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 questions, which require manual code changes to solve them.

NOTE: The tutorial scripts are located in RAVENdir/tutorial.

The following tutorials are available:

Tutorial	Script Name	Brief Description
Tutorial 1	tutorial1	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
Tutorial 2	tutorial2	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
Tutorial 3	tutorial3	Run FBA simulations, gene deletion analysis, and use GEMs as a scaffold for interpreting microarray data. Use a simplified model of yeast metabolism as an example.
Tutorial 4	tutorial4	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
Tutorial 5	tutorial5	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.
Tutorial 6	tutorial6	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
Tutorial 7	tutorial7	Use the biomass/ functions to calibrate a model's biomass pseudoreaction against measured condition-specific composition data, with a template data file (biomassConditions_template.tsv) to adapt for a new model

In addition, a book chapter is available from bioRxiv, which details a protocol where protein homology is used to generate a draft GEM using a functional GEM from another species as a template. It comes with its own GitHub repository.