Dynamical Systems Approach to Immune Response Modeling
DSAIRM is an R package containing a set of simulation modelss (apps) that teach within-host infection dynamics and immune response modeling from a dynamical system perspective.
All models can be explored through a graphical user interface, no reading or writing code is required. Each app comes with documenation and instructions which teach important concepts of within-host and immune response modeling, and how to use simulation models to understand such concepts.
It is also possible to go beyond the graphical interface and directly access and modify all simulations to adapt them to your needs.
The best approach to use this package is to install it, load it, and start the main menu, then you are ready to go. These lines of code typed into the
R console will get you there:
install.packages('DSAIRM') library('DSAIRM') dsairmmenu()
You can also give the package a quick try online, without having to install it. I still recommend you install it like any regular R package should you decide that you want to use it. It’s only 3 commands to get it up and running! Note that the shiny server on which I host the online version of the package is not regularly monitored and the package is not updated that frequently. If the online app doesn’t work, please let me know (through a Github Issue).
For a quick introduction to the package, step-by-step instructions on getting started, and more information on the different ways you can use the package see the tutorial (vignette).
If the DSAIRM package does in any way help you with your work such that it warrants citing it in one of your papers, please cite the DSAIRM publication in BMC Immunology.
This R package is developed and maintained by Andreas Handel. A full list of contributors and a Bibtex entry for the citation can be found here. The development of this package was partially supported by NIH grant U19AI117891.