In this repository, you will find every code and ressources used to reproduced the data presented in our paper.
Although the codes presented are in Matlab, the result can be reproduced with CNApy.

E_coli Data generated in the wet lab
Three_organisms Results of each of the analysis
Bacc_coli These codes should allow you to recreate your own thermodynamic models which are going to be the input of all further analysis. We used iML1515 directly retrieved from the BiGG database
Narringenin Contains the code used to directly take the data of what is feasible or not (Figure 3) and transforms it in way that makes it amenable for Escher maps.

All foldiers contain the same series of code doing the same task
Code_1 Create a community model
Code_2 Adds the shared compartiment allowing for the exchange of metabolites
Code_3 Sets up and run the MCS algorithm
Code_4 Converts the MCS solution into genes and validate that the community can still grow
Code_5 Test solutions on individual knock out to ensure no growth is possible with individual models
Code_6 Allows for the analysis of all valid solution
dFBA Code used to perform phenotypic phase plane analysis and dFBA\

Question? alexandre.tremblay@mail.utoronto.ca