Supercomputing
ELIXIR-CZ: Life science data services
The Czech National Infrastructure for Biological Data (ELIXIR-CZ) provides a research infrastructure for the storage, processing and analysing data in the field of life sciences. ELIXIR-CZ has launched a website dedicated to COVID-19, where experts and the general public can find information on activities related to the fight against COVID-19. The website provides recommendations for data storage and sharing and the information on access to relevant data. ELIXIR-CZ specifically provides assistance in setting up the FAIR data principles, special software and analytics tools, and computing resources to help analyse data sets.
EGI: HADDOCK, a biomolecular simulations platform
HADDOCK (High Ambiguity Driven protein-protein DOCKing) is an integrative platform developed at Utrecht University for the modelling of biomolecular complexes and is one of the WeNMR thematic services. HADDOCK can support complex simulation projects, and benefits from the distributed computing infrastructure of EGI. In the context of COVID-19 related research it can, for example, model interaction between virus proteins and human one, or support the docking of small molecules to targets such as the COVID-19 protease. The tool is offered by the Bijvoet Center of the Utrecht University, Netherlands, is supported by the EOSC-hub H2020 project and is also accessible through the European Open Science Cloud Portal.
CERN Against COVID-19 initiative
The objective of the CERN against COVID-19 initiative is to ensure effective and well-coordinated action, drawing on CERN’s many competencies and advanced technologies and working closely with experts in healthcare, drug development, epidemiology and emergency response so as to maximise the impact of CERN contributions. CERN is focusing these efforts in three action areas:
- Medical applications: design and production of medical supplies and equipment, ranging from producing sanitiser gel, to developing full-scale ventilators for use in hospitals.
- Computing and data analysis: the vast global computing resource, Worldwide LHC Computing Grid, (WLCG), and CERN openlab collaboration can provide considerable resources for fighting the pandemic.
- Help to society: emergency response teams available to support local ambulance services, donations of PPE, production of Perspex barriers to protect those working in public services.
LAPP: MUST data centre computational and storage capacities
The Particle Physics Laboratory of Annecy (LAPP), a joint research unit of CNRS and Savoie Mont-Blanc University, provides all the possible computational and storage support to the CNRS biologists with its MUST data centre, to contribute in the battle against the COVID-19 pandemic. Exceptionally, LAPP will offer special access to its MUST data centre for important insights into the behaviour of the virus. The computing power of MUST will be used for in-silico screening to select from a database of several million molecules, those that meet very precise specifications and that could attack some major COVID-19 enzymes responsible for the replication of the virus RNA in the human host cell.
GENCI: High performance computing and storage facilites
GENCI, the French HPC agency, is providing its HPC (high performance computing) and storage facilites (located into 3 national centers: TGCC for CEA, IDRIS for CNRS and CINES for French Universities), as well as the user support resources to researchers from academia and industry working on COVID-19. Such supercomputers are used to accelerate modelisation/simulation workloads, post-processing of massive amount of data and use at scale of artificial intelligence. Already 15 projects have been benefited from such fast track, in the fields of massive docking, development of vaccines and therapies, epidemiological research on the spread of the virus, and related applications.
CRESCO6: Free access to high-performance computers
The Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), in order to contribute to research on COVID-19, makes its high-performance computing infrastructure HPC CRESCO6 available - free-of-charge access - to the entire scientific community involved in research activities and application projects for the coronavirus emergency.
SIB: Bioinformatics data services and analysis tools
The SIB Swiss Institute for Bioinformatics, Swiss node of ELIXIR and a partner of EMBL-EBI, undertakes a wide range of initiatives against SARS-Cov-2, providing data services and analysis tools that can help researchers answer the following questions:
- From where did the new coronavirus arise, and how did it move to humans?
- How is it spreading and evolving?
- How can we develop therapies to treat it?
PRACE: Access to computing resources
PRACE (Partnership for Advanced Computing in Europe) is welcoming project proposals requesting computing resources to contribute to the mitigation of the impact of the COVID-19 pandemic. PRACE partners, HPC centres, and research infrastructures are doing their bit by opening up their facilities for urgent/priority access to the HPC systems and other resources to support the research to combat the coronavirus. Please find a list of these initiatives here.
ELIXIR: Life science data tools and resources
ELIXIR, the ESFRI Research Infrastructure for life science data, provides a range of services and resources, that can be used by researchers and consortia working on SARS-CoV-2 research via ELIXIR Nodes. ELIXIR has also initiated new community-driven initiatives (e.g. Hackathons) that help to open up and link COVID-19 data. As details become available, they will be published on the ELIXIR COVID-19 webpage linked below.
LINDAT/CLARIAH-CZ: Computing cluster capacities
LINDAT/CLARIAH-CZ and its host institution – the Institute of Formal and Applied Linguistics at the Faculty of Mathematics and Physics, Charles University, Prague – offers its computing cluster capacity for research computation devoted to fight the SARS-CoV-2 coronavirus and Covid-19 disease, in the amount of ~1000 CPUs, for the period of three months, starting 1st April 2020. More information on how to apply for an account and quota on the cluster, plus a technical description of the capabilities of the cluster, how to run jobs, transfer data etc., can be found here. Please note that decisions to allow access will be made at the discretion of the research infrastructure management and mainly on first-come first-serve basis if fulfilling the above criteria.
LINDAT/CLARIAH-CZ is a joint distributed Czech national node of the pan-European CLARIN ERIC (Common Language Resources and Technology Infrastructure) and DARIAH ERIC (Digital Research Infrastructure for the Arts and Humanities) networks.