Transfoam Metabolic Modeling

Instructions

COBRApy

• navigate to transfoam/bioreactor/library and activate virtual environment with 'source ../env/bin/activate'
  • start jupyter lab with 'jupyter lab'
  • run notebooks
    • model.ipynb adds plasmid reactions to model
    • data.ipynb extracts model data
    • yield.ipynb is for FBA and knockout analysis

MATLAB

• add transfoam/matlab to working path
  • run scripts
    • mostly for robustness analysis and optpipe

R

• open r.Rproj in RStudio
  • run scripts
    • figure generation with ggplot