Open Access Teaching

I make the material for all classes I teach available on github. These are released under the unrestrictive unlicense, which allows end users to use the teaching material however they wish.

Biochem and cellular physiology (B281H)


Course objectives

  • Survey the key molecular and cellular features shared by all organisms on earth, revealing how life can be understood in physical and chemical terms.
  • Begin to develop intuition and analytical tools to think about life quantitatively and molecularly.
  • Introduce several key, universal systems that are shared across organisms:
    • Serine protease
    • Hemoglobin
    • Glycolysis/gluconeogenesis
    • Citric Acid Cycle
    • Electron transport chain
    • ATP synthase

Scientific programming (CH410/510)


Conceptual Goals

By the end of the course, students should understand:

  • Basic python: data types, key words, control, functions and imports
  • Core python extensions for scientists: scipy, numpy, and jupyter
  • Strategies for dissecting problems and formulating solutions in code
  • Where to go to pick up skills in the future as the need arises

Skill Goals

By the end of the course, students should be able to:

  • Write basic python programs from scratch
  • Identify existing libraries for a problem and learn how to use them
  • Generate arbitrarily complex custom plots
  • Simulate experimental sampling
  • Manipulate scientific datasets of the following types (at a basic level):

  • High-throughput sequencing data

  • Chemical structure data from databases such as the PDB

Advanced Biochemistry (CH662)


Course objectives

  • Prepare PhD students to do research in molecular biology by helping them think molecularly and by introducing tools to study binding interactions.
  • This will be achieved by:
    • Introducing students to controlling conceptual frameworks in biochemistry, with an emphasis on quantitative reasoning.
    • Introducing methods used to study biomolecular properties and function, with an emphasis on binding interactions.
  • By the end of this course:
    • Understand the difference between microscopic and macroscopic phenomena and know the conceptual tools used by biochemists to link the two scales.
    • Be able to employ simple mathematical models to describe both the thermodynamics and kinetics of biomolecluar interactions.
    • Reason about the effects of mutations on molecular structure.
    • Have a working understanding of a collection of methods used to probe molecular mechanisms, with an emphasis on those used for binding interactions.

Physiological Biochemistry (CH360)


This course is under development.