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