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Published December 31, 2021 | Version 0.6
Project deliverable Open

BioExcel-2 Deliverable 6.3 – High Performance Computing in support of COVID-19 Research

Creators

  • 1. KTH
  • 2. UU
  • 3. JYU
  • 4. UNIMAN
  • 5. IRB
  • 6. MPG

Description

The unexpected emergence and spread of the SARS-CoV-2 virus and COVID-19 disease had a dramatic impact on societies across the world. Very soon it became clear that concerted efforts are needed in the fight against the pandemic.

As a focal point for the computational biomolecular research communities in Europe, BioExcel restructured its efforts in support of addressing the crisis. We developed and launched a number of portals for COVID-19 related data management and analysis. High-priority access to compute resources was provided by partner HPC centers.

We started numerous collaborative research projects including close partnerships with pharma industry. Community support was extended. We participated in dedicated webinars and presentations to cover methodologies, experience and results from our work.

We added a dedicated section to our website under category Research (https://bioexcel.eu/covid-19-research/) to present the various services and activities related to the disease. In this document we summarize the aforementioned activities.

Notes

Deliverable will be published after it is accepted by the funding agency.

Files

BioExcel-2_D6.3-High_performance_computing_in_support_of_COVID-19_research.pdf

Files (1.5 MB)

Additional details

Cites
Project deliverable: 10.5281/zenodo.5511704 (DOI)
Working paper: 10.5281/zenodo.4605654 (DOI)
Journal article: 10.1038/s41431-020-0637-5 (DOI)
Project deliverable: 10.5281/zenodo.5511684 (DOI)
Journal article: 10.1021/jacs.1c05301 (DOI)
Project deliverable: 10.5281/zenodo.4604924 (DOI)
https://www.bonvinlab.org/covid (URL)
Journal article: 10.1007/s10822-018-0148-4 (DOI)
Journal article: 10.1021/ci100031x (DOI)
Journal article: 10.1126/science.abb3405 (DOI)
Journal article: 10.1007/s10822-018-0148-4 (DOI)
Journal article: 10.1021/acs.jcim.1c00796 (DOI)
Working paper: 10.1101/2021.04.14.439284 (DOI)
Project deliverable: 10.5281/zenodo.5511717 (DOI)
10.5281/zenodo.4633655 (DOI)
Working paper: 10.1101/2020.06.21.163592 (DOI)
Working paper: 10.1101/2021.12.05.471263 (DOI)
Journal article: 10.1021/acs.jcim.0c00319 (DOI)
References
https://bioexcel.eu/covid-19-research/ (URL)
https://covid.bioexcel.eu/ (URL)
https://covid.molssi.org/ (URL)
https://about.workflowhub.eu/ (URL)
https://covid19.workflowhub.eu/ (URL)
https://elixir-europe.org/news/hacking-pandemic (URL)
https://elixir-europe.org/news/hacking-pandemic (URL)
https://covid19.galaxyproject.org/ (URL)
https://fairsharing.org/biodbcore-001581/ (URL)
https://www.covid19dataportal.org/ (URL)
https://about.workflowhub.eu/fair-computational-workflows/ (URL)
https://lifemonitor.eu/ (URL)
https://bioschemas.org/ (URL)
https://www.ga4gh.org/work_stream/cloud/ (URL)
http://w3id.org/ro/crate/ (URL)
https://www.commonwl.org/ (URL)
https://by-covid.org/news-events/by-covid-launch/ (URL)
https://by-covid.org/about#partners (URL)
https://sbnb.irbbarcelona.org/covid19/ (URL)
https://bioexcel-cv19.bsc.es/ (URL)
Dataset: https://bioexcel-cv19.bsc.es/#/browse/MCV1900002/trajectory (URL)
Software documentation: https://wenmr.science.uu.nl/haddock2.4/ (URL)
https://www.deshawresearch.com/downloads/download_trajectory_sarscov2.cgi/ (URL)
https://github.com/bioexcel/pmxlaunchCV19 (URL)
https://prace-ri.eu/prace-support-to-mitigate-impact-of-covid-19-pandemic/ (URL)
Software: https://github.com/MolSSI/covid (URL)
Software documentation: http://www.bonvinlab.org/software (URL)
Software documentation: https://www.eyesopen.com/omega (URL)
https://www.rcsb.org/structure/6y2f (URL)
https://www.imi-care.eu/ (URL)
Video/Audio: https://www.youtube.com/watch?v=8VJorSqIc2Q (URL)
https://www.exscalate4cov.eu/ (URL)
https://www.cecam.org/webinars-categories/hpc (URL)
https://www.cecam.org/webinar-details/prof-erik-lindhal-stockholm-university-prof-francesco-stellacci-epfl (URL)
https://fenix-ri.eu/events/9th-fenix-infrastructure-webinar-using-icei-resources-atomistic-molecular-dynamics (URL)
https://www.cecam.org/webinars-categories/covid (URL)
https://sites.google.com/view/icsp-online/events (URL)
https://euraxess.ec.europa.eu/worldwide/asean/eu-asean-hpc-initiative-fighting-covid-19-together (URL)
https://www.gla.ac.uk/research/az/scrc/ (URL)
https://scb.iec.cat/covid-19-viii-jornada-de-bioinformatica-i-genomica/ (URL)
https://www.escience2021.org/keynotes (URL)
https://sourceryinstitute.github.io/PAW/#Program (URL)
https://www.cecam.org/workshop-details/52 (URL)
https://www.cecam.org/workshop-details/1078 (URL)
https://bioexcel.eu/events/bioexcel-summer-school-on-biomolecular-simulations-2020/ (URL)
Video/Audio: https://www.youtube.com/watch?v=9IYsPH6iaw4&list=PLzLqYW5ci-2fhyTarjhpST9JT6qLTwBfL&index=15 (URL)
https://elixir-europe.org/news/hacking-pandemic (URL)
https://bioexcel.eu/covid-19-research/ (URL)
https://instruct-eric.eu/haddock-screen-of-2000-approved-drugs-for-covid19 (URL)
https://bioexcel.eu/category/webinar/ (URL)
https://bioexcel.eu/webinar-summerschool-2021/ (URL)
https://bioexcel.eu/webinar-covid-19-molecular-structure-and-therapeutics-hub-2020-06-25/ (URL)
https://bioexcel.eu/webinar-computationally-designing-therapeutic-antibodies-combining-immune-repertoire-data-and-structural-information-2021-11-09/ (URL)
https://bioexcel.eu/bioexcel-center-of-excellence-in-support-of-covid-19-research/ (URL)

Funding

BioExcel-2 – BioExcel Centre of Excellence for ComputationalBiomolecular Research 823830
European Commission