Resources

Infrastructures

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.

Estonian Scientific Computing Infrastructure (ETAIS)

ETAIS is a national research infrastructure that makes large-scale, high-performance computing resources, storage capacity and versatile user support available to Estonian researchers.

Data

Text data

See Text and Literature.

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/.

Clinical data and patient registries

LEOSS register

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

ASH RC COVID-19 Registry

COVID-19 Registry for Hematology.

COVID-Hep.net

Coronavirus (COVID-19) in liver disease reporting registry.

ELSO registry

COVID-19 patients on ECMO.

EUROELSO

ECMO use in adult COVID-19 patients in Europe.

IntubateCOVID

COVID-10 Intubation registry.

Pediatric COVID-19 U.S. Registry

PSOProtect

Psoriasis Registry for Outcomes, Therapy and Epidemiology of COVID-19 Infection.

SECURE-Cirrhosis

Reporting Registry for COVID-19 in liver disease.

SECURE-IBD

COVID-19 and Inflammatory Bowel Disease (IBD) Reporting Registry.

SECURE-SCD

COVID-19 and Sickle Cell Disease Registry.

The COVID-19 Global Rheumatology Alliance Global Registry

Registers with data provided by providers and patients.

VIRUS COVID-19 Registry

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.

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

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.

ECDC dashboard on variants

Variants of interest and concern in the EU/EEA

ECDC Response Measures Database

Database of non-pharmaceutical interventions (NPIs) introduced by 30 countries in the European Union (EU) and European Economic Area (EEA) since 1 January 2020 in response to the COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

WHO Coronavirus (COVID-19) Dashboard

Confirmed cases, deaths, vaccine doses administered.

COVID-19 Tracker USA, CDC and Vaccinations in the USA

epitweetr tool, ECDC

The R-based tool epitweetr allows users to automatically monitor trends of tweets by time, place and topic, with the aim of detecting health threats early through signals, such as an unusual increase in the number of tweets. It was designed to support public health experts with the early detection of threats from infectious diseases but can be extended to all hazards and other fields of study by modifying the topics and keywords. GitHub repository.

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.

National Library of Sweden - SweBERT models

Swedish BERT and ALBERT models for natural language processing.

Swedish Public Employment Service – Swedish BERT models

Swedish BERT models 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.

COVID-19 Data Repository on ICPSR

Social, behavioral, and health sciences research data.

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

Aitslab training collection

List of training resources related to data science and artificial intelligence curated by the Cell Death, Lysosomes and Artificial Intelligence Group at Lund University.

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.