This repository contains the scripts and documentation associated with the tutorial on working with genome-scale metabolic models (GEMs) and using them to interpret -omics data in the context of metabolism.
Launch a Jupyter notebook session
$ jupyter notebook
From the Jupyter browser, navigate to the scripts/ directory and open the COBRApy_tutorial.ipynb notebook. Follow the instructions within.
Regenerates the HumanGEM_metabolite_GSC.gmt and HumanGEM_subsystem_GSC.gmt files
Launch a Jupyter notebook session
$ jupyter notebook
From the Jupyter browser, navigate to the scripts/ directory and open the GEM_GSC_extraction.ipynb notebook. Follow the instructions within.
Launch RStudio from the command line
$ rstudio &
Follow the instructions found in the GEM_GSA.html document, located in the scripts/ directory. Optionally, the source RMarkdown file GEM_GSA.Rmd can be opened within RStudio, though it is not as easy to read as the HTML.