Metabolic Networks Modelling

Author/Creator: Paula Jouhten, Kiran Patil, Karin Sasaki, Aleksej Zelezniak
Curated By: Karin Sasaki
Language: python, COBRApy
Field(s): Constrained based modelling, flux balance analysis, stoichiometric models, modelling metabolic networks as a system on linear functions, optimisation of a system of linear functions using linear programming, metabolic networks, microbial metabolic networks


Introduction to constrained based modelling of metabolic networks and using COBRApy to simulate the systems at steady state. The tutorial introduces how to model metabolic networks, at steady state, using a system of linear equations and how to use the python library COBRApy, which employs the mathematical tool, of linear programming, to simulate the model. The tutorial is written in a Jupyter notebook and the exercises can be input directly in the file. The tutorial is designed for self instruction.

Level: Intermediate
Format: Online (browser-based)
Time Required: 6-8 hours
Prerequisites: python language, jupyter notebook, basic linear algebra (array manipulation)
Access: free
Last Curated: 08.08.2016