Course Description

The purpose of this course is to learn the basics of constraint-based metabolic cellular modeling and analysis, a subset of the larger world of systems biology. This course will focus on developing the programming skills to be able to interrogate cell models and develop new strains. It will focus on pragmatic skills.

Course Objectives

By the end of this course, you will be able to:

1. Explain flux balance analysis
2. Explain the basic E.coli core metabolic model
3. Demonstrate the ability to effectively use the COBRApy Toolbox
4. Explain and demonstrate flux variability analysis
5. Explain and demonstrate randomized sampling
6. Explain and demonstrate model interrogation
7. Explain and demonstrate the model creation and enhancement
8. Explain and demonstrate production envelopes
9. Explain and demonstrate gene/reaction knockout strategies
10. Explain and demonstrate gene/reaction modulation
11. Explain and demonstrate strain design

Course Content

1. Course Introduction Module
2. COBRA Models Module
3. Flux Balance Analysis Module
4. E.coli Core Metabolic Model Module
5. Flux Variability Analysis Module
6. Randomized Sampling Module
7. Model Interrogation Module
8. Model Creation/Enhancement Module
9. Production Envelopes Module
10. Gene/Reaction Knockout Strategies Module
11. Gene/Reaction Modulation Module
12. Strain Design Module
13. Omics Module

Instructor

Professor Scott Hinton, Professor emeritus, Utah State University

Warning

COBRApy has been updated to version 0.25.0 which has changed some of the input/output commands. To use these modules you should set up the following python environment.

pip install cobra==0.24.0

pip install cameo

pip install cobrapy_bigg_client