Skip to content
This repository has been archived by the owner on Dec 31, 2019. It is now read-only.

OriolLopezMassaguer/Hepatoxicity-SysBio

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

15 Commits
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

In this repository we provide the source code that computes the hepatoxicity for certain compounds based on the method described in:

Carbonell, P., Lopez, O., Amberg, A., Pastor, M., and Sanz, F. (2017) Hepatotoxicity prediction by systems biology modeling of disturbed metabolic pathways using gene expression data. ALTEX, 34, 219–234. doi:10.14573/altex.1602071

We provide a script to compute the FVA analysis of the human hepatocytes based on the Recon 2 metabolic models using the COBRA package in recon2_fva

We provide a smaple jupyter notebook that performs the hepatoxocity calculations for 3 statins in statins_notebook

All the python scripts and the jupyter notebook can be run on a conda environment that specifies completely the dependencies needed.

The conda environment can be created from them yml file provided

conda env create --name sysbio_hptx -f sysbio_hptx.yml

once the environment is created can be activated in Linux

source activate sysbio_hptx

This environment has been tested in Linux64 platforms

About

No description, website, or topics provided.

Resources

License

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published