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@pythonhealthdatascience

Reusable and Reproducible Healthcare Simulations in Python and R

For the UKRI-funded project STARS: Sharing Tools and Artefacts for Reproducible/Reusable Simulations

Welcome to thepythonhealthdatascience GitHub organisation!

Note on our name: We started as a Python-only initiative, but quickly expand to include R to, as another popular language for healthcare simulation.

This project tackles the challenges ofsharing, reusing, and reproducing discrete event simulation (DES) models in healthcare. Our goal is to create open resources using the two most popular open-source languages for DES: Python and R. Here you’ll find tutorials, code examples, and tools to help researchers and practitioners develop, validate, and share DES models more effectively.

This work has been centred around three important qualities for shared models - that they can be:

  • Reproducible - running code regenerates the published results - which verifies code is working as expected and increases trust.
  • Reusable - code can be adapted and used in new contexts - which saves time and increases impact.
  • Replicable - new code based on described methods produces consistent results - which gives confidence in results, their validity and reliability.

We have also been exploring how large language models (LLMs) could be used to support the development of simulation models.

Explore our repositories to get started, and feel free to reach out!

Project team members:

Tom Monks

  • ORCID
  • GitHub

Amy Heather

  • ORCID
  • GitHub

Alison Harper

  • ORCID
  • GitHub

Nav Mustafee

  • ORCID
  • GitHub

Andy Mayne

  • ORCID
  • GitHub

Fatemeh Alidoost

  • ORCID
  • GitHub

Reproducible simulations

Click to find out more

Assessing the reproducibility of published DES models

We attempted to reproduce the outputs from eight Python and R DES models, as described in:

Heather, A., Monks, T., Harper, A., Mustafee, N., & Mayne, A. (2025). On the reproducibility of discrete-event simulation studies in health research: an empirical study using open models. arxiv.https://doi.org/10.48550/arXiv.2501.13137.

RepositoriesDescription
stars-reproduction-protocolLatex files for reproduction protocol
stars-reproduce-allen-2020Test run of reproducibility protocol on Allen et al. 2020
stars-reproduction-templateTemplate for assessment of computational reproducibility
stars-reproduce-shoaib-2022Reproduction study 1: Shoaib and Ramamohan 2022 (Python)
stars-reproduce-huang-2019Reproduction study 2: Huang et al. 2019 (R)
stars-reproduce-lim-2020Reproduction study 3: Lim et al. 2020 (Python)
stars-reproduce-kim-2021Reproduction study 4: Kim et al. 2021 (R)
stars-reproduce-anagnostou-2022Reproduction study 5: Anagnostou et al. 2022 (Python)
stars-reproduce-johnson-2021Reproduction study 6: Johnson et al. 2021 (R)
stars-reproduce-hernandez-2015Reproduction study 7: Hernandez et al. 2015 (Python model + R figures)
stars-reproduce-wood-2021Reproduction study 8: Wood et al. 2021 (R)
stars_wp1_summarySummary of the eight computational reproducibility assessments conducted as part of STARS Work Package 1. These assessed discrete-event simulation papers with models in Python and R.

Online book guiding how to create reproducible Python and R DES models

We are developing a book which demonstrates how to create DES models in Python (SimPy) and R (simmer) which are reproducible - following the recommendations from our assessment above - and also, form a reproducible analytical pipeline. This is illustrated using a simple template model and an applied stroke model.

RepositoriesDescription
des_rap_bookOnline book providing detailed step-by-step guidance on developing reproducible DES models in Python and R
pydesrap_mmsReproducible analytical pipeline (RAP) for Python discrete-event simulation (DES) implementing an M/M/s queueing model.
rdesrap_mmsReproducible analytical pipeline (RAP) for R discrete-event simulation (DES) implementing an M/M/s queueing model.
pydesrap_strokeReproducible analytical pipeline (RAP) for Python discrete-event simulation (DES) implementing the Stroke Capacity Planning Model from Monks et al. 2016.
rdesrap_strokeReproducible analytical pipeline (RAP) for R discrete-event simulation (DES) implementing the Stroke Capacity Planning Model from Monks et al. 2016.

Reusable simulations

Click to find out more

Systematic review

We conducted a systematic review of how healthcare DES models (any software/language) are currently shared in the literature.

We identified common barriers to model reuse, including lack of documentation and standardised repositories.

Key takeaway: There is a clear need for better frameworks and tools to support reusable simulation models.

Monks, T., & Harper, A. (2023). Computer model and code sharing practices in healthcare discrete-event simulation: a systematic scoping review. Journal of Simulation, 19(1), 108–123.https://doi.org/10.1080/17477778.2023.2260772

STARS framework

Following this review, we developed the STARS framework, which provides essential and optional guidance to help make shared models more reusable. This is described in:

Monks, T., Harper, A., & Mustafee, N. (2024). Towards sharing tools and artefacts for reusable simulations in healthcare. Journal of Simulation, 1–20.https://doi.org/10.1080/17477778.2024.2347882

This paper included three examples of the STARS framework implemented in Python:

RepositoriesDescription
stars-treat-simSTARS paper example 1. Implements essential components + annotated notebook to run code executable online with Binder
stars-simpy-example-docs

stars-streamlit-example
STARS paper example 2. Fully implements essential + optional components including enhanced documentation hosted online and web app
stars-ciw-exampleSTARS paper example 3. Fully implements essential + optional components, but with different licence, documentation publishing software, web app framework and web app hosting

Subsequently, we have been developing similar examples in R, as well as looking at webassembly:

RepositoriesDescription
stars-treat-simmerR simmer implementation of treatment simulation model
stars-shiny-simmerTemplate for shiny interface to simmer DES model
stars-stlite-examplestlite template for SimPy models
stars-simpy-jupterliteJupyterLite template for SimPy models

Applying STARS

We applied the STARS framework to an oncology cost-effectiveness model developed by PenTAG and collaborates for the NICE Pathways Pilot appraisal.

RepositoriesDescription
stars-eom-rccModifications to the "Exeter Oncology Model: Renal Cell Carcinoma edition (EOM-RCC)" as part of STARS work package 3.

Replicable simulations

Click to find out more

STRESS guidelines

Tom was involved in developing the Strengthening The Reporting of Empirical Simulation Studies (STRESS) guidelines. They are a 20-item checklist (with guidelines for DES, agent-based simulation, and system dynamics) which outline the details authors should include about their model in their reports/publications.

Monks, T., Currie, C. S. M., Onggo, B. S., Robinson, S., Kunc, M., & Taylor, S. J. E. (2018). Strengthening the reporting of empirical simulation studies: Introducing the STRESS guidelines. Journal of Simulation, 13(1), 55–67.https://doi.org/10.1080/17477778.2018.1442155.

Updating STRESS

We are currently undergoing a review and update of the STRESS guidelines.

RepositoriesDescription
stress_updateA review and update of the Strengthening the Reporting of Empirical Simulation Studies guidelines for DES, SD, and ABS.

Using LLMs

Click to find out more

Generating DES models using LLMS

We investigated the ability to replicate Discrete-Event Simulation models reported in the literature using iterative prompting of Perplexity.AI's foundational model:

Monks, T., Harper, A., & Heather, A. (2025). Unlocking the Potential of Past Research: Using Generative AI to Reconstruct Healthcare Simulation Models. arxiv.https://doi.org/10.48550/arXiv.2503.21646

RepositoriesDescription
llm_simpyCode for exploring the ability of LLMs to generate SimPy models and streamlit interfaces.
llm_simpy_modelsThe SimPy models and apps generated by LLMs, deployed as a single app.

Other repositories

Click to find out more

SW25 DES in Python tutorial

There is a tutorial on discrete-event simulation for the Operational Research Society Simulation Workshop 2025:

Monks, T., Harper, A., Heather, A., Mayne, A., & Mustafee, N. (2025). Building healthcare discrete-event simulation models in free and open source software: an introductory tutorial. Proceedings of the Operational Research Society Simulation Workshop 2025 (SW25).https://doi.org/10.36819/SW25.004.

RepositoriesDescription
intro-open-simAn introduction to Discrete-Event Simulation using Free and Open Source Software.

GW4 Open Research Prize

Amy was shortlisted for the GW4 Open Research Prize for her work on assessing the computational reproducibility of published models. The slides from her presentation at the prize ceremony are here:

RepositoriesDescription
gw4_prize_presentationAmy Heather's presentation for the GW4 Open Research Prize 2024/25.

Review of computer simulation in orthopaedic services

We used a topic modelling approach to examine and map the computational simulation literature applied to operational-level orthopedics services, combined with a structured analysis of the papers. The repository below serves as supplementary material for the paper:

Mapping Applications of Computer Simulation in Orthopedic Services: A Topic Modeling Approach.

RepositoriesDescription
scope_wsc_2025Data and analysis for a literature review of simulation for orthopaedics services

Other STARS repositories

RepositoriesDescription
stars-publicationsList of all STARS publications
stars-logoSVG and PNG files with logo
stars_wp3_summaryReflections from prospective and retrospective application of the STARS framework

Popular repositoriesLoading

  1. intro-open-simintro-open-simPublic

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  2. stars-simpy-jupterlitestars-simpy-jupterlitePublic template

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  3. pydesrap_mmspydesrap_mmsPublic template

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  4. stars-treat-simmerstars-treat-simmerPublic

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  5. stars-shiny-simmerstars-shiny-simmerPublic

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  6. stars-eom-rccstars-eom-rccPublic

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    Modifications to the "Exeter Oncology Model: Renal Cell Carcinoma edition (EOM-RCC)" as part of STARS work package 3.

    R 3

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