**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**

- This is the last day of the previous module

- Read Sections 1, 2, and 3 of the course notes.
- Read the notebooks called "1 expressionOfAnUnregulatedGene-Dist-X.nb", "2 transcriptionAndTranslation-Dist-X.nb", and "3 repressorAndTarget-Dist-X.nb", where X represents the largest release number in the same directory as this module guide. Evaluate all expressions and complete all exercises found in the notebooks. Turn the notebooks in before class.

**Day 1**

**In class**

- Introduction to transcriptional modeling in Mathematica: Analytic and numerical solutions to differential equations.

- Complete the assignment repressionSimulation-Dist.X.zip, where X is the largest release number in the same directory as this module guide.

In class

Discussion:

- Modeling transcriptional repression in Mathematica.

- Study the toggle switch paper. Be prepared to answer questions.
- Read Section 4 of the course notes.
- Look at this web page on stable and unstable equilibria. You can stop before reading the section "Stability in discrete-time models".
- Complete the Mathematica notebook called "4 ToggleSwitchGraphing-Dist.X.nb" where X is the largest release number in the same directory as this module guide. This notebook gives you some tools for visualizing the dynamical system described in the paper.

In class

- Brief quiz on the assigned reading.
- Discussion of the toggle switch paper and other assigned materials.

- Study the repressilator paper. Be prepared to answer questions.
- Read Section 5 of the course notes, complete any exercises found it that section, and turn them in before the next class.
- Complete the Mathematica notebook called "5 Repressilator.nb", which gives you a tool for visualizing the dynamical system described in the paper.

In class

- Brief quiz on the assigned reading.
- Discussion of the repressilator Paper.
- Multirepressor model (Course notes section 6.1).

In class

Discussion:

- Brief quiz on the assigned reading.
- Parameter estimation in a regulatory network. (Course notes 6 and 6.1).

- Read Section 6.2 of the course notes. Do this first.
- 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.

In class

Discussion:

- Parameter estimation for a specific pathway (Section 6.2).

- Read Section 7 of the course notes.

In class

Discussion:

- A thermodynamic model of transcriptional regulation (Section 7).

- Study this paper. Be prepared to answer questions. You will probably need to read parts of the supplement .
- Complete Exercises 7.1, 7.2, and 7.3.
- 2015: Complete Part 4 the repression system lab.

In class

Discussion:

- Brief quiz on the assigned reading.
- Application of the thermodynamic model to synthetic promoters (Section 9).

- Complete Exercises 8.1.