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Reproducible Healthcare Simulations in Python and R

For the UKRI-funded project STARS: Sharing Tools and Artefacts for Reproducible Simulations
README.md

The STARS Framework

Several repositories are related to our recent paper 'Towards sharing tools and artefacts for reusable simulations in healthcare', which includes three examples of the implemented STARS framework in Python:

Repositories Description
stars-treat-sim STARS 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-example STARS 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:

Repositories Description
stars-treat-simmer R simmer implementation of treatment simulation model
stars-shiny-simmer Template for shiny interface to simmer DES model
stars-stlite-example stlite template for SimPy models
stars-simpy-jupterlite JupyterLite template for SimPy models

Generating DES models using LLMS

Repositories Description
llm_simpy Code for exploring the ability of LLMs to generate SimPy models and streamlit interfaces.
llm_simpy_models The SimPy models and apps generated by LLMs, deployed as a single app.

Computational reproducibility of published DES models

As part of STARS, we haved assessed the reproducibility of published simualation models, as described in 'On the reproducibility of discrete-event simulation studies in health research: an empirical study using open models'.

Repositories Description
stars-reproduction-protocol Latex files for reproduction protocol
stars-reproduce-allen-2020 Test run of reproducibility protocol on Allen et al. 2020
stars-reproduction-template Template for assessment of computational reproducibility
stars-reproduce-shoaib-2022 Reproduction study 1: Shoaib and Ramamohan 2022 (Python)
stars-reproduce-huang-2019 Reproduction study 2: Huang et al. 2019 (R)
stars-reproduce-lim-2020 Reproduction study 3: Lim et al. 2020 (Python)
stars-reproduce-kim-2021 Reproduction study 4: Kim et al. 2021 (R)
stars-reproduce-anagnostou-2022 Reproduction study 5: Anagnostou et al. 2022 (Python)
stars-reproduce-johnson-2021 Reproduction study 6: Johnson et al. 2021 (R)
stars-reproduce-hernandez-2015 Reproduction study 7: Hernandez et al. 2015 (Python model + R figures)
stars-reproduce-wood-2021 Reproduction study 8: Wood et al. 2021 (R)
stars_wp1_summary Summary 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.

Template DES models

We have developed template reproducible analytical pipeline (RAP) for DES in python and R.

Repositories Description
rap_template_python_des Template reproducible analytical pipeline (RAP) for simple python discrete-event simulation (DES) model.
rap_template_r_des Template reproducible analytical pipeline (RAP) for simple R discrete-event simulation (DES) model.

DES in Python tutorial

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

Repositories Description
intro-open-sim An introduction to Discrete-Event Simulation using Free and Open Source Software.

Other repositories

Repositories Description
stars-publications List of all STARS publications
stars-logo SVG and PNG files with logo
stress_update A review and update of the Strengthening the Reporting of Empirical Simulation Studies guidelines for DES, SD, and ABS.
stars-eom-rcc Modifications to the "Exeter Oncology Model: Renal Cell Carcinoma edition (EOM-RCC)" as part of STARS work package 3.
stars_wp3_summary Reflections from prospective and retrospective application of the STARS framework
gw4_prize_presentation Amy Heather's presentation for the GW4 Open Research Prize 2024/25.

Team

Member ORCID GitHub
Thomas Monks ORCID: Monks https://github.com/TomMonks
Alison Harper ORCID: Harper https://github.com/AliHarp
Amy Heather ORCID: Heather https://github.com/amyheather
Navonil Mustafee ORCID: Mustafee https://github.com/NavonilNM
Andrew Mayne ORCID: Mayne https://github.com/andy-mayne

Popular repositories Loading

  1. intro-open-sim intro-open-sim Public

    An introduction to building open Descrete-Event Simulation (DES) in Python

    Jupyter Notebook 6

  2. stars-simpy-jupterlite stars-simpy-jupterlite Public template

    A template for Discrete-Event Simulation (DES) repositories that use JupyerLite and xeus-python to enable reproducible environments and models

    Jupyter Notebook 3

  3. stars-shiny-simmer stars-shiny-simmer Public

    WORK IN PROGRESS: An example R shiny interface to a simmer DES model.

    JavaScript 3

  4. stars-eom-rcc stars-eom-rcc Public

    Forked from nice-digital/NICE-model-repo

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

    R 3

  5. rap_template_python_des rap_template_python_des Public template

    Template reproducible analytical pipeline (RAP) for simple python discrete-event simulation (DES) model.

    Jupyter Notebook 3

  6. llm_simpy llm_simpy Public

    Research Compendium for exploring the ability of LLMs to generate SimPy models and streamlit interfaces.

    Jupyter Notebook 2

Repositories

Showing 10 of 38 repositories
  • stroke_rap_python Public

    Applying the Python DES RAP Template to the Stroke Capacity Planning Model from Monks et al. 2016

    pythonhealthdatascience/stroke_rap_python’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Apr 3, 2025
  • intro-open-sim Public

    An introduction to building open Descrete-Event Simulation (DES) in Python

    pythonhealthdatascience/intro-open-sim’s past year of commit activity
    Jupyter Notebook 6 MIT 0 0 0 Updated Apr 3, 2025
  • llm_simpy Public

    Research Compendium for exploring the ability of LLMs to generate SimPy models and streamlit interfaces.

    pythonhealthdatascience/llm_simpy’s past year of commit activity
    Jupyter Notebook 2 MIT 0 0 0 Updated Mar 28, 2025
  • gw4_prize_presentation Public

    Amy Heather's presentation for the GW4 Open Research Prize 2024/25

    pythonhealthdatascience/gw4_prize_presentation’s past year of commit activity
    HTML 1 CC-BY-4.0 0 0 0 Updated Mar 28, 2025
  • rap_template_python_des Public template

    Template reproducible analytical pipeline (RAP) for simple python discrete-event simulation (DES) model.

    pythonhealthdatascience/rap_template_python_des’s past year of commit activity
    Jupyter Notebook 3 MIT 0 2 0 Updated Mar 26, 2025
  • rap_template_r_des Public template

    Template reproducible analytical pipeline (RAP) for simple R discrete-event simulation (DES) model.

    pythonhealthdatascience/rap_template_r_des’s past year of commit activity
    R 1 1 4 (1 issue needs help) 0 Updated Mar 25, 2025
  • llm_simpy_models Public

    The SimPy models and apps generated by LLMs, deployed as a single app.

    pythonhealthdatascience/llm_simpy_models’s past year of commit activity
    Python 1 MIT 0 0 0 Updated Mar 25, 2025
  • .github Public

    GitHub profile

    pythonhealthdatascience/.github’s past year of commit activity
    0 MIT 0 0 0 Updated Mar 25, 2025
  • stars-ciw-example Public

    A treatment simulation model implemented in CiW

    pythonhealthdatascience/stars-ciw-example’s past year of commit activity
    Python 1 GPL-3.0 3 0 0 Updated Jan 22, 2025
  • stars_wp1_summary Public

    Summary 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.

    pythonhealthdatascience/stars_wp1_summary’s past year of commit activity
    TeX 1 CC-BY-4.0 0 0 0 Updated Jan 22, 2025
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