Workshop Materials:

Link to Escher

How to build a model from scratch in COBRApy

How to convert a COBRApy model to a json file for making an Escher pathway map: type, in COBRApy “cobra.io.save_json_model(model, “my_model_fbc2.json”)”

Getting started in COBRApy

Some code showing how to load a model from BiGG into COBRApy and how to do some basic analysis

Code from the COBRApy tutorial

Project 2 (FBA primer)

Project 3 (strain design)

 

Slides:

Network Reconstruction Slides

Resources and Databases: KEGG

A short introduction to SBML and its software support

Making maps with Escher and COBRApy

Lect 4 FBA

Extra reading:

BiGG_Models

Escher

COBRApy

kegg_translator

What_is_FBA