Welcome and opening remarks

Safety first

🔥🔥🔥 In case of fire 🔥🔥🔥

🛜 WIFI

  • EDUROAM
  • for non-Academic participants

The Cloud

  1. Connect to ’_The Cloud’ on your device
  2. Follow the instructions

Support

A brief history of odin

🏺 “Classic” odin - the beginnings (2016-2019)

  • odin created to integrate ODEs (e.g. for compartmental models) in R with a domain-specific language (DSL)
  • Limited support for difference (discrete-time) equations
  • Automatic translation to C; efficient solutions in little code
  • Used at Imperial for malaria, HIV, ebola and other diseases
  • No support for inference

😷 COVID-19 response (2020-2022)

(Knock et al 2021, Science Translational Medicine)

😷 COVID-19 response (2020-2022)

  • mcstate for statistical machinery (particle filter, pMCMC)
  • dust for efficient parallel simulation
  • odin.dust compile odin code to use dust
  • Collaborative work by the UK real-time modelling & research software engineers teams at Imperial College
  • Many, many, rough edges

Meanwhile…

  • Different versions of the stack have been picked up outside of Imperial
    • Zurich, Munster, LSHTM, CDC, Fudan, Lancaster, Pasteur, NC State, Norway, Switzerland
  • People tried to repurpose statistical machinery in mcstate
  • We hit limits of computational efficiency and ability to manage inputs and outputs with the COVID model
  • The documentation (22 vignettes) and packages (>5) were hard to navigate and discover

Version 2

New software

  • Design of a new architecture, rewiring data, model and parameters
  • New statistical interface, monty
    • A new small BUGS-inspired DSL for priors
    • Works well with odin models, but usable on its own
    • Modular, and eventually easy to extend
    • Fully replaces mcstate

New community

  • We want to understand how people are using these tools
  • What have you built, what do you want to build?

🙌 For us to know

Who identifies as

  1. 🟢 Novices (no prior tool experience)
  2. 🟡 Users of other tools (e.g. Stan, JAGS, BayesTools)
  3. 🔵 odin/mcstate/monty users

Aim of the workshop

  1. Introducing the 2nd generation of the toolkit
  2. Collecting feedback
  3. Building a community and fostering collaboration

Overview of workshop

Day 1: Introducing the Tools and Applications

Day 2: Feedback, Development, and Support

📸 Group photo 1:40PM

🥂 Reception 5:30PM

🍽️ Workshop Dinner @ “The BroadCaster” 7PM