This is the python functions used based for the HIV-1 generation (Also could be used for generating VBOF of viruses).
- Viranet: https://github.com/seanaller/viranet
- Cobrapy: https://opencobra.github.io/cobrapy/
Genome-scale models (GEMs) of 4 CD4+ T cells generated by Puniya et al. were acquired from BioModels, under the acession number MODEL1909260003, MODEL1909260004, MODEL1909260005, MODEL1909260006. Models integrated with HIV-1 VBOF were deposited in the host-virus-model folder and used for analysis
All the analysis were conducted using the IDE Jupyter nobebook and the codes were uploaded in the .ipynb file.