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COVID 19 Resources

COVID-19 resources

Infrastructures

SLING – Slovenian national supercomputing network

The Slovenian national supercomputing network is available for researchers in universities, research institutions and industrial development centers who need significant computing capacities to run compute-intensive algorithms and massively parallel algorithms (HPC/supercomputing) and use distributed processing of large numbers of tasks across several clusters (compute grid, HTC/high throughput computing) and big data processing. The network provides access to cluster-based Slovenian and international computing and storage capacities. It is available to eligible ARNES network users, members of industry research teams and SLING members. As part of international collaborations and projects, users can also access the network through the EGI network and collaborations, such as ELIXIR and CLARIN.

COVID-19 HPC Consortium

The consortium encompasses computing capabilities from some of the most powerful and advanced computers in the world. It is possible to request allocations of up to 6 months.

ELIXIR Computing Resources

ELIXIR nodes have made available a broad variety of computing resources.

European Galaxy COVID-19 Project

Publicly accessible infrastructure and workflows for SARS-CoV-2 data analyses from different scientific domains (genomics, proteomics, metabolomics, cheminformatics…).

Partnership for Advanced Computing in Europe (PRACE)

PRACE provides access to world-class high performance computing resources for researchers from academia and industry. PRACE has a fast review track for project proposals requesting computing resources to contribute to the mitigation of the impact of the COVID-19 pandemic.

Slovenian-Clarin

CLARIN.SI is the Slovene national consortium of the European research infrastructure CLARIN. Its goal is to support research communities from Humanities, Social Sciences and other language-related disciplines with:

Its vision is to broaden the scope of technological solutions for language studies, with the emphasis on Slovene and other South Slavic languages, as well as encourage cross-disciplinary cooperation.

Text and literature

For central COVID-19 hubs of text and literature, please see:

CDC COVID-19 Research Articles

A downloadable database of COVID-19 literature. This database is updated by systematically searching various bibliographic databases and hand searching selected grey literature sources.

CORD-19 dataset

Large collection of scientific articles (currently 130000) related to coronaviruses from Pubmed, biorxiv, medrxiv and other sources. All articles are provided in a standardized JSON format.

CORD-19-on-FHIR

A version of the CORD-19 dataset with semantic annotations in FHIR RDF format.

Elsevier Novel Coronavirus Information Centre

Bulk download of Elsevier fulltext articles related to COVID-19 and other resources.

LitCovid

A curated database of COVID-19 articles in PubMed compiled by the National Library of Medicine.

medRxiv and bioRxiv COVID-19 preprints

Combined page for all COVID-19 publications posted on medRxiv and bioRxiv.

Elsevier COVID-19 articles

Articles available for bulk download.

WHO database of COVID-19 publications

Data

Clinical data and clinical trials

Clinicaltrial.gov

US clinical trials register.

EU Clinical Trials Register

Official database of clinical trials within the EU.

Global Clinical Trial Tracker

Map of clinical trials related to COVID-19 world wide.

International Clinical Trials Registry Platform

WHO database of clinical trials. See also https://apps.who.int/trialsearch/.

LEOSS register

Anonymous register with COVID-19 patient data from over 200 hospitals.

Epidemiology and mobility data

Apple Mobility Trends

COVID-19 mobility data from Apple Maps.

COVID-19 Global Forecasting Kaggle Competition

Training and testing data for a weekly competition in forecasting COVID-19 cases and fatalities.

European Centre for Disease Prevention and Control (ECDC)

Reports on worldwide COVID-19 cases.

GISAID/Nexstrain genomic epidemiology

Evolution and worldwide distribution of SARS-CoV-2 genotypes.

See also https://www.gisaid.org/epiflu-applications/next-hcov-19-app/.

Google Mobility Reports

COVID-19 mobility data from Google Maps.

Institute for Health Metrics and Evaluation (IHME) - COVID19 Projections

Predictions for cases, tests, deaths and required hospital resources.

Johns Hopkins COVID-19 Dashboard

See also https://systems.jhu.edu/research/public-health/ncov/.

Our World in Data

Worldwide COVID-19 statistics.

UNCOVER COVID-19 Challenge

This dataset is a curated collection of over 200 publicly available COVID-19 datasets from sources like Johns Hopkins, the WHO, the World Bank, the New York Times, and many others. It includes data on a wide variety of potentially powerful statistics and indicators, like local and national infection rates, global social distancing policies, geospatial data on movement of people, and more. The data comes with a Kaggle competition hosted by the Roche Data Science Coalition (RDSC) which comprises number of tasks developed and evaluated by global frontline healthcare providers, hospitals, suppliers, and policy makers.

Image data

Structural data

Deepmind structure predictions

Structure predictions for COVID-19-related proteins from AlphaFold.

Xchem fragment screen data

Results from a large crystallographic fragment screen against the SARS-CoV-2 main protease (MPro, PDB ID: 6YB7) conducted by XChem at the Diamond Light Source.

Tools and other resources

Artificial intelligence models

COVID_BERT_base model

A BERT base model fine-tuned on COVID-19-related texts for natural language processing.

Other COVID-19 tools

COVID-19 Cell Atlas

Repository for cell-specific expression data.

COVID-19 Disease Map

The COVID-19 Disease Map is an assembly of molecular interaction diagrams, established based on literature evidence. The focus is on host-pathogen interactions specific to the SARS-CoV-2 virus.

General tools

BIAFlows

BIAFLOWS is an open-source web platform to benchmark and reproducibly deploy Bio Image Analysis (BIA) workflows.

Bioimage Informatics Search Engine (BISE)

BISE is a search engine for tools, training materials and data for bioimage analysis.

ImJoy

ImJoy is a plugin powered hybrid computing platform for deploying deep learning applications such as advanced image analysis tools.

scispaCy

scispaCy is a Python package containing spaCy models for processing medical text.

spaCy

spacy is a natural language processing library which integrates deep learning models for a variety of text analysis tasks.

Discussion groups, online workshops, networks

Crowdfight COVID-19

A platform that connects COVID-19 researchers with expert volunteers from various domains.

Data against COVID-19 forum

A forum that connects clinicians, virologists, immunologists with machine learners, bioinformaticians, epidemiologists and statisticians. For posting questions and finding collaborations.

ELLIS against COVID-19 online workshops

This series of online workshops presents projects on how to tackle COVID-19 using methods of machine learning and AI, carried out by leading international researchers. Research topics include outbreak prediction, epidemiological modelling, drug development, viral and host genome sequencing, and health care management. Meetings can be attended by live streaming or watched as recordings.

Image.sc Forum

The forum’s focus is software-oriented aspects of scientific imaging, particularly (but not limited to) image analysis, processing, acquisition, storage, and management of digital scientific images. It is the primary discussion forum of the bioimaging community.

NEUBIAS

NEUBIAS is a network of bioimage analysts in Europe, aiming at strengthening the bridge between life science, computer science and digital image processing. It also offers many training activities including online workshops and a YouTube channel.

Training and teaching resources

ELLIS against COVID-19

Recordings from workshops presenting different AI projects related to COVID-19.

Galaxy Training

Collection of tutorials developed and maintained by the worldwide Galaxy community.

NEUBIAS youtube channel

Videos related to bioimage analysis.

Aitslab COVID-19 Resource List

List of COVID-19 resources curated by the Cell Death, Lysosomes and Artificial Intelligence Group at Lund University.

data-against-covid.org community wiki

A list of data, services and other resources compiled by the data-against-covid.org community.

CDC Link list

Secondary data and statistics sources for COVID-19 researchers compiled by the CDC.

Open-Source-COVID-19

A global collection of Open Source projects related to COVID-19.

Hack the Crisis – Inspiration & resources

A list of resources compiled to support participants of the Swedish Hack the Crisis hackathon.

COVID-19 Biohackathon Resources

A list of resources compiled to support participants of the COVID-19 Biohackathon.

COVID-19 Research Funding Monitor

A curated list of open funding calls and other support for researchers, non-profit organizations and commercial organizations, specifically for COVID-19 research.