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 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.

Background image: Sunset from Spencer's Butte, 5 miles from the lab.