Science Infrastructure

Tools to help the Research Community

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For Studies Currently Recruiting: coronavirustechhandbook.com/science/studies-recruiting
For Monitoring Ongoing Clinical Trials: http://covid19.trialstracker.net/data_viz.html
For NLP Initiatives and Solutions:
coronavirustechhandbook.com/nlp

Technical Tools & Resources

Useful Tools

AI algorithm trained from radiology images

🔗http://medicalsegmentation.com/covid19/
AI segmentation tool and algorithm trained on a compilation of COVID-19 radiology imageps

Open-source project for low cost detection

🔗 Slack channel for JOGL-covid-19
join this first as much more active than website

Pypi epydemic

🔗https://pypi.org/project/epydemic/ 
Python library that implements simulations of epidemic (and other) processes over networks.

Commercial tools for high cost detection

🔗https://www.randox.com/coronavirus-randox/
📧@randox.com 
According to the website, the test identifies the lethal strain and differentiates between other non-lethal variants with the same symptoms.

Strain sequences map (Global Initiative on Sharing All Influenza Data)

🔗GISAIDepydemic
🗣https://www.gisaid.org/help/contact/
Sequence and strain info from GISAID.  Provides a publicly accessible database designed by scientists for scientists, to improve the sharing of influenza data. 

Genomic epidemiology of novel Coronavirus (hCoV-19)

🔗 nextstrain.org/ 
🗣[email protected]
Open source virus sequence tracker. Use visualisations to show pathogen evolution.  Open issues, some of them marked as `good first issues`: https://github.com/orgs/nextstrain/projects/5 from a quick glance skills required are Python and JS

Better and faster decision making

🔗https://www.contextlabs.com/provenpaths
Allows analysts, researchers, and business users to make better and faster decisions using data that was previously inaccessible or unusable. #PROVENPATHS™ via @contextlabsbv

Software Free Trials

Vccafe

🔗https://www.vccafe.com/2020/03/18/100-startups-offering-free-products-and-services-in-response-to-coronavirus/?fbclid=IwAR0YcEaHhVbOOfgK7_9G7Lvy
Free products and services being offered to people working on Coronavirus

Delve

🔗https://docs.google.com/forms/d/e/1FAIpQLScdqhFqddSaQg3M_NmMiELyk4lylCIge_7wOLnJXGJTOiIrng/viewform
Delve (transcript analysis and synthesis tool) is offering a free 6-month membership for Coronavirus-related studies.

Castor

🔗 https://www.castoredc.com/for-researchers/
📧 [email protected] 
Research Data Capture Platform made free for those researching COV-19. Get in contact using the details above.

Computing Resources Offers

Rescale

🔗www.rescale.com
📧 [email protected]
Anyone in need of virtually unlimited high performance computing resources with no queue, for a special offer in this time of need. 


Gridrepublic

📧[email protected]
Anyone in need of high-throughput computing resources, please get in touch: [email protected] and we’ll get you what you need.

Large Memory Computing Resources

📧[email protected]
If anyone has large memory requirements for COVID-19 simulation work, get in touch. We have 3TB nodes, 48 cores each, that could be made available. 

Data & Modelling

See also: https://coronavirustechhandbook.com/infographics
See also: https://coronavirustechhandbook.com/data


Dynamic Dataset

🔗https://worldhealthorg-my.sharepoint.com/:f:/g/personal/garnicacarrenoj_who_int/EnzxnSJt68pIqLBwPYdqkqcB1KHboCAQJRN3mkTt3ZqDAA?e=OtxhHb
COVID-19 Database files

Rosetta molecular modeling suite

🔗 https://www.ipd.uw.edu/coronavirus/
📧 https://twitter.com/uwproteindesign
The Rosetta protein prediction server has been used to produce models of SARS-CoV-2 proteins [example paper]. 


The Big Data Institute at Oxford University

🔗El equipo de la Universidad de Oxford
📧https://045.medsci.ox.ac.uk/contact-info
Is it possible to stop a pandemic? The Big Data Institute at Oxford University with expertise in epidemiology, medicine, virology, immunology, mathematical modelling, phylogenetics, behavioural economics, and ethics, have redirected their usual research on stopping virus spread to address the new pathogen SARS-CoV-2. They suggest high adoption of a mobile app to trace contacts and track user movement.

Our World In Data - Coronavirus Disease (COVID-19) – Research and Statistics

🔗https://ourworldindata.org/coronavirus
📧[email protected]  (no need to contact to use the visualisations)
Uses data from the World Health Organisation’s daily ‘Situation Updates’. They visualise growth rate, testing, cases, trajectories, symptoms, incubation period, severity of symptoms, fatality rates. They also have short accompanying explanations. (See description of WHO Situation Updates and description of other datasets in the data handbook).

Data Visualisation of COVID-19 cases

🔗https://covy.app/?lat=40.29399&lng=-104.81659&dlat=-20.90077&dlng=-28.95996&z=4&c=7206
Visualises COVID-19 cases

Figure 1; Clinical Cases

🔗https://www.figure1.com/covid-19-clinical-cases
During previous emerging public health threats, such as Zika and MERS, Figure 1 played a pivotal role in disseminating real-time clinical knowledge, enabling healthcare professionals to share cases about how the viruses presented.

Corona Open Datasources

🔗https://docs.google.com/document/d/1agNknLycm9o6UfFCW_5P-0RUuubwf4M-XoTQvQe4pnM/edit
Coronavirus Open Data Sources and more

Corona Radiology Images (CT Scans and x-rays)

🔗https://github.com/coyotespike/covid19-images
The largest aggregation of relevant images, being assembled into useful datasets

Research

Important Research/ Collections

COVID-19 Resource Centre

🇬🇧🔗https://www.thelancet.com/coronavirus
Lancet Comments and correspondence from the medical research community relating to the corona outbreak.

Research Analysis Tools

WHO website with built-in search:

🔗https://www.who.int/emergencies/diseases/novel-coronavirus-2019/global-research-on-novel-coronavirus-2019-ncov
WHO is gathering the latest scientific findings and knowledge on Coronavirus disease (COVID-19) and compiling it in a database. We update the database daily from searches of bibliographic databases, hand searches of the table of contents of relevant journals, and the addition of other relevant scientific articles that come to our attention. The entries in the database may not be exhaustive and new research will be added regularly.

scite

🔗 scite.ai
🗣 https://twitter.com/scite
scite is a new platform that allows anyone to see how a scientific paper has been cited, not just how many times and, specifically, if it has been supported or contradicted.
On this platform you can:


Extracting Genes from Published Pathway Figures

🔗 https://github.com/wikipathways/cord-19
🗣 https://twitter.com/xanderpico
Pipeline for detecting gene mentions from pathway figures in the literature. 1.1M gene mentions in 60k figures so far from 1995-2019. Almost 5000 gene mentions found in 216 pathway figures from the CORD-19 dataset. Repo includes raw OCR, identified genes and initial characterization under CC0 waiver.

Causaly - Complete Coronavirus Drug Discovery Dataset 

🔗 https://www.causaly.com/
🗣[email protected]
Causaly’s relationship database was co-created for Novartis, and maps all biomedical literature, including related Corona diseases, most likely targets and potential treatments. Causaly’s dataset has been provided to the Global Health Drug Discovery Institute (GHDDI) to support COVID-19 research. If you are a researcher or health official for COVID-19 research, reach out on the details above.

Extracting Data From Preprints

🔗 medRxiv, bioRxiv, arXiv
 🗣 https://twitter.com/L_Brierley
Graphs about number and category of posts to different preprint servers.
Data Sources: The above 3 preprint servers via https://github.com/lbrierley/epi_preprint

Reviewing Pre-prints

COVID Preprints

🔗http://covidpreprints.com/
A new website showing a timeline of landmark COVID-19-related preprints, including their short summaries


Outbreak Science

🔗 https://outbreaksci.prereview.org
🗣 https://twitter.com/outbreaksci
Outbreak Science Rapid PREreview is a web application for open, rapid reviews of outbreak-related preprints.
On this platform you can:


Biorxiv

🔗https://connect.biorxiv.org/relate/content/181
Review pre-prints related to COVID-19. Consider reading through submissions, providing feedback, and flagging any concerns.

The Lancet

🇬🇧🔗https://www.thelancet.com/pdfs/journals/langlo/PIIS2214-109X(20)30113-3.pdf
Preprint platforms facilitate discourse about COVID-19, Science by The Lancet

preLights - The Company of Biologists

🔗 http://covidpreprints.com/
A timeline of landmark preprints including their short summaries, curated and regularly updated by researchers who are members of preLights, a preprint highlighting platform supported by The Company of Biologists.


Open Access Journals and Research Articles on COVID-19 

Oxford Journals

🔗https://academic.oup.com/journals/pages/coronavirus
Coronavirus | Journals | Oxford Academic Oxford Journals

Cambridge

🔗https://www.cambridge.org/core/browse-subjects/medicine/coronavirus-free-access-collection
Cambridge journals

Clarivate resources

🔗https://clarivate.com/coronavirus-resources/
(request needed) 

Elsevier

🔗 https://www.elsevier.com/connect/coronavirus-information-center 

Taylor and Francis

🔗https://newsroom.taylorandfrancisgroup.com/coronavirus-reading-list/ 

Springer

🔗https://www.springernature.com/gp/researchers/campaigns/coronavirus 

JoVE

🔗https://info2.jove.com/coronavirusvideo?utm_source=joveglobal&utm_medium=twitter&utm_campaign=coronavirus 

ACS Pubs

🔗 https://pubs.acs.org/doi/10.1021/acscentsci.0c00272

COVID-19 Registered Trials

🔗 https://www.cebm.net/oxford-covid-19/covid-19-registered-trials-and-analysis/

The Lancet

🔗https://www.thelancet.com/coronavirus?dgcid=kr_pop-up_tlcoronavirus20
A number of journals have made articles on COVID-19 free to access.

Science Compilation on Covid-19

🔗https://medium.com/@gweninvestor/science-compilation-on-covid-19-750574c16ac9
Daily digest of current COVID-19 research articles.

Wiley

🔗https://novel-coronavirus.onlinelibrary.wiley.com/
More than 5,000 #Coronavirus related articles freely available in support of the global efforts in its diagnosis, treatment and prevention.

Related Research, suggested articles.

Annual Reviews

🔗https://www.annualreviews.org/doi/pdf/10.1146/annurev-virology-012420-022445
Seasonality of Respiratory Viral Infections. March 2020

BMJ

🔗https://www.bmj.com/content/368/bmj.m1165?
COVID-19: identifying and isolating asymptomatic people helped eliminate virus in Italian village
Medicine

Applied Research Associates, Inc

🔗https://www.ara.com/news/ara-research-mitigate-shortage-respiratory-protection-devices-during-public-health-emergencies
Research to Mitigate a Shortage of Respiratory Protection Devices During Public Health Emergencies: recommendations for sterilization of face masks, supply chain shortage mitigation and links for healthcare professionals.

Nature

🌏🔗https://www.nature.com/articles/d41586-020-00837-4?
Map clusters of diseases to tackle multimorbidity: article defines at risk groups for severe COVID-19 infection


The Lancet

🇨🇳🔗https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(20)30198-5/fulltext
Clinical and epidemiological features of 36 children with Coronavirus disease 2019 (COVID-19) in Zhejiang, China: an observational cohort study, primary research article
Epidemiology/Medicine by The Lancet: Infectious Disease

Science

🇨🇳🔗https://science.sciencemag.org/content/early/2020/03/25/science.abb4218?
Effect of Social Distancing on the Spread of COVID-19, primary research article


Medrxiv

🔗https://www.medrxiv.org/content/10.1101/2020.03.09.20033357v1.full.pdf
Estimates of the severity of COVID-19 disease

https://clinmedjournals.org/articles/jide/journal-of-infectious-diseases-and-epidemiology-jide-6-113.php?jid=jide
A Plausible "Penny" Costing Effective Treatment for Corona Virus - Ozone Therapy

🔗https://www.rivm.nl/node/153991
COVID-19 found in wastewater, good way to monitor in population

Citizen Science and Crowdsourcing

See also : https://coronavirustechhandbook.com/techcommunities
See also : https://coronavirustechhandbook.com/self-reporting

Crowdsourced Science

Analysis Mode

🔗https://www.analysismode.com/
This game empowers people to find patterns and configurations that later will be used to teach an artificial intelligence (AI) to predict vaccine formulas

EU Citizen science

🔗http://eu-citizen.science/citizen-science-resources-related-to-the-covid19-pandemic/
Compilation of Citizen Science and Crowdsourcing projects focused on COVID-19

COVID-19 Pandemic Shareable Scientist Response Database

🔗https://datastudio.google.com/u/0/reporting/715dc546-0160-419d-976d-f87b219f2d5d/page/veXJB?fbclid=IwAR00IdW7AeIw46RUKiWsQYkqpkdGCzecbMQKKoS_NB7gKEi9Xc1MSFMhmFk
Database of scientists who are volunteering help

Crowdfight Covid

🔗https://crowdfightcovid19.org/
📧 [email protected]
Crowdsourcing Platform Tasks for Researchers of COVID-19 to outsource needs 

Impact of Government Measures

🔗https://docs.google.com/document/d/1kZj44-Gvau1zeVedkbSQxRihdRywnDqKAbu_heYEEb8/edit#
Collaborative project to estimate and quantify the impact of government measures on the growth rate, to create an informed-decision tool for governments. Please reason and calculate along, help is very welcome! The results will be valuable as such, and also be used to back an open-source simulator where the effect of up to 50 government measures on the epidemic can be simulated.

Challenges

Sage Health Coronavirus Drug Discovery Competition

🔗 https://www.sage-health.org/coronavirus/
📧[email protected] 
Sage Health’s open source competition to find potential Coronavirus treatments by machine learning. Page has descriptions of the methodology and datasets used by the three winners, and links to github repositories of their code.

COVID-19 Open Research Dataset Challenge 

🔗https://www.kaggle.com/allen-institute-for-ai/CORD-19-research-challenge
Challenge to develop text mining tools to extract data from a machine-readable literature collection. 

Citizen Science

Quantified Flu

🔗 https://quantifiedflu.org
🗣 https://www.twitter.com/gedankenstuecke / [email protected]
An open source, collaborative citizen science project to understand whether our wearable devices can be used to predict when we're sick!

[email protected] for Coronavirus Research

🔗 https://twitter.com/drGregBowman
By downloading [email protected], you can donate your unused computational resources to the [email protected] Consortium, where researchers are working to advance our understanding of the structures of potential drug targets for 2019-nCoV that could aid in the design of new therapies. The data you help generate will be quickly and openly disseminated as part of an open science collaboration of multiple laboratories around the world, giving researchers new tools that may unlock new opportunities for developing lifesaving drugs.

Stanford University Folding Project

🔗https://pcmasterrace.org/folding/
Folding at home is a project started at Stanford University, also involving many other top universities and laboratories all around the world, and that uses our computing power to help study the process of protein folding so as to aid research on various diseases, including many forms of cancer, Alzheimer's, Huntington's and Parkinson's.

The Zooniverse

🔗 https://www.zooniverse.org/
🗣 Twitter: https://twitter.com/the_zooniverse / online forum: talk.zooniverse.org
📧 [email protected]
The Zooniverse is an online citizen science platform with over 2 million registered volunteers who have participated in hundreds of projects on a variety of topics, including biomedical research and time-sensitive projects for e.g. disaster relief. Specialities include advanced pattern detection in images and other datasets, and interfaces with machine learning algorithms in a variety of disciplines.
If you have a dataset that urgently needs help sorting through, please get in touch. We have expertise in building effective projects that collect results at expert-level accuracies. Some research councils have told us funding is available to support this work. 

Fundings and Grants

See also: https://coronavirustechhandbook.com/funding


NSERC Alliance COVID-19 grants
🇨🇦🔗https://www.nserc-crsng.gc.ca/Innovate-Innover/COVID-19/index_eng.asp
Natural Sciences and Engineering Research Council (NSERC) of Canada offers grants of up to $50,000 to university researchers collaborating with private-sector, public-sector or not-for-profit organizations.

Informing the Public

Skype a scientist

🔗https://www.skypeascientist.com/
Skype a Scientist matches scientists with classrooms around the world! 

Edit wikipedia

🔗https://en.wikipedia.org/wiki/2019%E2%80%9320_coronavirus_pandemic
Help wikipedians edit the relevant pages surrounding the Coronavirus pandemic. Here’s a handy tutorial for beginners.

Experts to follow

🔗https://www.ucl.ac.uk/oppenheim/Covid-19_tweeps.shtml?
A list of scientists and organisations with expertise who are themselves highly followed by experts

Science Chatbots

COVID-19 BOT

🔗https://covid19.fas.org/l/en
The Federation of American Scientists, the New Jersey Office of Innovation and the Governance Lab have developed an COVID-19 Ask-A-Scientist ChatBot service, which is powered by volunteers.

Jennifer

🔗https://www.newvoicesnasem.org/jennifer-ai-chatbot
National Academies of Science, Engineering and Medicine (NASEM) have developed the Jennifer COVID-19 Chatbot. You can sign up as a volunteer to help answer questions and expand the ChatBot’s knowledge base.

Trusted Voices

🌏🔗https://www.ucl.ac.uk/oppenheim/Covid-19_tweeps.shtml?
A list of scientists and organisations with expertise who are themselves highly followed by experts

Blogs

A blog on Coronavirus & Academia

🔗 https://bryanalexander.org/category/coronavirus/
🗣 https://twitter.com/BryanAlexander
Bryan Alexander is a futurist. He is currently posting every 1-2 days about Coronavirus and higher education.

80000 Hours

🔗https://80000hours.org/covid-19/
List of resources by 80000hrs.org, including numbers of scientific works and decision-making stuff

How science is changing

🌏🔗https://www.sciencemag.org/news/2020/02/completely-new-culture-doing-research-coronavirus-outbreak-changes-how-scientists
pre-print publishing, slack, twitter -Restoring the culture of doing research - outbreak changes how scientists communicate, lay article.

Project Ideas (add your own!)

Using infrared camera images to test for fever

🔗https://err.ersjournals.com/content/28/152/190011
🔗https://support.owlstonenanotech.com/hc/en-us/community/topics?_ga=2.172014691.1757891918.1583628709-1120005712.1583628709
📧[email protected]
I have multiple methods to screen images, I have found indicators specific to COVID-19 not fever/flu. This can be done on long range military optics. Using the sensor (gyroscope, accelerometer) data in your phone to detect cough pattern via algorithm, based on how phone is being held, or microphone to listen/apply AI to cough with distinguishing characteristics to pneumonia specific to COVID-19 - Also Smartphone or other Breath Biopsy to detect 

CRISPR-based therapies

🔗http://bit.ly/coronavirus-guides
See CRISPR guide RNA design tutorial here for the spike (S) protein

Seasonal Mimicry Approaches for Combating COVID-19

🔗https://docs.google.com/document/d/1wCZ2floqy25CwTgNPj7CDxJE3JW53NqpE_7T13ZGZ4E/edit?usp=sharing
Collaborative research document investigating potential tactics and strategies to combat COVID-19 transmission and human susceptibility through exploiting its apparent sensitivity to seasonal conditions. Is it possible to recreate these conditions - whatever they are - out-of-season?

Vaccination Ideas

a. mass vaccination against influenza (less doubt re: flu symptoms)
b. vaccinate against pneumonia (reduce complications that many die from)
c. design a very cheap, fast test to roll out en masse (see S-Korea)
d. efficient tracking of who has it and with whom they have been in contact (see China)
e. local sustainable production of ventilators/masks.  
For c. People are working on better identification at genetic level. More is possible re smartphone-based testing from symptoms. Ex: animals can be tested for disease on the basis of their sounds. Try powerful ML to analyze coughs (frequency + intensity), temp, facial change, other characteristics easily measurable w mobile phones -- to estimate the probability of corona.
For d. Think of linking existing gps data to an app, as in many asian countries: what’s a v we could use comfortably?