Our team is providing technical and software support to the ongoing 2019-nCoV-SARS/COVID-19 pandemic. Much of this builds on tools that we have developed over the previous 5 years, with some ongoing development of these tools to track the research needs:
- orderly and OrderlyWeb, our reproducible reporting framework developed for the Vaccine Impact Modelling Consortium, is being used to coordinate research results amongst our (now distributed) team of researchers in a reproducible and traceable way. During the response we have developed extensions such as sharepoint support and an Rstudio addin, as well as a lot of new features
- cyphr is being used to encrypt data at rest
We are working directly with researchers as they develop models and analyses, supporting
- CovidSim (an individual-based simulation requiring significant HPC capacity to run)
- sircovid an odin model for the epidemic through the UK hospital system, fit using particle filter MCMC
- squire an odin model with both a stochastic version used to fit to data (with nightly reports fitting to 110 countries) and a deterministic version that is available on the web (the web app was created by Bio Nano consulting, and the embedded model runs purely client side, compiled with odin.js)
- Tooling and strategies for processing multiple daily streams of incoming unstandardised data.