Computational Molecular Biology, aka Algorithms for Computational Biology

Systems Biology Module Guide

This module is intended to introduce you dynamical systems modeling of gene regulation.

The source for the material in this module is text that I have written: Systems Biology Course Notes. Any references to course notes below refer to this. There are also Mathematica notebooks that go with it that are used at various steps.

Day 0
In class

Before the first class

Day 1
In class

Before the next class
Day 2
In class

Discussion:

Before the next class

Day 3
In class
Before the next class

Day 4
In class
Before the next class Before class on Day 6
  • Complete Parts 1-3 of the lab in repressionSystem-Dist-X where X is the largest release number found in the directory containing this page.
  • If you have extra time you may want to get started early on Part 4, which is due on Day 8. It may be challenging and / or time consuming.

    Day 5
    In class

    Discussion:

    Before the next class
    Day 6
    In class

    Discussion:

    Before the next class Before class on Day 8
  • Complete Part 4 the repression system lab.

    Day 7
    In class

    Discussion:

    Before the next class

    Day 8
    In class

    Discussion:

    • Brief quiz on the assigned reading.
    • Application of the thermodynamic model to synthetic promoters (Section 9).
    Before the next class
    • Complete Exercises 8.1.