Repository includes matlab scripts of the whole cell model from: Weiße, A. Y., Oyarzún, D. A., Danos, V., & Swain, P. S. (2015). Mechanistic links between cellular trade-offs, gene expression, and growth. Proceedings of the National Academy of Sciences, 201416533.
Files:
- cellmodel_Driver.m & cellmodel_odes.m - Files to run the original model from the paper
- cellmodel_Driver_MolarParamSpecies.m - File includes parameters and initial species values in concentration-based units 3,4) Annotated files: contain a thorough annotation of the original code from the paper with the 'zombie' species being removed for clarity. Recommended to look at these when starting out with this code.