Fighting COVID19 with data science and bioinformatics

by Paul Agapow
in science

tagged data-science, bioinformatics, infectious-disease

Last updated 2020/4/4. Originally published on LinkedIn

I won't be updating this list further as the intention was to point people to the right places to help in a crisis.

Should you have an potentially useful information set or data source, the best course of action is you for to add it to existing data sources, making it widely available, rather than working in isolation. Some of the below links will help you to the right place.

As a bioinformaticist / genomicist / lab scientist / whatever, you might rightly want to help efforts against COVID. Here are a few that have come up in discussions, with a bias towards the UK and bioinformatics / biomedical data science / healthcare.

But first

There's lots that you can do which is non-technical:

The Red Cross is looking for donations and volunteers to do driving, take supplies to people, make phone calls to the isolated.

The NHS is looking for volunteers including those with technical and lab skills

Technical efforts

Quick editorial: there's a lot of low-value information out there, and we don't need more data scientists without epidemiology banging out graphs that will just scare people. The below list aims to capture projects with work to do, that can use warm bodies with the right skills. Please, use your time wisely on meaningful projects that can help and be respectful of the time of those who are in the frontline of this crisis.

The Royal Society is calling for modellers, not necessarily in epidemiology, to aid in "rapid assistance in modelling the pandemic (RAMP)"

HDR-UK is maintaining a HDR UK COVID-19 Knowledge + Skills Matchmaker "a sharing space for expertise and experience, as well as a forum to post queries which might need input." Note this is more for established teams.

ELIXIR & European Bioinformatics Communities are organising the Global COVID-19 Biohackathon on April 5 – 11, 2020

Data Against Covid (website) (twitter) are "a community of medical professionals, life and data scientists on a quest to defeat Covid-19. Let's beat this pandemic together!" Looking for scientists, people who can code or debug, or curate data.

The Turing Institute is heading a Call for COVID-19 rapid response data science taskforce. Possibly more for established research groups, but give it a look.

Hack from Home is a virtual hackathon running April 4-5

MIT COVID19 Virtual hackathon April 3-5

Crowdfight COVID19 is a site where scientists may look for help and other can list their skills that may be of help: "They only need to state a wish or a task, which can go from a simple time-intensive task to be performed (e.g. transcribe data, manually annotate images), to answering a technical question which is beyond their expertise, or to setting up a collaboration. They only need to explain their request in a few lines. Then, another scientist makes the effort of understanding that request and making it reality."

Mishal Patel at AstraZeneca is looking to "develop an algorithm for immediate diagnosis of COVID-19 from X-Rays and CT scans in the UK. If you know of anyone with DICOM format X-Ray or CT data of COVID-19 patients that would be interested in collaborating on this project please let them know of this project."

The COVID19 Global Online Hackathon "is an opportunity for developers to build software solutions that drive social impact, with the aim of tackling some of the challenges related to the current coronavirus (COVID-19) pandemic ... The hackathon welcomes locally and globally focused solutions, and is open to all developers - with support from technology companies and platforms including AWS, Facebook, Giphy, Microsoft, Pinterest, Salesforce, Slack, TikTok, Twitter and WeChat, who will be sharing resources to support participants throughout the submission period."

The Overflow: ways to fight COVID19 from home: a variety of links including folding at home, and various coordinating forums

A few tech companies and startups are turning their resources and skills towards the fight. An incomplete list:

  • scibite
  • Causaly has a large corpus of potentially useful data in their knowledge base that needs mining and expert insight. This may be a good resource for already ongoing efforts. See Yiannis Kiachopoulos.

The OHDSI COVID-19 Study-A-Thon is already in progress, but those with EHR and observational data expertise may watch that space for forthcoming developments.

There are numerous COVID-relevant data tranches and projects on Kaggle, including some massive document dumps, requiring NLP. While these could be important, remember that this is not a programming competition and that methods and results should be shared.

There are reports that PHE could use genomicists, but it's unclear how accurate or recent this is. Research carefully.](https://www.hpcwire.com/off-the-wire/global-covid-19-biohackathon-announced/)