Course information for From Enzyme Kinetics to Models of Metabolism

Welcome to the website that supports the June 21-23 course at the TU Delft.

The last version of the course material you can download below (note the date, I may sometimes upload a new version)

You can also download all the Mathematica files that I used to make all the plots in the syllabus.

The course syllabus teaches you enzyme kinetics to a level that I suspect is sufficient to make mathematical models of metabolic networks. I do not think that you need any pre-existing knowledge, other than basic chemistry and chemical kinetics. The syllabus also discusses recurrent regulatory mechanisms of enzymes and enzyme networks, using simple mathematical models made to illustrate the essence of a mechanism. The books ends with realistic models and a few examples of the analysis of their features. The course should give you a basic understanding of what mathematical models of metabolism involve and how they can be used. 

Mathematical modelling requires tools for numerical analysis and simulations. Many of them exist and they vary in their approach. Some are GUI based such as Copasi, others are in Python (requiring script writing in and dedicated packages such as Pysces), while others are more general purpose mathematical and numerical analysis software such as Matlab and Mathematica. If you want to become a Mathematica user then this video may be helpful https://youtu.be/EP2THAvZecY and the following introduction files as well:

Other simulation tools are completely online and offer many published models, such as JWS Online, which is a great resource for the analysis and retrieval of published models.

When you are starter with modelling, I advise Copasi. When you are Python user or want to learn it, I advise Pycses. When you want to do analytical mathematics and numerical analysis then I advise Mathematica (which is what I always use and all figures of the course syllabus are made in it). When you are familiar with Matlab for numerical analysis choose that. Finally, if you just want to become familiar with models from the literature then stick to JWS Online. 

Should you read anything to prepare? If you are a modeller and do not know much about metabolism then I advise the book Cell biology by the numbers by Phillips and Milo and The way of the cell by Harold. If you are a biochemist or biotechnologist then you do not need anything, but if you are curious have a look at Understanding the control of metabolism by Fell. If you are unsure whether your level of chemical kinetics and mathematics is sufficient to get started with the course then check Chapter 2 and 3 of the following syllabus to get an impression.