IGTC Graduate Summer School in Mathematical Biology

A PIMS/Accelerate BC sponsored Summer School in Mathematical Biology

University of British Columbia, Vancouver, May 11-June 11, 2008

Course Content and Material

This page presents details of the main Course Content.

For a detailed daily schedule click HERE.

For an overview of the month-long schedule click HERE.

For a summary of events by category and/or lecturer(s) click HERE.

For abstracts of talks click HERE.

Unless otherwise indicated, events will take place at the UBC campus of PIMS. Directions for PIMS can be found HERE.

Useful links

  1. Information for IGTC computer labs is HERE

  2. Leah's Worksheet/Chapter on Enzyme Kinetics in PDF and in Latex form. (May 13, 2008). Note: may contain typos.

  3. Leah's Preliminary Worksheet/Chapter on Biochemical Dynamics in PDF and in Latex form. (May 14, 2008). Note: may contain typos.

  4. Some literature papers that you may want to read and present as a project are given at the last pages of the worksheet on Biochemical Dynamics.

  5. A simple guide on using XPP AUTO for a simple bistable equation is given PDF form. (May 14, 2008). (This example was done in tutorial on May 14).

  6. A summary of what was discussed on the Tyson models for cell cycle appears here in PDF form. This includes a guide to the literature for possible projects/class presentations. A shortened version of the powerpoint slides appears here in PDF form. UPDATE: The chapter has been edited to reflect the revision that includes better AUTO settings and file to produce the stable limit cycle. The ode file that was contributed by Anmar Khadra is HERE.

  7. A worksheet/chapter on simple polymerization can be found HERE. An XPP ode file to simulate polymer size distribution (asizedistr.ode) will be posted on the lab webpage.

  8. Notes and a guided exercise to how scaling arguments can be used to reconstruct the mechanism of polymer self-assembly are HERE. An excel file containing data for the Flyvbjerg polymer self-assembly problem is HERE. Your challenge is to use this data together with scaling arguments to determine how this polymer self-assembles (i.e., what are the steps).

  9. A few of you have been asking for This File, that for some reason is bouncing from email.

  10. A short example and exercise for the Gillespie Method, from Bard's XPP book.

  11. Some quick notes about Bard Ermentrout's XPP-AUTO lab, including the two .ode files (ml.ode and hhh.ode) and AUTO setting can be found HERE.

  12. Here are three documents that Bard has assembled to help you read up about the material in his lectures: Bard's Chap7 , Bard's Chap7's Figures , and Bard's MBI Chapter .

  13. Here is an example of how to get XPP to plot the solutions of reaction-diffusion pde's. The example is different from the one we did in class, but the XPP instructions are the same. (Figures in the Turing chapter were produced in the same way.)

  14. Here is a selection of a few projects that Bard Ermentrout suggested in a workshop he gave at Utah. One or two of these may be suitable, but many are outside of the scope of what he talked about here.

  15. Here is the summary of the XPP lab tutorial by Bard Ermentrout showing how to use AUTO for the tyson.ode problem and for hhh.ode. Notes were kindly written by Jiafen Gong and edited slightly (with graphs inserted) by Leah.

  16. Another list (from Leah) with ideas and general instructions for projects that you may want to consider.. or feel free to suggest your own.

  17. I have updated this chapter on the Turing reaction-Diffusion system. It now includes more of what I talked about in class.

  18. Here are the slides from the lectures by Alex Mogilner in .pdf file format: Lecture 1, Lecture 2, Lecture 3, Lecture 4, Lecture 5.

  19. Here are Leah's slides for the lecture about Rho proteins, cell polarization, and wave pinning from the final few days.

  20. A link to a paper by Omer Dushek and others about how to combine diffusion of two chemicals (related to what was discussed in class).

  21. Here is an updated summary of the course in case you need to present this to get credit from your university.

Lectures by Prof Karl Hadeler (May 12-23, 2008)

Lectures by Prof Bard Ermentrout (May 26-29, 2008)

Here is some basic reading material for lectures by Prof Bard Ermentrout:

Lectures by Prof Alex Mogilner (June 4-10, 2008)

The following readings are suggested by Prof Mogilner:

Course Sylabus

Lectures by Leah Keshet (May 11-June 11, 2008)

Other details about the content of the course will be posted here from time to time.