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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.

Swe-Clarin

Swe-Clarin makes text-based materials and text analysis tools available. It is a national node in the European CLARIN (Common Language Resources and Technology Infrastructure).

Swedish National Infrastructure for Computing (SNIC)

SNIC is a national research infrastructure that makes available large-scale high performance computing resources, storage capacity, and advanced user support, for Swedish researchers.

Data

Text data

See Text and Literature.

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.

LIF coronavirus overview

Overview over global vaccine and drug development projects

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.

COVID-19 Symptom Tracker

Maps with self-reported symptom data from a Swedish self-reporting app.

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.

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.

Skåne University Hospital 3D Printing Centre

Project descriptions for COVID-19 3D printing projects and contacts for volunteers.

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

AI Innovation of Sweden

National centre for applied AI research and innovation. Hosts projects, data lab, workshops and networking events.

AI Lund

AI Lund is a network for research, education and innovation in the area of artificial intelligence. It is hosted by Lund University and open to everyone. AI Lund organizes a bi-weekly online discussion (AI Lund drop-in), regular workshops, training events and other activities. The website also has a channel with videos from past events.

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.

MakersofSweden Forum – Pandemihack channel

Discussion forum and link list for makers engaged in COVID-19 projects.

SciLifeLab Forum – COVID-19 channel

Discussion forum for the Swedish COVID-19 community and SciLifeLab infrastructures.

Training and teaching resources

AI Competence for Sweden

Artificial intelligence courses and training for professionals provided by Swedish universities.

AI Lund TV

Videos from AI Lund workshops, seminars and training events, including technology-oriented topics and topics related to medicine, ethics and privacy.

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.

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.

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.

Swelife COVID-19 Resource List

A list of funding opportunities and other resources for COVID-19 projects.

Utveckling i VGR – COVID-19 Resource List

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.