See this page for talks and posters given by the group.

Teaching Resources

Here we’ve included a bunch of teaching resources from Peter and Andy (and others) in the group, including classes and workshops we have taught in the past.

Peter’s classes

• Advanced Biological Statistics, a two-quarter graduate-level statistics course at UO that covers many advanced statistical topics, including Bayesian methods using Stan, from a nonmathematical point of view. In R, slides in Rmarkdown.

  • website: uo-biostats.github.io/UO_ABS/
  • github: github.com/UO-Biostats/UO_ABS

• Applied Mathematics, an first-year graduate course in (an eclectic subset of) applied mathematics, with a heavy focus on stochastic processes (and applications).

  • website: uo-applied-math.github.io/applied_math/
  • github: github.com/uo-applied-math/applied_math

• Population Biology, a short (three-week) introduction course at UO on modeling population dyanmics, using python (in jupyter notebooks).

  • github: github.com/petrelharp/popbio

• Probability Theory, the second quarter of a first-year graduate course in probability theory.

  • website: petrelharp.github.io/probability_theory/
  • github: github.com/petrelharp/probability_theory/

• Introduction to Statistics for Biologists, taught as BISC 305 at USC around 2015.

  • Slides and examples on github: github.com/petrelharp/bisc305

Andy’s classes

• Computational Genetics, an undergraduate course at UO taught as Bio 399. This course aims to introduce upper level biology students to fundemental concepts in computational biology and genetics using a hands-on, code workshop context. Topics covered include population growth, sequence alignment, phylogenetic tree construction, clustering, dimensionality reduction, simulation, and supervised machine learning.

  • github: github.com/andrewkern/bio399

• Scientific Programming, a short (three-week) introduction course at UO on using the python scientific programing stack

  • github: github.com/andrewkern/bio610

Workshops

• stdpopsim: adding species workshop, taught by Andy in March 2021, this workshop was aimed at potential contributors to the stdpopsim project and guiding folks through the process of adding a species to the stdpopsim catalog

  • github: https://github.com/popsim-consortium/workshops/tree/main/adding_species