Simulating COVID-19 with the Francis Crick Institute


Read about how Hadean continued to grow even in a pandemic.

3 min read

Why We’re Delighted to Renew Our Partnership with the FCI

The last three months have changed the world irrevocably and the COVID-19 outbreak has highlighted our limitations in understanding the transmission of disease. Governments, organisations and businesses are all to some extent operating in the dark as they race to take action. Against this backdrop, Hadean have renewed our partnership with the Francis Crick Institute, tracking how viruses spread – both within an individual, and through urban areas.

Together we hope to uncover valuable insights into virus transmission, enabling effective measures to be put in place, quickly and reliably. Although the project is focussed on data from COVID-19, the algorithms will be generic and applicable to future epidemics, providing a reliable model on which to predicate mitigating actions.

Simulating Virus Transmission

Hadean Simulate (previously known as Aether Engine) will combine analysis of person-to-person interaction with insight into how the virus transmits within an individual, providing a complete picture of the pathogen’s spread.

The project will utilise massive complex data sets, mapping the millions of movements and interactions that take place every day within a city, across public transport, social gatherings and work environments for covid-19 outbreak simulation. At the same time in-vivo data is ingested, addressing how the virus currently enters human cells, multiplies and spreads to the lungs, bearing in mind the genetic differences that exist person to person, such as immune system strength.

The simulation will then forecast how susceptible an individual is to infection and the likelihood that they can pass on the virus. It will provide near real-time analysis necessary for planning protective measures, easing the burden on healthcare infrastructure and saving lives.

The project builds upon Hadean’s prior work with the Francis Crick Institute, which involved simulating proteins and formulating mathematical models, leading to a co-published paper. Dr Paul Bates, leading the project, commented, ‘I’m very excited about the Crick’s collaboration with Hadean. We believe our algorithms will have future applications in the advent of other virus-driven epidemics, predicting the consequences and protocols that governments could adopt to help save lives.’

He went on to say, ‘Gaining access to parallel compute expertise and Hadean Simulate will be critical to how we model SARS-CoV-2, the virus that causes COVID-19. Simulations developed on Hadean Simulate will enable us to significantly speed up predictions on how the virus interacts with humans.’

The Role of Hadean Simulate

A library for spatially partitioning agent-based simulations, Hadean Simulate, is underpinned by the Hadean platform – a proprietary compute model, which ensures any programme written on it is distributed by default.

The distributed octree data structure dynamically partitions physical simulations to provide additional computing power as required, reducing the expense and engineering challenges typically associated with running hyper-scale simulations. Instead, Hadean Simulate enables scientists and organisations to build spatial simulations that achieve newfound levels of scale and fidelity.

Ultimately, researchers at the Francis Crick Institute will be able to run complex simulations at speed, deriving accurate conclusions despite the size and complexity of the data sets involved.