- Course overview
- Search within this course
- What is a mathematical model?
- Introduction to networks and graphs
- How to get from biology to mathematics
- Introduction to three mathematical model formalisms
- Case study – Infectious diseases (SIR Models)
- Other modelling approaches
- Sustainable modelling and sharing
- Summary
- Check your learning
- Your feedback
- References
All materials are free cultural works licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, except where further licensing details are provided.
Sustainable modelling and sharing
When we build models, we want them to be useful not just for ourselves right now, but also for others (or ourselves!) in the future. Therefore, it is important to think about reproducibility (can others run your model and get the same results?) and sustainability (can the model be reused, tested, or extended?). Here we provide you with a list of useful resources for you to explore:
Model databases and resources
- BioModels – a large, free database where many published models are stored in standard formats, so they can be reused and cited.
- JWS Online – is a model database and lets you simulate and visualise models directly in your web browser.
- Menelmacar – Making Execution of (Nearly) Every Life-science Model ACcessible to All Researchers, helps to visualise models from the EMBL-EBI’s BioModels database.
- BioSimulators – a registry of tools that can run models in standard formats, helping ensure models work across different software.
- Epirecipes – a collection of infectious disease transmission models in various coding languages
Standards and formats
- COMBINE is a community that develops standards like SBML (for models) and SED-ML (for simulation setups). Using these helps others run your model as you intended and makes models interoperable between different modelling tools.
Code sharing and good practices
- Share your model code and simulation scripts on platforms like GitHub, GitLab, or Zenodo. This makes it easier for others to find and cite your work.
- Document clearly: What does your model represent? Where did the parameters come from? What assumptions did you make?
- Provide example simulations so others can check that your model behaves as expected.
Further learning
- A great guide for biologists on how to make biochemical models reproducible: Best Practices for Making Reproducible Biochemical Models (Porubsky VL et al, 2020).