Math 563: Mathematical Cell Biology (Graduate Course)
University of British Columbia, Vancouver, Jan-April 2020
Instructor: Leah Edelstein-Keshet
Course Details
- Overview Overview of this course and some goals.
- Schedule (List of Topics and dates). This file evolves to reflect the progress of the course. It also lists the homework assignments,
- Lecture Notes, codes, and papers: This course has no recommended book. Students receive links to evolving lecture notes, and to various files and publications to read.
- We are learning to use the open source Morpheus in this class for multi scale cell biology simulations.
Link to Morpheus HomePage
- Here is a link to a
Morpheus User's Manual.
- Here is a link to the free software XPP by Bard Ermentrout. This free software can produce simulations of ODEs, bifurcation diagrams, and other helpful output.
Videos of interest
Bacteria run and tumble
video
- Lecture about actin and cell motility by Julie Theriot
Part I.
- Lecture about actin and cell motility by Julie Theriot
Part II.
- Lecture by Eric Wieschaus about patterning development in the early embryo
Part I.
- Lecture by Eric Wieschaus about patterning development in the early embryo
Part II.
- Cartoon video about
Turing pattern formation
General Information
Meetings: Class on Mondays 1:30-5:00PM in UBC Math Bldg Room 126. Tutorial: Thursday 10-11:30AM (same room).
On the week of Feb 3-7, we will not have a lecture on Monday. Instead, we will have a tutorial on Monday afternoon and a Morpheus presentation and tutorial (involving the Dresden group that developed Morpheus) on Thursday Feb 6 at 9:30-11AM in M126.
There may be other occasional changes to make up for weeks when Monday is a holiday.
Grading
The grading will be based on 4-6 homework sets (10% each), a short presentation of paper(s) from the literature (10%) and/or various class discussion and group work, and a final term project (30-40%).
Academic Conduct
Students are encouraged to work together and help one another in all respects. Assignments are meant as opportunities for learning. However, any material you submit for grading should be work you have written up on your own, in your own words, and that you understand completely. Copying calculations, code, or writing (from any source) without full and clear attribution is plagiarism, a form of academic misconduct not tolerated in any UBC course.
For more information: keshet@math.ubc.ca