This project contains scripts allowing to add a "virus biomass function" to a cell metabolic model (a SBML model), and then to perform an analysis of this "Host-Virus Model" (HVM).
The scripts allowing to create the HVM and to analyse it are stored in the
modelAnalysis module. The analyse_model.py script in the root directory of
this project consists in a command-line interface to this module. An example
of invokation (using the Recon2.2 model) would be
python analyse_model.py SARS_CoV_2.txt recon2.xml biomass_reaction
where "SARS_CoV_2.txt" is the genbank file for SARS_CoV_2, "recon2.xml" is
the SBML file for the Recon2.2 model and "biomass_reaction" is the id of the
biomass reaction in the Recon2.2 model. For informations about the other
options of the command-line interface of analyse_model.py, refer to its
documentation.
The minimalMediaCreation directory contains a script to determine the
composition of the minimal medium allowing growth for a given model.
The scripts create_reaction.py and get_tissue-specific_stoichiometry.sh in
the root directory are used to produce modified versions of the Recon2.2 model
where the biomass_protein reaction is modified such that its stoichiometry
reflects the RNA expression data from a specific tissue, from the human
protein atlas project (https://www.proteinatlas.org/). In order to use it,
use the get_tissue-specific_stoichiometry.sh script.
The scripts have been used in the following article: hadrien delattre, Kalesh Sasidharan, orkun soyer. Inhibiting the reproduction of COVID-19-causing SARS-CoV-2 through perturbations in human cell metabolic network. Authorea. May 12, 2020. Preprint available here.
The analysis codes provided here are “AS IS" and covered under a BSD2 Licence. They are intended solely for non-commercial, academic use in the hope that they will be useful for analysing other host-virus pairs in the context of infection or viral ecology. If you would like to explore application of the provided code and analysis approach in a commercial setting, please get in touch with the project developers or University Warwick tech transfer office at “ventures@warwick.ac.uk” quoting reference ‘host-virus metabolic modelling