We are working on multiple software projects, some of which are ever-evolving, involve large teams, are distributed for different systems, and have many associated publications. Some other projects consist of many standalone packages that serve their own purposes but are designed to “play well” together and adhere to common conventions and standards.

tdaverse: An R package collection for topological data analysis

Topological data analysis (TDA) relies heavily on a handful of C++ libraries developed primarily by and for statistical topologists. As TDA matures and standard workflows emerge, more accessible and modular implementations become necessary. The tdaverse is a collection of R packages designed to integrate TDA functionality into the tidyverse–tidymodels ecosystem in R.

Multiscale model of nutritional immunity in invasive pulmonary aspergillosis

The purpose of the work is to develop a multiscale computational model to simulate the invasion of the human lungs by spores of the opportunistic fungus Aspergillus fumigatus. In particular, we explore the role of nutritional immunity in clearing infection, with a focus on iron. This project is currently funded by The National Institutes of Health and The National Science Foundation of the United States of America. The team includes members from UF Health and Kitware.