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This repository contains supplementary files for the metabolic modeling analysis in the manuscript:
Hove PR, Nealon NJ, Chan SHJ, Bover SM, Haberecht HB and Ryan EP. (Submitted) Metabolomics and proteomics of L. rhamnosus GG and E. coli Nissle probiotic supernatants identify distinct pathways that mediate growth suppression of antimicrobial-resistant pathogens.

ECN_20200729.mat/xml
Draft Cobra model reconstructed using KBase and a genome for E. coli Nissle 1917 (NCBI Reference Sequence: NZ_CP007799)

LGG_20200729.mat/xml
Draft Cobra model reconstructed using KBase and a genome for Lactobacillus rhamnosus GG (NCBI Reference Sequence: NC_013198.1)

.mat files are directly readable by Matlab
.xml files are in Systems Biology Markup Language (SBML) level 3 version 1 with flux balance constraints (fbc) version 2

metabolomicData.mat Matlab data file containing the fold change in metabolite abundance in ECN or LGG culture relative to the blank MRS media
variables therein:

  • mappedMets: the metabolites mapped to the models
  • metsFoldChangeEc, metsFoldChangeLg: fold change of and mapping from the metabolites to the exchange reactions in the models
  • metsFoldChangeHeader: header for the columns in metsFoldChangeEc/Lg

pFBAconstrainedByExoMetabolomes.m
Matlab m-file for constructing the optimizing model for analysis from the metabolic models and metabolomic data.

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