JuliaCon 2026
Three talks on composable infectious disease modelling in Julia
Sam Abbott · samabbott.co.uk · github.com/seabbs · epiaware.org
The talks
All three are on Friday 14 August 2026 in Muschel — N3, times Europe/Berlin.
14:30–14:45
A composable Julia ecosystem for infectious disease modelling
A roadmap, challenges, and questions
Where EpiAware is going, what we have got wrong so far, and the questions we would like the Julia community to answer.
14:45–15:00
Estimating epidemiological delay distributions
From R/Stan to Julia
CensoredDistributions.jl, and an honest comparison with the R and Stan implementation it grew out of.
16:45–17:00
Composable probabilistic models
Lowering barriers to rigorous infectious disease modelling
Why composition might be how modelling evidence gets to be timely, rigorous and collaborative at once, and what is still missing.
My submitted conference bio
🤖 The following was drafted by @seabbs-bot, who has a very suspiciously high opinion of me, so take it with a pinch of salt.
I am an Assistant Professor at the London School of Hygiene & Tropical Medicine. I did my PhD in the optimal usage of the BCG vaccine, transitioning to work on real-time modelling of infectious disease outbreaks on the 3rd of January 2020. Four days later, I switched to work on what was then known as 2019-NCoV. I did early work on the size and scale of the initial outbreak, tracking transmissions in different countries, and exploring the potential role of different interventions. Throughout the pandemic, I ran a dashboard that was used by over a million people. I also provided estimates, forecasts, and analyses weekly to the UK government advisory bodies. I developed the tools and methods we used into open source software and these were used by upwards of 30 public health agencies around the world. I have continued to work in this area with a focus on improving tools and methods used both in research and in public health practice. I have recently transitioned to Julia for my work and am exploring how to propagate Julia based tools to the users of our current tooling and to the wider infectious disease modelling community.
Other recent work you might like
Julia
- CensoredDistributions.jl. Censoring and truncation for Distributions.jl.
- ConvolvedDistributions.jl. The next layer up, combining delays.
- EpiAware. The organisation these talks are about.
- EpiAwarePackageTools.jl. One rigid package template.
- EpiAwareADTools.jl. AD workarounds we host until the upstream fix lands.
R
- epinowcast. The ecosystem this is trying to become in Julia, with a community forum and seminar series.
- primarycensored. The R and Stan package behind the delays talk.
- epidist. Individual-level delay estimation.
- EpiNow2 and scoringutils. Widely used, and what I want a better foundation for.
Papers and talks
- ComposableTuringIDModels.jl and what we want from an approach. The prototype behind the composable models talk, and the design considerations it is built to meet. The paper is in CDC clearance.
- A workflow for infectious disease modelling. The paper behind the roadmap talk.
- BVDOutbreakSize. A live report on the size of the 2026 DRC outbreak of Ebola disease caused by Bundibugyo virus. It builds on the Imperial (McCabe et al.) report. Source.
- How I am LLM. What coding agents do and do not do in a research workflow.
- How to serial interval?. Delays, censoring, and the serial interval as a composition.
The prompts page has the brief I wrote for this site and the steers that followed.