Better software, better COVID-19 research

Posted by g.law on 7 May 2020 - 8:59am
Mike Jackson
Mike Jackson

By Mike Jackson, EPCC

This blog post was originally published on the EPCC blog

A friend recently forwarded me a tweet from Professor Neil Ferguson, director of J-IDEA and the MRC Centre for Global Infectious Disease Analysis at Imperial College London, concerning their COVID-19 pandemic modeller, used by the UK Government:

Prof. Ferguson's follow-up tweet was to announce that refactoring of the COVID-19 pandemic modeller had begun:

There proceeded a (remarkably civilised by Twitter standards) thread touching upon issues including software as critical infrastructure, research software development best practice (or lack of), open science, open source (or lack of) and reproducibility. "Should have gone to The Software Sustainability Institute," I thought. The Institute has been assisting researchers with exactly those challenges for 10 years now!

Some of the Twitter reactions reminded me of the furore around GISS Surface Temperature Analysis (GISTEMP), NASA's simulation to calculate and compare global surface temperature anomalies. In 2007, responding to demands from climate bloggers, the GISTEMP source code was released, to a less than positive reaction. GISTEMP was deemed to be poorly organised, incomplete, bug-ridden and would not run. Indeed, there were accusations that the code that was released was not the actual source code. This motivated the formation of the Clear Climate Code Project to reimplement GISTEMP with an emphasis on code clarity, to encourage people to download, inspect and run the code, and to increase public confidence in climate science results. Nick Barnes and David Jones give a great overview of the project and how it came into being in "Clear Climate Code: Rewriting Legacy Science Software for Clarity" (doi: 10.1109/MS.2011.113).

Prof. Ferguson and his team have now released their refactored C++ code on GitHub, within the covid-sim project, available under the GNU General Public License v3.0.


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