PHYS 847/492 - Quantitative Biology

Instructor: Eldon Emberly         Office: SCB9684      Phone: 3701        e-mail: eemberly_at_sfu_dot_ca

Syllabus


Lecture Material:

Review of Molecular Biology

Random Polymer Results

RNA notes     RNA 2ndary structure prediction     RNA folding game

Protein folding notes     Protein folding game

Network mechanics     Molecular motors

Equilibrium Binding: Promoter regulation     Genetic Switches: Stability analysis

Biochemical oscillators: limit cycles

Gillespie Algorithm

Class Questions/Readings:

Random polymer problems (Sept 11 discussion)
RNA papers discussion (Sept 18 discussion)     Paper 1     Paper 2
Protein papers discussion (Sept 25 discussion)     Paper 1     Paper 2
Gene regulation discussion (Oct. 9 discussion)     Paper 1     Paper 2
Biological oscillators discussion (Oct. 23 discussion)
Noise in biochemical systems (Oct. 30 discussion)
Spatial patterning: Min system
Information optimization: morphogen gradients

Problem Sets:

Assignment #1 Due Oct 2 in class

   Hamiltonian Paths Generator Script    Paper detaling algorithm

   Data for PCA: 2D data    5D data choose 'Save As'

Assignment #2 Due Oct 30 in class
Assignment #3 Due Nov 27 in class