Tutorial
========

The tutorial is composed of nine distinct Jupyter notebooks, which systematically 
guide the user through the workflows of creating, modifying, and optimizing various 
genome-scale extended models. These models are used as a case study to illustrate 
the principles and applications of genome-scale modeling. The latest FBA model of *E. coli* 
serves as a representative example throughout the tutorial.

jupyter notebooks
-----------------

.. toctree::
   :maxdepth: 2

   notebooks/1_Create_iML1515_default_GECKO
   notebooks/2_Create_iML1515_modified_GECKO
   notebooks/3_Create_iML1515_predicted_GECKO
   notebooks/4_Create_iML1515_manually_adjusted_GECKO
   notebooks/5_Create_iML1515_auto_fitted_GECKO
   notebooks/6_Create_iML1515_RBA
   notebooks/7_Create_iML1515_TFA
   notebooks/8_Create_iML1515_TGECKO
   notebooks/9_Create_iML1515_TRBA