Skip to content
@pythonhealthdatascience

Reproducible Healthcare Simulations in Python and R

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

STARS: Sharing Tools and Artefacts for Reproducible Simulations

STARS Framework

The STARS framework is a set of open practices, tools and learning materials to produce enhanced versions of research artefacts that intend to increase accessibility for others to (re)use, adapt and build on work.

Essential components of STARS framework (shaded in green below):

  • Open license
  • Dependency management
  • Model created using free and open-source software (FOSS)
  • Minimum documentation
  • Research artefact meta data (ORCID ID + citation information)
  • Remote code repository
  • Open science archive

Optional components of STARS framework (shaded in blue below):

  • Enhanced documentation
  • Documentation hosting
  • Online coding environment
  • Model interface
  • Web app hosting

STARS framework overview

Repositories

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:

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

Repositories as part of work package 1:

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

Other repositories are:

Repositories Description
stars-publications List of all STARS publications
stars-simpy-jupterlite JupyterLite template for SimPy models
stars-stlite-example stlite template for SimPy models
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.

Team

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

Popular repositories

  1. stars-publications stars-publications Public

    A list of all STARS publications including journals articles, conference papers, book chapters, pre-prints and presentations

    2

  2. stars-simpy-example-docs stars-simpy-example-docs Public

    STARS Project: Example `simpy` model documentation using JupyterBook, GitHub Pages, and STRESS

    Jupyter Notebook 1 1

  3. 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 1

  4. stars-treat-simmer stars-treat-simmer Public

    R Simmer implemention of the treatment simulation model

    R 1

  5. stars-reproduce-allen-2020 stars-reproduce-allen-2020 Public

    Test-run of our reproducibility protocol on Allen et al. 2020 (A simulation modelling toolkit for organising outpatient dialysis services during the COVID-19 pandemic)

    Jupyter Notebook 1

  6. stars-ciw-example stars-ciw-example Public

    A treatment simulation model implemented in CiW

    Jupyter Notebook

Repositories

Showing 10 of 15 repositories

Top languages

Loading…

Most used topics

Loading…