OxidizeME: computing multiscale cellular responses to reactive oxygen species

OxidizeME model and notebooks.

• Author: Laurence Yang

• Systems Biology Research Group, UCSD

• Citation: Yang et al. (2018) bioRxiv, doi:10.1101/227892

Requirements

1. Python
   • tested on Python 2.7
2. cobrapy
   • tested on 0.5.11
   • not yet fully compatible with cobrapy >= 0.6
3. cobrame: follow installation instructions here: https://github.com/SBRG/cobrame
4. ecolime: follow installation instructions here: https://github.com/SBRG/ecolime
5. solvemepy: follow installation instructions here: https://github.com/SBRG/solvemepy