Some tools and resources for modeling
Slides: https://www.andreashandel.com/presentations/
2025-05-27
Acknowledgements
- Lot’s of people contributed. See the websites for each tool/resource.
- NIH funding.
Format for this presentation
- I’ll give a very short introduction to the tools/resources.
- The bulk will be show & tell demonstration and Q&A.
- I’ll focus on tools/resources we developed.
Upcoming SISMID Course
- Summer Institute in Statistics and Modeling in Infectious Diseases.
- 2.5 day workshop “Infectious Diseases, Immunology and Within Host Models” with Paul Thomas and me.
- (Thursday workshop is a shortened version of my introductory presentation).
Simulation Modeling in Immunology (SMI)
- Free online website hosts videos, slides, readings: https://andreashandel.github.io/SMIcourse/
SMI Strengths/Weaknesses
- The good
- Decent amount of introductory material (videos, slides, readings)
- Immunology and modeling
- All free
- The bad
- No guided/curated experience
- Coverage of topics is uneven/idiosyncratic
- Not fully polished
DSAIRM R package
Dynamical Systems Approach to Immune Response Modeling
- R package to learn/explore mechanistic simulation models: https://ahgroup.github.io/DSAIRM/
- Modular design, starts with no-code approach, allows advancement to coding.
- Each simulation app comes with model description and a set of suggested tasks that teach a specific modeling concept.
- Full solutions to all tasks are available (on request).
Learning DSAIRM
- The goal is to have a very low barrier to use. If you can use Excel/Prism, you can use this 😁.
- Main resource is package website: https://ahgroup.github.io/DSAIRM/
- See some materials on the SMI site.
- Also this paper in BMC Immunology.
DSAIRM Strengths/Weaknesses
- The good
- Starts out completely code-free.
- Good number of within-host modeling topics are covered.
- Set of guided exercises/tasks to help learn the material.
- Full access to underlying model code.
- The bad
- Only the models I wrote are available.
- Custom models (e.g., for research) will require adapting one of the existing models, which means having to write code.
- Package name is maybe awkward (taking suggestions for better naming).
modelbuilder R package
- Graphical/non-coding approach to building custom models.
- Usable (I think) but still in progress.
- Main resource is package website: https://ahgroup.github.io/modelbuilder/
modelbuilder Strengths/Weaknesses
- The good
- You can build your own models (or adapt existing ones).
- You can explore your models through the graphical interface.
- You can get different versions of the model code for further use.
- Has lots of overall potential 😀.
- The bad
- User interface not fully polished and robust.
- No option to load and fit data (do stats).
- Not suitable for big models.
- Potential only partially realized 😁.
flowdiagramr R package
- Side project: automated way to make model diagrams.
- Can produce nice diagrams of not-too-complex models.
- Main resource is package website: https://andreashandel.github.io/flowdiagramr/
flowdiagramr Strengths/Weaknesses
- The good
- Helps with potentially annoying model drawing task.
- Is highly configurable and easy to use.
- The bad
- Currently can’t handle more complex models (e.g. 3-way interaction).
- Still not fully tested, might still contain a good bit of bugs.
agdist package
- R package to compute antigenic distances.
- Main resource is package website: https://ahgroup.github.io/agdist/
- Very early stages, barely functional (but hopefully fairly functional in the next 1-2 months).
- Learn more about it from Zane at the CMC lunch on Thursday.
Questions/Discussion
Some tools and resources for modeling Slides: https://www.andreashandel.com/presentations/ 2025-05-27