Tools
We are developing open source tools for research and education at the intersection of molecular/systems modeling, machine learning and optimization. These tools include foundational resources that enable therapeutic design and application specific models.
Research
![FFT Protein](/images/fftML.png)
Python package for developing and analyzing machine learned models of protein function and properties that leverage periodicities in physicochemical properties along protein sequences.
![PyBio3D](/images/proteinGNN.png)
Provides basic tools for manipulating PDB files, including visualization through dash.bio, and provides a framework for developing Graph Neural Networks based portein structural data.
![smolyay](/images/smolyak.png)
Work in collaboration with Mike Howard (Auburn University) aimed at developing tools for multi-scale modeling based on Smolyak sparse grids.
Education
![introCSB](/images/shiny.png)
These resources include interactive modules that are generally applicable to learning the basics of systems biology modeling, as well as, coding examples for using R to develop and analyze various types of systems biology models.