BE 262 - Physical Biology Bootcamp


This course provides an intensive introduction to thinking like a quantitative biologist. Students will use Python to write computer code to analyze real-world quantitative experiments. No previous experience in coding is presumed, though for those with previous coding experience, advanced projects will be available. Students will use “street fighting mathematics” to perform order of magnitude estimates on problems ranging from how many photons it takes to make a cyanobacterium to the forces that can be applied by cytoskeletal filaments. These modeling efforts will be complemented by the development of physical models of phenomena such as gene expression, phase separation in nuclei and cytoskeletal polymerization.

Where and When?

For this year’s pandemic edition of the course, all sessions will happen online via zoom. Each day will have a schedule roughly of the form: 9 - 1130am class, 1130am - 1pm break, 1-2pm talk, 215pm - 415pm class, 415 pm - 515pm computational session. Our first meeting will take place on on September 7th, Sunday, September 13th is a day off, and the course will be finished on Tuesday, September 15th. There will be a brief introduction to the course, and then each of you will have 60 seconds to deliver a lightning talk in which you quickly tell us who you are, where you are from, and what you are excited about. For these talks, send your single-slide presentation as a PDF to Rob (phillips [at] pboc [dot] caltech [dot] edu) by 5pm on Sunday, Sept. 6 in PDF FORMAT (no exceptions).

Zoom link to lectures

Course Syllabus

The course syllabus (subject to change depending on our progress) will be of the form:

  • Day 1 Monday, Sept. 7: A feeling for the numbers in biology, Faculty talk 1-2pm, Frances Arnold.

  • Day 2 Tuesday Sept. 8: The great probability distributions and the rules of right reasoning, Faculty talk 1-2pm - Magda Zernicka-Goetz.

  • Day 3 Weds. Sept. 9: Diffusion as biology’s null hypothesis for dynamics, Faculty talk 1-2pm, TBD.

  • Day 4 Thursday, Sept. 10: Equilibrium Thinking for Nonequilibrium Systems, Faculty talk 1-2pm, TBD.

  • Day 5 Friday Sept. 11: Life as Defiance: How Energy Expenditure Makes Biological Systems Lifey, Faculty talk 1-2pm, TBD.

  • Day 6 Monday Sept. 14: A potpourri of Physical Biology, Faculty Talk -1pm - 2pm, Justin Bois.

  • Day 7 Tuesday Sept. 15:  Final lecture  - end by noon.