How should we build methods and tools to prepare for future pandemics?

There are several models that we could take to develop methods and tools in order to prepare for future pandemics. We should talk about them.

Sam Abbott

Pandemic preparedness has been in vogue for a while (for obvious reasons)1. The majority of the conversation I’ve seen has been on how to get more, and longer term, funding and on specific initiatives we should focus on2. I have seen much less discussion about how we go about doing this work, whether our traditional research models are a good fit, or if something more is needed. When this is discussed the impression I get is that if traditional research is not the way to go then new organisations, that have provider/user models, are favoured but to me this seems like a potentially very risky way to go about things3.

Over the last several years I have been working on real-time infectious disease modelling4 with the aim of providing evidence faster, and better, than was previously possible. In the main this has proved very very hard, as I know many others have found. In many cases the major issue has not been technical ability (though for me at least perhaps this is a limitation5), or a lack of understanding of what the problem is, but rather the sheer scope of the task. This is compounded by the lack of resources that are connected to the appropriate communities of practice. This makse it hard to even start answering some of the more pressing questions, or in some cases even to understand what they are, in the amount of time available. This has been the case for both reactive work but also preparedness work where the timelines are longer (a few years) but the resources still seem insufficient for the task in hand.

For a while I have been convinced that a community approach6 is the right way to go about this. What do I mean by this? I mean creating something where people (and ideally users) can contribute to a large project - or body of knowledge - whilst retaining ownership, and the credit that comes with it, of their contributions. On the face of it this is how science already works but in practice I think contrasts with the traditional model where separate groups/organisations create competing tools and methodologies and then in theory (but often not in practice) provide these as a service to others7. This is a hard sell but quite a few practioners appear to agree.

This could all just be my echo chamber and there are a wide range of views8. For a while I have been running Twitter polls9 to scope out what people think. I recently came across which is a platform designed for these sort of conversations. From a first pass it seems great. Below is a conversation I’ve started aiming to find out what people think. Currently the questions are a pretty eclectic mix that I put together but you can and should submit your own. Initial results are shaping up to be pretty interesting.

If you find this useful/interesting please consider sharing it in your network. I think it’s important we think more about how we do work before attention from this problem fades yet again.

  1. There is a lot to this but here I just focus in on my domain interest which is processing data to get useful signals to inform decisions.↩︎

  2. For example certain groups are very in faviour of metagenomic scanning and others want to develop a weather forecasting service for infectious disease.↩︎

  3. Borne out I think by the recent shuttering of the Pandemic Preparedness Institute:↩︎

  4. A very biased round-up for a (sadly unsuccessful) promotion application:↩︎

  5. Some thoughts on limitations with my work here:↩︎

  6. See this starting to take shape here:↩︎

  7. Sound good? Get involved:↩︎

  8. Clearly given the numerous projects starting to take shape based on similar ideas but with very different approaches.↩︎

  9. I am a very serious scientist.↩︎


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For attribution, please cite this work as

Abbott (2022, Oct. 13). Sam Abbott: How should we build methods and tools to prepare for future pandemics?. Retrieved from

BibTeX citation

  author = {Abbott, Sam},
  title = {Sam Abbott: How should we build methods and tools to prepare for future pandemics?},
  url = {},
  year = {2022}