{
  "m-model-path": "./helper_files/inputs/m_model.json",
  "genbank-path": "./helper_files/inputs/genome.gb",
  "biocyc.genes": "./helper_files/inputs/genes.txt",
  "biocyc.prots": "./helper_files/inputs/proteins.txt",
  "biocyc.TUs": "./helper_files/inputs/TUs.txt",
  "biocyc.RNAs": "./helper_files/inputs/RNAs.txt",
  "biocyc.seqs": "./helper_files/inputs/sequences.fasta",
  "df_gene_cplxs_mods_rxns": "./helper_files/building_data/automated-org-with-refs.xlsx",
  "df_TranscriptionalUnits": "",
  "out_directory": "./helper_files/",
  "log_directory": "./helper_files/",
  "run_bbh_blast": true,
  "e_value_cutoff": 1e-10,
  "dev_reference": true,
  "include_pseudo_genes": true,
  "locus_tag" : "old_locus_tag"
}