Source code, resources and results for comparative assessment of automatic GEM reconstruction methods.
/AuReMe_test: Contains GEMs generated using AuReMe alternative modes.
/biomass_analysis: Contains descriptions of reference model biomass composition and, for each draft model, classifications of such biomass metabolites according to presence and producibility.
/compartment_analysis: Contains a summary of duplicated reactions (i.e. appearing in multiple compartments) and the relation between the GPRs of such reactions.
/DB: Metabolite and reaction databases (from KEGG, BiGG, modelSEED and MetaNetX).
/figures: Figures included in the body of the manuscript.
/mappings: Contains model reaction and metabolite mappings to the common MetaNetX namespace, for model content comparison.
/memote_results: Contains JSON files summarizing Memote analysis results for each draft and reference model. These files are organized in subfolders named after each reconstruction method (including a "reference" subfolder).
/models: Contains the generated draft models and the reference models. These are organized in subfolders named after each reconstruction method (including a "reference" subfolder).
/specialized_metabolites: Contains lists of metabolites which are present in specific organisms according to metabolomic datasets.
/supplementary_material: Supplementary material.
main.ipynb: Main script for analyzing and comparing draft and reference models and generating manuscript Figures.
mergem_mapping.ipynb: Script for mapping reaction and metabolite names to MetaNetX namespace using the library mergem.
gene_mapping.ipynb: Script for mapping gene names to a common namespace.
gene_comparison.ipynb: Script for exploring genes and GPRs across models.
GPR_comparisons.ipynb: Previous version of gene_mapping.ipynb.