Code

Data, code, and analysis for publications

We regularly publish code and analysis accompanying our publications. Associated repositories are linked on the Papers page. Just follow the links labeled [code]. Most relevant code repositories can also be found on our lab GitHub page.

Software

• mplot
  Simple Python scripts for high quality figures in matplotlib.

• ACE
  Fast and flexible code for solving the inverse Ising/Potts inference problem.

• simple-rebound-simulation
  Code to simulate HIV-1 rebound following the model of Hill et al., PNAS 2014.

Teaching materials

• popgen-lectures
  This repository contains a set of Jupyter notebooks accompanying a brief series of introductory lectures in population genetics.

• Python-workshop
  Material for a set of workshops introducing new coders to Python. Workshops include example activities and exercises that may also interest more experienced coders.

• Physics-177
  Lecture notes, exercises, and homework assignments for the course Physics 177: Computational Physics taught at UC Riverside. Credit to Flip Tanedo for earlier versions of this course.