switch_lcts_to_glc.yaml

model: '../../tutorials/models/SlackModel iJO1366_vETFL_tp_441_enz_128_bins__20190620_144322.json'
tag: 'vETFL_switch_lcts_to_glc'
simulation:
  timestep: 0.05
  tfinal: 3
  mode: switch1
assumptions:
  v0:
    EX_o2_e: -15 # mmol/gDW/h
    EX_glc__D_e: 0 # mmol/gDW/h
    EX_lcts_e: -5 # mmol/gDW/h
    EX_ac_e: 0 # mmol/L
  S0:
    EX_o2_e: 0.21 # mmol/L
    EX_glc__D_e: 0 # mmol/L
    EX_lcts_e: 1 # mmol/L
    EX_ac_e: 0 # mmol/L

  X0: 0.05
  uptake_enz:
#    EX_ac_e:
#      - ACt4pp
#      - ACt2rpp
    EX_glc__D_e:
      - GLCDpp
      - GLCabcpp
      - GLCptspp
      - GLCt2pp
    EX_lcts_e:
      - LACZpp
      - LCTSt3ipp
      - LCTStpp

options:
  verbose: false
  inplace: true
  chebyshev_include:
    - ForwardCatalyticConstraint
    - BackwardCatalyticConstraint
#    - EnzymeDeltaPos
#    - EnzymeDeltaNeg
#    - ExpressionCoupling
  constraints:
    mRNA_degradation: no
    mRNA_synthesis  : no
    enzyme_degradation: yes
    enzyme_synthesis: no