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 sample 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.ymlonce the environment is created can be activated in Linux
source activate sysbio_hptxThis environment has been tested in Linux64 platforms