgwzhob3cbayfdp4tgxcqzutwu

BioExcel-2 Deliverable 2.4 – Development of a framework for the combination of HPC and HPDA operations

Adam Hospital, Genis Bayarri, Josep Lluis Gelpi, Pau Andrio, Daniele Lezzi, Rosa M Badia, Jorge Ejarque, Javier Alvarez, Salvi Sola, Sandro Barissi, Federica Battistini, Diego Gallego (+2 others)
2020 Zenodo  
This deliverable presents the different approaches of the BioExcel CoE regarding the design and development of a framework for the combination of High Performance Computing (HPC) and High Performance Data  ...  In parallel with the biobb_ml module, a new ML library, offering large-scale data analytics on HPC infrastructures, has been developed: dislib.  ...  The project aims at being an interactive and graphical extension for the BioExcel-MolSSI COVID-19 Molecular Structure and Therapeutics Hub.  ... 
doi:10.5281/zenodo.4916029 fatcat:yqr2fvusv5ftlkyy6nbkyelzoa

IMPECCABLE: Integrated Modeling PipelinE for COVID Cure by Assessing Better LEads [article]

Aymen Al Saadi, Dario Alfe, Yadu Babuji, Agastya Bhati, Ben Blaiszik, Thomas Brettin, Kyle Chard, Ryan Chard, Peter Coveney, Anda Trifan, Alex Brace, Austin Clyde (+24 others)
2020 arXiv   pre-print
This is both too expensive and too slow, especially in emergencies like the COVID-19 pandemic.  ...  The capabilities outlined here have been used in production for several months as the workhorse of the computational infrastructure to support the capabilities of the US-DOE National Virtual Biotechnology  ...  The IMPECCABLE Solution Artificial intelligence (AI) and machine learning (ML) have played a pivotal role in COVID-19 drug discovery [61] .  ... 
arXiv:2010.06574v1 fatcat:scmq2ge6ufgpzi5uckr6bxxvgu

Intelligent Resolution: Integrating Cryo-EM with AI-driven Multi-resolution Simulations to Observe the SARS-CoV-2 Replication-Transcription Machinery in Action [article]

Anda Trifan, Defne Gorgun, Zongyi Li, Alexander Brace, Maxim Zvyagin, Heng Ma, Austin R Clyde, David A Clark, Michael Salim, David Hardy, Tom Burnley, Lei Huang (+21 others)
2021 bioRxiv   pre-print
Attacking RTC function with pharmaceutical compounds is a pathway to treating COVID-19.  ...  We leverage a multi-site distributed workflow manager to orchestrate AI, FFEA, and AAMD jobs, providing optimal resource utilization across HPC centers.  ...  OVERVIEW OF THE PROBLEM The novel coronavirus 2019 (COVID-19) pandemic has led to a massive acceleration in the pace of development in experimental structural biology.  ... 
doi:10.1101/2021.10.09.463779 fatcat:4oluasz3jbgnvhwryercs6jts4

Pandemic Drugs at Pandemic Speed: Infrastructure for Accelerating COVID-19 Drug Discovery with Hybrid Machine Learning- and Physics-based Simulations on High Performance Computers [article]

Agastya P. Bhati, Shunzhou Wan, Dario Alfè, Austin R. Clyde, Mathis Bode, Li Tan, Mikhail Titov, Andre Merzky, Matteo Turilli, Shantenu Jha, Roger R. Highfield, Walter Rocchia (+17 others)
2021 arXiv   pre-print
We have demonstrated the viability of this workflow for the study of inhibitors for four COVID-19 target proteins and our ability to perform the required large-scale calculations to identify lead antiviral  ...  Here, we present an innovative infrastructural development that combines both approaches to accelerate drug discovery.  ...  Acknowledgements Access to SuperMUC-NG, at the Leibniz Supercomputing Centre in Garching, was made possible by a special COVID-19 allocation award (award ID COVID-19-SNG1) from the Gauss Centre for Supercomputing  ... 
arXiv:2103.02843v2 fatcat:k2x6by6ojrgqlkdhb4lpoq7cj4

Pandemic drugs at pandemic speed: infrastructure for accelerating COVID-19 drug discovery with hybrid machine learning- and physics-based simulations on high-performance computers

Agastya P. Bhati, Shunzhou Wan, Dario Alfè, Austin R. Clyde, Mathis Bode, Li Tan, Mikhail Titov, Andre Merzky, Matteo Turilli, Shantenu Jha, Roger R. Highfield, Walter Rocchia (+17 others)
2021 Interface Focus  
We have demonstrated the viability of this workflow for the study of inhibitors for four COVID-19 target proteins and our ability to perform the required large-scale calculations to identify lead antiviral  ...  Here, we present an innovative infrastructural development that combines both approaches to accelerate drug discovery.  ...  Access to SuperMUC-NG, at the Leibniz Supercomputing Centre in Garching, was made possible by a special COVID-19 allocation award (award ID COVID-19-SNG1) from the Gauss Centre for Supercomputing in Germany  ... 
doi:10.1098/rsfs.2021.0018 pmid:34956592 pmcid:PMC8504892 fatcat:rvalq6bwkfcmfapzwnowova6se

A Dynamic, Hierarchical Resource Model for Converged Computing [article]

Daniel J. Milroy, Claudia Misale, Stephen Herbein, Dong H. Ahn
2021 arXiv   pre-print
flexibility, performance and scalability across all three problems in comparison to limited traditional approaches.  ...  Extreme dynamic heterogeneity in high performance computing systems and the convergence of traditional HPC with new simulation, analysis, and data science approaches impose increasingly more complex requirements  ...  We wish to thank Jeff Buseman, David Fox, and Robin Goldstone for creating and configuring our test cluster and for enabling our AWS EC2 tests. This work was performed under the auspices of the U.S.  ... 
arXiv:2109.03739v1 fatcat:zl7z4hjrsvg53ju2ltbnhwul2y

Linking brain structure, activity and cognitive function through computation

Katrin Amunts, Javier DeFelipe, Cyriel Pennartz, Alain Destexhe, Michele Migliore, Philippe Ryvlin, Steve Furber, Alois Knoll, Lise Bitsch, Jan G. Bjaalie, Yannis Ioannidis, Thomas Lippert (+3 others)
2022 eNeuro  
research infrastructure EBRAINS.  ...  Understanding the human brain is a 'Grand Challenge' for 21st century research.  ...  The Fenix infrastructure federates scalable storage and computing resources at multiple leading HPC sites in Europe to provide a single and readily available base infrastructure for data exchange and demanding  ... 
doi:10.1523/eneuro.0316-21.2022 pmid:35217544 pmcid:PMC8925650 fatcat:k7obyuqb5vcenossdwrlcbg4eu

Rapid community-driven development of a SARS-CoV-2 tissue simulator [article]

Yafei Wang, Randy Heiland, Morgan Craig, Courtney L. Davis, Ashlee N Ford Versypt, Adrianne Jenner, Jonathan Ozik, Nicholson Collier, Chase Cockrell, Andrew Becker, Gary An, James A. Glazier (+3 others)
2020 biorxiv/medrxiv  
points" for pharmacologic interactions, screen potential therapies, and identify potential biomarkers that differentiate response dynamics.  ...  A critical question for treatment and protection is why it appears that the severity of infection may correlate with the initial level of virus exposure.  ...  Acknowledgements PM thanks the Jayne Koskinas Ted Giovanis Foundation for Health and Policy for generous support. PM, RH, and YW thank the National Institutes of Health (U01-CA232137-01) for support.  ... 
doi:10.1101/2020.04.02.019075 pmid:32511322 pmcid:PMC7239052 fatcat:swatm4xmjrdtnjzpidriauhqae

Academic Data Science Alliance: Founding Member Book, 2021-2022 [article]

Academic Data Science Alliance
2022 Zenodo  
In the years to come, we will continue to offer institutional membership and Member Books to provide a resource for students, administrators, and leaders of data science programs.  ...  The Academic Data Science Alliance is a community network for data science leaders, practitioners, and educators who take responsibility for a just, equitable future where data science approaches are thoughtfully  ...  In the Tripods REU and STEM for All summer research programs, students investigate the mathematical foundations of data science.  ... 
doi:10.5281/zenodo.6395103 fatcat:67pkbp3szzd2varr4u67svkib4

54. Jahrestagung der Deutschen Gesellschaft für Transfusionsmedizin und Immunhämatologie (DGTI), 22.–24. September 2021, DIGITAL, Abstracts

2021 Transfusion Medicine and Hemotherapy  
option for COVID-19.  ...  For this reason, we produced convalescent plasma from individuals after overcome COVID-19, as a possible therapeutic option.  ...  will contribute to resolve the question of the therapeutic benefit of CCP in Covid-19.  ... 
doi:10.1159/000518751 fatcat:fhykwocxwnbjvdxeve5zptljyq

Rapid, accurate, precise and reproducible ligand–protein binding free energy prediction

Shunzhou Wan, Agastya P. Bhati, Stefan J. Zasada, Peter V. Coveney
2020 Interface Focus  
Here, we review computational approaches for both relative and absolute binding free energy calculations, and illustrate their application to a diverse set of ligands bound to a range of proteins with  ...  They can be used in real-world problems such as hit-to-lead and lead optimization stages in drug discovery, and in personalized medicine.  ...  We thank a multitude of people for their assistance  ... 
doi:10.1098/rsfs.2020.0007 pmid:33178418 pmcid:PMC7653346 fatcat:z6m7p6rgrvgvxdf6fzmtxebooa

User Communities' test-cases [article]

Chrysovalantis Constantinou, Andreas Athenodorou, Hrachya Astsatryan, Bojana Koteska, Theodoros Christoudias, Georgios Artopoulos, Zoe Cournia, Milutin Radonjic, Ognjen Prnjat
2020 Zenodo  
It describes cross-border use cases for the target scientific areas of Life Science, Climate Science and Digital Cultural Heritage as well as for the area of Computational Physics.  ...  This deliverable provides a detailed description of cross-border test-cases including research groups involved and their mapping to generic, thematic and repository services which will be tested.  ...  products against COVID-19.  ... 
doi:10.5281/zenodo.3971646 fatcat:f3dz4ca7bre6dhk4xw62n4v4wy
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