Open Epidemiology for pandemic modelling: a transparent, traceable, reusable, open source pipeline for reproducible science

Historically, models used to support advice to government have not been publicly available, at least not readily, prior to publication. Technological advances and the growth of open source and reproducible science mean this is no longer tenable. Although current models feeding into UK policy are publicly available, they still lack the transparent and readily traceable chain of evidence connecting data and assumptions with model outputs that allows them to be readily independently assessed.

Our Data Pipeline supports the implementation of COVID-19 epidemiological models that we, the Scottish COVID-19 Response Consortium (SCRC), have developed using volunteer resources within the RAMP initiative, to create new, complementary models. The Data Pipeline fulfils a critical role in our assessment of fitness for purpose for the models in providing policy advice, by managing and documenting a chain of trust that connects the primary data, analyses, and published and unpublished literature on COVID-19 to model outputs, documenting provenance of the conclusions being reached. The software interfaces we develop will be powerful, generic tools that will be useful to any policy-oriented modelling community.