Modeling Metabolic Networks
Welcome to the module of Modeling Metabolic Networks! Below, you will find all the required material.
In this module, we will explore the study of metabolic networks from mathematical and computational perspectives.
You will learn the theory and be able to apply it by running your own metabolic engineering projects and
software.
Overview
Brief description of the schedule, split into Theoretical Classes (T1, T2, T3) and Practical Classes (P1, P2, P3,
each with 2 possible shifts). Green are the initial classes.
Please note: In red are the classes that had to be rescheduled due to the bank holidays (April 25th
and May 1st).
Announcements: The class from Wednesday, 1st of May at 9-11h Q4.2 will move to Tuesday, 30th of April at 16h30-18h30 Q4.7. Those that can not make this time, can join the other class in the morning (i.e. Tuesday, 30th of April 9-11h P8).
Theoretical
Practical
In the practical classes we will use this handbook as a guide for the exercises: [PracticalExercices_v1.4.pdf]- P1 - Introduction to Python and Google Colaboratory - Exercise 1. [Solutions]
- P2 - Exercise 2 (linear programming) [Solution], Exercise 3 (Cobrapy) [Solution], and Exercise 4 (gene/reaction deletions).
- P3 - Ethanol optimization problem [pdf].
Software Installation
In this module, we will use Python and Google Colaboratory.
You won't have to install any software locally on your computer. The provided scripts will run in your web
browser and automatically install all the necessary
Python modules.
- We provide a simple structure of for your Google Colaboratory Ipython Notebook example ipynb.
- Cobrapy will be used to read, edit and simulate metabolic models.
- StrainDesign will be used for strain optimization.