Xanthomonas phaseoli pv. manihotis Metabolic Model

This is the repository of Xanthomonas phaseoli pv. manihotis (Xpm) metabolic models (Xpm M-model), maps (constructed in Escher) and code used for analyses. This repository is divided in three folders:

Code Folder

This folder includer four subfolders, each one with a jupyter notebook and the corresponding input files to run the code. Results are included into the folders. The code was run in pyhton 3.6 and COBRApy 0.17.1v. The analyses included are:

• Clustering: hierarchical clustering of Context Specific Models (CSM) of Xpm WT and mutant strains with and without the addition of Xanthan production in the objective function.

• Loops: analyses of Xpm M-model loops using pyCOBRA.

• S-Matrix: loops calculations using null space.

• Tradeoff: tradeoff between xanthan and biomass production in growth rate.

Metabolic Maps

Inlcuding all the metabolic maps of Xpm M-model generate with Escher

• Metabolic map of the central metabolism and carbohydrate sources of Xpm : Xpm_Central_metabolism_map.json

• Metabolic map of amino acid biosynthesis of Xpm: Xpm-Aminoacid_map.json

• Metabolic map of xanthan biosynthesis of Xpm: Xpm-Xanthan_biosynthesis_map.json

Models

Including all the models versions used in the analyses:

• Xpm_model_May_29_2020.xml: Full Xpm M-model with metabolite annotations (sbml format)

• Xam_Biomass&Xanthan(completed_mar15)_model.xml: Full Xpm M-model without metabolite annotations (sbml format)

• Xpm_model_May_29_2020.mat: Full Xpm M-model with metabolite annotations (matlab format)

• Xam_Biomass&Xanthan(completed_mar15)_model.json: Full Xpm M-model without metabolite annotations (json format)

• Xam_void_CSM.mat: Context Specific Metabolic Model of Xpm CIO151 EV strain (matlab format)

• Xam_rpfCGH_CSM.mat: Context Specific Metabolic Model of Xpm CIO151 ΔrpfCGH-EV strain (matlab format)

• Xam_BiGG_full_media.json: Xpm M-model used for loops and null space calculations (json format)