Tutorials

Tutorials

The RAVEN Toolbox contains several tutorials which highlight the basic RAVEN functionality. While several scripts only demonstrate the RAVEN functions, the other ones have exercises, which require the manual code changes to solve them.

NOTE: The tutorial scripts are located in RAVENdir/tutorial

The following tutorials are available:

Exercise	Script Name	Brief Description
Exercise 0	tutorial0	Use the Penicillium chrysogenum GEM iAL1006 to show some functionality of RAVEN, with a focus on GEM import, modification, simulations and the ways to interpret the simulation results
Exercise 1	tutorial1	Deal with the RAVEN model format and the most basic aspects of GEM modelling: build a simple model from scratch, set parameters and perform simple simulations
Exercise 2	tutorial2	Run FBA and MOMA simulations and use GEMs as a scaffold for interpreting microarray data. Use a simplified model of yeast metabolism as an example.
Exercise 3	tutorial3	While having a supplied version of the small yeast model with errors inserted, find and fix these errors to ensure that the model could predict growth
Exercise 4	tutorial4	Show how to de novo generate a draft GEM from KEGG, based on protein sequences in a FASTA file, and doing some functionality checks on the model.
Exercise 5	tutorial2018	Show how to de novo generate a combined draft GEM from KEGG and MetaCyc. Shows the case study for bacterium Streptomyces coelicolor together with additional curation steps

Coming soon:

Exercise	Script Name	Brief Description
Exercise 6	tutorial6	Show how to generate a draft GEM from another finalized (template) GEM while performing the homology search