ewels
commented
4 years ago Many thanks for this @SonjaAits - super impressive!
This is now merged and up on the website: https://www.covid19dataportal.se/support_services/resources/
Note that I moved the Text Data section to the Text and literature page: https://www.covid19dataportal.se/support_services/text_and_literature/
If you'd like to edit / add to this, the relevant files are:
content/english/support_services/resources.mdcontent/english/support_services/text_and_literature.mdcontent/svenska/support_services/resources.mdcontent/svenska/support_services/text_and_literature.md
I made the Swedish translations by simply passing through Google Translate. Feel free to do the same yourself. If any native Swedes spot stuff that looks strange then they can submit fixes directly. It's better to have the content on the Swedish version, even if the language is poor I think.
Thanks again, and let me know if you have any questions (here, or on Slack).
Phil
Here is a long list to be copied into the Resources section:
Resources
Infrastructures
COVID-19 HPC Consortium https://www.xsede.org/covid19-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 https://elixir-europe.org/services/tag/compute ELIXIR nodes have made available a broad variety of computing resources.
European Galaxy COVID-19 Project https://covid19.galaxyproject.org/ 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) https://prace-ri.eu/prace-support-to-mitigate-impact-of-covid-19-pandemic/ 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.
SciLifeLab BioImage Informatics https://www.scilifelab.se/facilities/bioimage-informatics/ The BioImage Informatics Facility provides support and training needed to perform state-of-the-art analyses on image data, including machine learning. It also organizes monthly Call4Help sessions.
Swe-Clarin https://sweclarin.se/ 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) https://www.snic.se/ 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
CDC COVID-19 Research Articles https://www.cdc.gov/library/researchguides/2019novelcoronavirus/researcharticles.html 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 https://pages.semanticscholar.org/coronavirus-research Large collection of scientific articles (currently 128000) related to coronaviruses from Pubmed, biorxiv, medrxiv and other sources. All articles are provided in a standardized json format.
CORD-19-on-FHIR https://github.com/fhircat/CORD-19-on-FHIR A version of the CORD-19 dataset with semantic annotations in FHIR RDF format.
Elsevier Novel Coronavirus Information Centre https://www.elsevier.com/connect/coronavirus-information-center Bulk download of Elsevier fulltext articles related to COVID-19 and other resources.
LitCovid https://www.ncbi.nlm.nih.gov/research/coronavirus/ A curated database of COVID-19 articles in PubMed compiled by the National Library of Medicine.
medRxiv and bioRxiv COVID-19 preprints https://connect.medrxiv.org/relate/content/181 Combined page for all COVID-19 publications posted on medRxiv and bioRxiv.
Elsevier COVID-19 articles https://www.elsevier.com/connect/coronavirus-information-center Articles available for bulk download.
WHO database of COVID-19 publications https://www.who.int/emergencies/diseases/novel-coronavirus-2019/global-research-on-novel-coronavirus-2019-ncov
Clinical data and clinical trials
Clinicaltrial.gov https://clinicaltrials.gov/ US clinical trials register.
EU Clinical Trials Register https://www.clinicaltrialsregister.eu/ctr-search/search?query=covid-19&page=2 Official database of clinical trials within the EU.
Global Clinical Trial Tracker https://www.covid-trials.org/ Map of clinical trials related to COVID-19 world wide.
International Clinical Trials Registry Platform https://www.who.int/ictrp/en/ https://apps.who.int/trialsearch/ WHO database of clinical trials.
LEOSS register https://leoss.net/ Anonymous register with COVID-19 patient data from over 200 hospitals.
LIF coronavirus overview https://www.lif.se/forskningsoversikt-coronavirus/ Overview over global vaccine and drug development projects
Epidemiology and mobility data
Apple Mobility Trends https://www.apple.com/covid19/mobility COVID-19 mobility data from Apple Maps.
COVID-19 Global Forecasting Kaggle Competition https://www.kaggle.com/c/covid19-global-forecasting-week-5 Training and testing data for a weekly competition in forecasting COVID-19 cases and fatalities.
COVID-19 Symptom Tracker https://www.covid19app.lu.se/ Maps with self-reported symptom data from a Swedish self-reporting app.
European Centre for Disease Prevention and Control (ECDC) https://www.ecdc.europa.eu/en/covid-19-pandemic Reports on worldwide COVID-19 cases.
GISAID/Nexstrain genomic epidemiology https://nextstrain.org/ncov https://www.gisaid.org/epiflu-applications/next-hcov-19-app/ Evolution and worldwide distribution of SARS-CoV-2 genotypes.
Google Mobility Reports https://www.google.com/covid19/mobility/ COVID-19 mobility data from Google Maps.
Institute for Health Metrics and Evaluation (IHME) - COVID19 Projections https://covid19.healthdata.org/ Predictions for cases, tests, deaths and required hospital resources.
Johns Hopkins COVID-19 Dashboard https://www.arcgis.com/apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6 https://systems.jhu.edu/research/public-health/ncov/
Our World in Data https://ourworldindata.org/coronavirus Worldwide COVID-19 statistics.
Swedish Intensive Care Register https://www.icuregswe.org/data--resultat/covid-19-i-svensk-intensivvard/ Statistics about ICU admissions in Sweden.
Swedish Public Health Authorities (Folkhälsomyndigheten) https://www.folkhalsomyndigheten.se/smittskydd-beredskap/utbrott/aktuella-utbrott/covid-19/bekraftade-fall-i-sverige/ Official statistics about COVID-19 cases and tests in Sweden.
UNCOVER COVID-19 Challenge https://www.kaggle.com/roche-data-science-coalition/uncover 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 https://deepmind.com/research/open-source/computational-predictions-of-protein-structures-associated-with-COVID-19 Structure predictions for COVID-19-related proteins from AlphaFold.
Xchem fragment screen data https://covid.postera.ai/covid 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 https://huggingface.co/deepset/covid_bert_base A BERT base model fine-tuned on Covid-19-related texts for natural language processing.
National Library of Sweden - SweBERT models https://github.com/Kungbib/swedish-bert-models Swedish BERT and ALBERT models for natural language processing.
Swedish Public Employment Service – Swedish BERT models https://github.com/af-ai-center/SweBERT Swedish BERT models for natural language processing.
Other COVID-19 tools
COVID-19 Cell Atlas https://www.covid19cellatlas.org/ Repository for cell-specific expression data.
COVID-19 Disease Map https://covid.pages.uni.lu/ 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 http://3dskane.se/ Project descriptions for COVID-19 3D printing projects and contacts for volunteers.
General tools
BIAFlows https://biaflows.neubias.org/ BIAFLOWS is an open-source web platform to benchmark and reproducibly deploy Bio Image Analysis (BIA) workflows.
Bioimage Informatics Search Engine (BISE) http://biii.eu/ BISE is a search engine for tools, training materials and data for bioimage analysis.
ImJoy https://imjoy.io/ ImJoy is a plugin powered hybrid computing platform for deploying deep learning applications such as advanced image analysis tools.
scispaCy https://allenai.github.io/scispacy/ scispaCy is a Python package containing spaCy models for processing medical text.
spaCy https://spacy.io/ 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 https://www.ai.se National centre for applied AI research and innovation. Hosts projects, data lab, workshops and networking events.
AI Lund http://ai.lu.se/ 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 https://crowdfightcovid19.org/ A platform that connects COVID-19 researchers with expert volunteers from various domains.
Data-against-Covid.org forum https://discourse.data-against-covid.org/ 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 https://ellis.eu/covid-19 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 https://forum.image.sc/ 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 http://eubias.org/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: https://www.youtube.com/channel/UC-oy7UpEhRfHQ-5ePCviKFg.
MakersofSweden Forum – Pandemihack channel https://forum.makersofsweden.se/c/pandemihack/ Discussion forum and link list for makers engaged in COVID-19 projects.
SciLifeLab Forum – Covid-19 channel https://forum.scilifelab.se/c/covid-19/ Discussion forum for the Swedish Covid-19 community and SciLifeLab infrastructures.
Training and teaching resources
AI Competence for Sweden https://ai-competence.se/ Artificial intelligence courses and training for professionals provided by Swedish universities.
AI Lund TV http://ai.lu.se/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 https://github.com/Aitslab/training 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 https://ellis.eu/covid-19 Recordings from workshops presenting different AI projects related to COVID-19.
Galaxy Training https://training.galaxyproject.org/ Collection of tutorials developed and maintained by the worldwide Galaxy community.
NEUBIAS youtube channel https://www.youtube.com/channel/UC-oy7UpEhRfHQ-5ePCviKFg Videos related to bioimage analysis.
Link lists with COVID-19 projects and resources
Aitslab COVID-19 Resource List https://github.com/Aitslab/corona List of COVID-19 resources curated by the Cell Death, Lysosomes and Artificial Intelligence Group at Lund University.
data-against-covid.org community wiki https://discourse.data-against-covid.org/t/community-wiki-resources-on-data-science-and-friends-vs-covid-19/731 A list of data, services and other resources compiled by the data-against-covid.org community.
CDC Link list https://www.cdc.gov/library/researchguides/2019novelcoronavirus/datastatistics.html Secondary data and statistics sources for COVID-19 researchers compiled by the CDC.
Open-Source-COVID-19 http://open-source-covid-19.weileizeng.com/index A global collection of Open Source projects related to COVID-19.
Hack the Crisis – Inspiration & resources https://www.hackthecrisis.se/inspiration A list of resources compiled to support participants of the Swedish Hack the Crisis hackathon.
Swelife COVID-19 Resource List https://swelife.se/verktyg/covid-19/ A list of funding opportunities and other resources for COVID-19 projects.
Utveckling i VGR – COVID-19 Resource List https://vgrblogg.se/utveckling/2020/03/31/covid19-resurser-for-dig-som-vill-hacka-krisen/ A list of resources compiled to support participants of the Swedish Hack the Crisis hackathon.
COVID-19 Biohackathon Resources https://github.com/virtual-biohackathons/covid-19-bh20/blob/master/datasets_and_tools.md A list of resources compiled to support participants of the COVID-19 Biohackathon.