model_23BDO.yaml

name: iCbes, Genome-scale metabolic model of Cladicellulosiruptor bescii
biomass: Biomass_Cbescii
default_flux_limit: 1000
default_compartment: c
extracellular: e
compartments:
- id: c
  adjacent_to: e
  name: Cytoplasm
- id: e
  adjacent_to: c
  name: Extracellular
compounds:
- include: compounds.yaml
reactions:
- include: reactions.yaml
- include: engineered_reactions_products.yaml #added to simulate the TLC2 engineering designs
exchange:
#- include: EX_DG25.tsv # used to test the growth and product yields of wild-type and dLdh strain grown on glucose or fructose, as well as the carbon utilization for model validation
#  format: tsv
#- include: EX_modified_DSMZ516_v1.tsv # used to test the growth yields of wild-type strain on cellulose
#  format: tsv
#- include: EX_modified_DSMZ516_v2.tsv # used to test the ethanol production of the engineered ethano strain MACB1062 on cellulose
#  format: tsv
- include: EX_modified_DSMZ516_v3.tsv #used to teset the 2,3BDO strains
  format: tsv
- include: EX_products.yaml
  format: tsv
model:
- include: WT_model_def.tsv
- include: model_def_23BDO.tsv
limits:
- include: limits_mutant.yaml