# stageCD
# aerobic, acetate
marciez.sh ecoli_core_2010_A_tmall_meta.andl 4 1000 1000 1000 k_R_EX_h_e=0,k_re_R_EX_h_e=0,k_R_EX_h2o_e=0,k_R_EX_h_e_fix=1,k_re_R_EX_h_e_fix=1,k_R_EX_h2o_e_fix=1,k_re_R_PPS=1,k_re_R_FRUpts2=1,k_re_R_GLCpts=1,k_re_R_PPC=1,k_re_R_EX_o2_e=1,k_re_R_EX_ac_e=1 stageCD aerobic acetate
# aerobic, acetaldehyde
marciez.sh ecoli_core_2010_A_tmall_meta.andl 4 1000 1000 1000 k_R_EX_h_e=0,k_re_R_EX_h_e=0,k_R_EX_h2o_e=0,k_R_EX_h_e_fix=1,k_re_R_EX_h_e_fix=1,k_R_EX_h2o_e_fix=1,k_re_R_PPS=1,k_re_R_FRUpts2=1,k_re_R_GLCpts=1,k_re_R_PPC=1,k_re_R_EX_o2_e=1,k_re_R_EX_acald_e=1 stageCD aerobic acetaldehyde
# aerobic, 2-oxoglutarate
marciez.sh ecoli_core_2010_A_tmall_meta.andl 4 1000 1000 1000 k_R_EX_h_e=0,k_re_R_EX_h_e=0,k_R_EX_h2o_e=0,k_R_EX_h_e_fix=1,k_re_R_EX_h_e_fix=1,k_R_EX_h2o_e_fix=1,k_re_R_PPS=1,k_re_R_FRUpts2=1,k_re_R_GLCpts=1,k_re_R_PPC=1,k_re_R_EX_o2_e=1,k_re_R_EX_akg_e=1 stageCD aerobic 2-oxoglutarate
# aerobic, ethanol
marciez.sh ecoli_core_2010_A_tmall_meta.andl 4 1000 1000 1000 k_R_EX_h_e=0,k_re_R_EX_h_e=0,k_R_EX_h2o_e=0,k_R_EX_h_e_fix=1,k_re_R_EX_h_e_fix=1,k_R_EX_h2o_e_fix=1,k_re_R_PPS=1,k_re_R_FRUpts2=1,k_re_R_GLCpts=1,k_re_R_PPC=1,k_re_R_EX_o2_e=1,k_re_R_EX_etoh_e=1 stageCD aerobic ethanol
# aerobic, D-fructose
marciez.sh ecoli_core_2010_A_tmall_meta.andl 4 1000 1000 1000 k_R_EX_h_e=0,k_re_R_EX_h_e=0,k_R_EX_h2o_e=0,k_R_EX_h_e_fix=1,k_re_R_EX_h_e_fix=1,k_R_EX_h2o_e_fix=1,k_re_R_PPS=1,k_re_R_FRUpts2=1,k_re_R_GLCpts=1,k_re_R_PPC=1,k_re_R_EX_o2_e=1,k_re_R_EX_fru_e=1 stageCD aerobic D-fructose
# aerobic, fumarate
marciez.sh ecoli_core_2010_A_tmall_meta.andl 4 1000 1000 1000 k_R_EX_h_e=0,k_re_R_EX_h_e=0,k_R_EX_h2o_e=0,k_R_EX_h_e_fix=1,k_re_R_EX_h_e_fix=1,k_R_EX_h2o_e_fix=1,k_re_R_PPS=1,k_re_R_FRUpts2=1,k_re_R_GLCpts=1,k_re_R_PPC=1,k_re_R_EX_o2_e=1,k_re_R_EX_fum_e=1 stageCD aerobic fumarate
# aerobic, formate
marciez.sh ecoli_core_2010_A_tmall_meta.andl 4 1000 1000 1000 k_R_EX_h_e=0,k_re_R_EX_h_e=0,k_R_EX_h2o_e=0,k_R_EX_h_e_fix=1,k_re_R_EX_h_e_fix=1,k_R_EX_h2o_e_fix=1,k_re_R_PPS=1,k_re_R_FRUpts2=1,k_re_R_GLCpts=1,k_re_R_PPC=1,k_re_R_EX_o2_e=1,k_re_R_EX_for_e=1 stageCD aerobic formate
# aerobic, L-glutamine
marciez.sh ecoli_core_2010_A_tmall_meta.andl 4 1000 1000 1000 k_R_EX_h_e=0,k_re_R_EX_h_e=0,k_R_EX_h2o_e=0,k_R_EX_h_e_fix=1,k_re_R_EX_h_e_fix=1,k_R_EX_h2o_e_fix=1,k_re_R_PPS=1,k_re_R_FRUpts2=1,k_re_R_GLCpts=1,k_re_R_PPC=1,k_re_R_EX_o2_e=1,k_re_R_EX_gln_L_e=1 stageCD aerobic L-glutamine
# aerobic, L-glutamate
marciez.sh ecoli_core_2010_A_tmall_meta.andl 4 1000 1000 1000 k_R_EX_h_e=0,k_re_R_EX_h_e=0,k_R_EX_h2o_e=0,k_R_EX_h_e_fix=1,k_re_R_EX_h_e_fix=1,k_R_EX_h2o_e_fix=1,k_re_R_PPS=1,k_re_R_FRUpts2=1,k_re_R_GLCpts=1,k_re_R_PPC=1,k_re_R_EX_o2_e=1,k_re_R_EX_glu_L_e=1 stageCD aerobic L-glutamate
# aerobic, D-lactate
marciez.sh ecoli_core_2010_A_tmall_meta.andl 4 1000 1000 1000 k_R_EX_h_e=0,k_re_R_EX_h_e=0,k_R_EX_h2o_e=0,k_R_EX_h_e_fix=1,k_re_R_EX_h_e_fix=1,k_R_EX_h2o_e_fix=1,k_re_R_PPS=1,k_re_R_FRUpts2=1,k_re_R_GLCpts=1,k_re_R_PPC=1,k_re_R_EX_o2_e=1,k_re_R_EX_lac_D_e=1 stageCD aerobic D-lactate
# aerobic, L-malate
marciez.sh ecoli_core_2010_A_tmall_meta.andl 4 1000 1000 1000 k_R_EX_h_e=0,k_re_R_EX_h_e=0,k_R_EX_h2o_e=0,k_R_EX_h_e_fix=1,k_re_R_EX_h_e_fix=1,k_R_EX_h2o_e_fix=1,k_re_R_PPS=1,k_re_R_FRUpts2=1,k_re_R_GLCpts=1,k_re_R_PPC=1,k_re_R_EX_o2_e=1,k_re_R_EX_mal_L_e=1 stageCD aerobic L-malate
# aerobic, pyruvate
marciez.sh ecoli_core_2010_A_tmall_meta.andl 4 1000 1000 1000 k_R_EX_h_e=0,k_re_R_EX_h_e=0,k_R_EX_h2o_e=0,k_R_EX_h_e_fix=1,k_re_R_EX_h_e_fix=1,k_R_EX_h2o_e_fix=1,k_re_R_PPS=1,k_re_R_FRUpts2=1,k_re_R_GLCpts=1,k_re_R_PPC=1,k_re_R_EX_o2_e=1,k_re_R_EX_pyr_e=1 stageCD aerobic pyruvate
# aerobic, succinate
marciez.sh ecoli_core_2010_A_tmall_meta.andl 4 1000 1000 1000 k_R_EX_h_e=0,k_re_R_EX_h_e=0,k_R_EX_h2o_e=0,k_R_EX_h_e_fix=1,k_re_R_EX_h_e_fix=1,k_R_EX_h2o_e_fix=1,k_re_R_PPS=1,k_re_R_FRUpts2=1,k_re_R_GLCpts=1,k_re_R_PPC=1,k_re_R_EX_o2_e=1,k_re_R_EX_succ_e=1 stageCD aerobic succinate
# aerobic, D-glucose
marciez.sh ecoli_core_2010_A_tmall_meta.andl 4 1000 1000 1000 k_R_EX_h_e=0,k_re_R_EX_h_e=0,k_R_EX_h2o_e=0,k_R_EX_h_e_fix=1,k_re_R_EX_h_e_fix=1,k_R_EX_h2o_e_fix=1,k_re_R_PPS=1,k_re_R_FRUpts2=1,k_re_R_GLCpts=1,k_re_R_PPC=1,k_re_R_EX_o2_e=1,k_re_R_EX_glc_e=1 stageCD aerobic D-glucose
# aerobic, AllOn
marciez.sh ecoli_core_2010_A_tmall_meta.andl 4 1000 1000 1000 k_R_EX_h_e=0,k_re_R_EX_h_e=0,k_R_EX_h2o_e=0,k_R_EX_h_e_fix=1,k_re_R_EX_h_e_fix=1,k_R_EX_h2o_e_fix=1,k_re_R_PPS=1,k_re_R_FRUpts2=1,k_re_R_GLCpts=1,k_re_R_PPC=1,k_re_R_EX_o2_e=1,k_re_R_EX_ac_e=1,k_re_R_EX_acald_e=1,k_re_R_EX_akg_e=1,k_re_R_EX_etoh_e=1,k_re_R_EX_for_e=1,k_re_R_EX_fru_e=1,k_re_R_EX_fum_e=1,k_re_R_EX_glc_e=1,k_re_R_EX_gln_L_e=1,k_re_R_EX_glu_L_e=1,k_re_R_EX_lac_D_e=1,k_re_R_EX_mal_L_e=1,k_re_R_EX_pyr_e=1,k_re_R_EX_succ_e=1 stageCD aerobic AllOn
# aerobic, AllOff
marciez.sh ecoli_core_2010_A_tmall_meta.andl 4 1000 1000 1000 k_R_EX_h_e=0,k_re_R_EX_h_e=0,k_R_EX_h2o_e=0,k_R_EX_h_e_fix=1,k_re_R_EX_h_e_fix=1,k_R_EX_h2o_e_fix=1,k_re_R_PPS=1,k_re_R_FRUpts2=1,k_re_R_GLCpts=1,k_re_R_PPC=1,k_re_R_EX_o2_e=1,k_re_R_EX_ac_e=0,k_re_R_EX_acald_e=0,k_re_R_EX_akg_e=0,k_re_R_EX_etoh_e=0,k_re_R_EX_for_e=0,k_re_R_EX_fru_e=0,k_re_R_EX_fum_e=0,k_re_R_EX_glc_e=0,k_re_R_EX_gln_L_e=0,k_re_R_EX_glu_L_e=0,k_re_R_EX_lac_D_e=0,k_re_R_EX_mal_L_e=0,k_re_R_EX_pyr_e=0,k_re_R_EX_succ_e=0 stageCD aerobic AllOff
# anaerobic, acetate
marciez.sh ecoli_core_2010_A_tmall_meta.andl 4 1000 1000 1000 k_R_EX_h_e=0,k_re_R_EX_h_e=0,k_R_EX_h2o_e=0,k_R_EX_h_e_fix=1,k_re_R_EX_h_e_fix=1,k_R_EX_h2o_e_fix=1,k_re_R_PPS=1,k_re_R_FRUpts2=1,k_re_R_GLCpts=1,k_re_R_PPC=1,k_re_R_EX_o2_e=0,k_re_R_EX_ac_e=1 stageCD anaerobic acetate
# anaerobic, acetaldehyde
marciez.sh ecoli_core_2010_A_tmall_meta.andl 4 1000 1000 1000 k_R_EX_h_e=0,k_re_R_EX_h_e=0,k_R_EX_h2o_e=0,k_R_EX_h_e_fix=1,k_re_R_EX_h_e_fix=1,k_R_EX_h2o_e_fix=1,k_re_R_PPS=1,k_re_R_FRUpts2=1,k_re_R_GLCpts=1,k_re_R_PPC=1,k_re_R_EX_o2_e=0,k_re_R_EX_acald_e=1 stageCD anaerobic acetaldehyde
# anaerobic, 2-oxoglutarate
marciez.sh ecoli_core_2010_A_tmall_meta.andl 4 1000 1000 1000 k_R_EX_h_e=0,k_re_R_EX_h_e=0,k_R_EX_h2o_e=0,k_R_EX_h_e_fix=1,k_re_R_EX_h_e_fix=1,k_R_EX_h2o_e_fix=1,k_re_R_PPS=1,k_re_R_FRUpts2=1,k_re_R_GLCpts=1,k_re_R_PPC=1,k_re_R_EX_o2_e=0,k_re_R_EX_akg_e=1 stageCD anaerobic 2-oxoglutarate
# anaerobic, ethanol
marciez.sh ecoli_core_2010_A_tmall_meta.andl 4 1000 1000 1000 k_R_EX_h_e=0,k_re_R_EX_h_e=0,k_R_EX_h2o_e=0,k_R_EX_h_e_fix=1,k_re_R_EX_h_e_fix=1,k_R_EX_h2o_e_fix=1,k_re_R_PPS=1,k_re_R_FRUpts2=1,k_re_R_GLCpts=1,k_re_R_PPC=1,k_re_R_EX_o2_e=0,k_re_R_EX_etoh_e=1 stageCD anaerobic ethanol
# anaerobic, D-fructose
marciez.sh ecoli_core_2010_A_tmall_meta.andl 4 1000 1000 1000 k_R_EX_h_e=0,k_re_R_EX_h_e=0,k_R_EX_h2o_e=0,k_R_EX_h_e_fix=1,k_re_R_EX_h_e_fix=1,k_R_EX_h2o_e_fix=1,k_re_R_PPS=1,k_re_R_FRUpts2=1,k_re_R_GLCpts=1,k_re_R_PPC=1,k_re_R_EX_o2_e=0,k_re_R_EX_fru_e=1 stageCD anaerobic D-fructose
# anaerobic, fumarate
marciez.sh ecoli_core_2010_A_tmall_meta.andl 4 1000 1000 1000 k_R_EX_h_e=0,k_re_R_EX_h_e=0,k_R_EX_h2o_e=0,k_R_EX_h_e_fix=1,k_re_R_EX_h_e_fix=1,k_R_EX_h2o_e_fix=1,k_re_R_PPS=1,k_re_R_FRUpts2=1,k_re_R_GLCpts=1,k_re_R_PPC=1,k_re_R_EX_o2_e=0,k_re_R_EX_fum_e=1 stageCD anaerobic fumarate
# anaerobic, formate
marciez.sh ecoli_core_2010_A_tmall_meta.andl 4 1000 1000 1000 k_R_EX_h_e=0,k_re_R_EX_h_e=0,k_R_EX_h2o_e=0,k_R_EX_h_e_fix=1,k_re_R_EX_h_e_fix=1,k_R_EX_h2o_e_fix=1,k_re_R_PPS=1,k_re_R_FRUpts2=1,k_re_R_GLCpts=1,k_re_R_PPC=1,k_re_R_EX_o2_e=0,k_re_R_EX_for_e=1 stageCD anaerobic formate
# anaerobic, L-glutamine
marciez.sh ecoli_core_2010_A_tmall_meta.andl 4 1000 1000 1000 k_R_EX_h_e=0,k_re_R_EX_h_e=0,k_R_EX_h2o_e=0,k_R_EX_h_e_fix=1,k_re_R_EX_h_e_fix=1,k_R_EX_h2o_e_fix=1,k_re_R_PPS=1,k_re_R_FRUpts2=1,k_re_R_GLCpts=1,k_re_R_PPC=1,k_re_R_EX_o2_e=0,k_re_R_EX_gln_L_e=1 stageCD anaerobic L-glutamine
# anaerobic, L-glutamate
marciez.sh ecoli_core_2010_A_tmall_meta.andl 4 1000 1000 1000 k_R_EX_h_e=0,k_re_R_EX_h_e=0,k_R_EX_h2o_e=0,k_R_EX_h_e_fix=1,k_re_R_EX_h_e_fix=1,k_R_EX_h2o_e_fix=1,k_re_R_PPS=1,k_re_R_FRUpts2=1,k_re_R_GLCpts=1,k_re_R_PPC=1,k_re_R_EX_o2_e=0,k_re_R_EX_glu_L_e=1 stageCD anaerobic L-glutamate
# anaerobic, D-lactate
marciez.sh ecoli_core_2010_A_tmall_meta.andl 4 1000 1000 1000 k_R_EX_h_e=0,k_re_R_EX_h_e=0,k_R_EX_h2o_e=0,k_R_EX_h_e_fix=1,k_re_R_EX_h_e_fix=1,k_R_EX_h2o_e_fix=1,k_re_R_PPS=1,k_re_R_FRUpts2=1,k_re_R_GLCpts=1,k_re_R_PPC=1,k_re_R_EX_o2_e=0,k_re_R_EX_lac_D_e=1 stageCD anaerobic D-lactate
# anaerobic, L-malate
marciez.sh ecoli_core_2010_A_tmall_meta.andl 4 1000 1000 1000 k_R_EX_h_e=0,k_re_R_EX_h_e=0,k_R_EX_h2o_e=0,k_R_EX_h_e_fix=1,k_re_R_EX_h_e_fix=1,k_R_EX_h2o_e_fix=1,k_re_R_PPS=1,k_re_R_FRUpts2=1,k_re_R_GLCpts=1,k_re_R_PPC=1,k_re_R_EX_o2_e=0,k_re_R_EX_mal_L_e=1 stageCD anaerobic L-malate
# anaerobic, pyruvate
marciez.sh ecoli_core_2010_A_tmall_meta.andl 4 1000 1000 1000 k_R_EX_h_e=0,k_re_R_EX_h_e=0,k_R_EX_h2o_e=0,k_R_EX_h_e_fix=1,k_re_R_EX_h_e_fix=1,k_R_EX_h2o_e_fix=1,k_re_R_PPS=1,k_re_R_FRUpts2=1,k_re_R_GLCpts=1,k_re_R_PPC=1,k_re_R_EX_o2_e=0,k_re_R_EX_pyr_e=1 stageCD anaerobic pyruvate
# anaerobic, succinate
marciez.sh ecoli_core_2010_A_tmall_meta.andl 4 1000 1000 1000 k_R_EX_h_e=0,k_re_R_EX_h_e=0,k_R_EX_h2o_e=0,k_R_EX_h_e_fix=1,k_re_R_EX_h_e_fix=1,k_R_EX_h2o_e_fix=1,k_re_R_PPS=1,k_re_R_FRUpts2=1,k_re_R_GLCpts=1,k_re_R_PPC=1,k_re_R_EX_o2_e=0,k_re_R_EX_succ_e=1 stageCD anaerobic succinate
# anaerobic, D-glucose
marciez.sh ecoli_core_2010_A_tmall_meta.andl 4 1000 1000 1000 k_R_EX_h_e=0,k_re_R_EX_h_e=0,k_R_EX_h2o_e=0,k_R_EX_h_e_fix=1,k_re_R_EX_h_e_fix=1,k_R_EX_h2o_e_fix=1,k_re_R_PPS=1,k_re_R_FRUpts2=1,k_re_R_GLCpts=1,k_re_R_PPC=1,k_re_R_EX_o2_e=0,k_re_R_EX_glc_e=1 stageCD anaerobic D-glucose
# anaerobic, AllOn
marciez.sh ecoli_core_2010_A_tmall_meta.andl 4 1000 1000 1000 k_R_EX_h_e=0,k_re_R_EX_h_e=0,k_R_EX_h2o_e=0,k_R_EX_h_e_fix=1,k_re_R_EX_h_e_fix=1,k_R_EX_h2o_e_fix=1,k_re_R_PPS=1,k_re_R_FRUpts2=1,k_re_R_GLCpts=1,k_re_R_PPC=1,k_re_R_EX_o2_e=0,k_re_R_EX_ac_e=1,k_re_R_EX_acald_e=1,k_re_R_EX_akg_e=1,k_re_R_EX_etoh_e=1,k_re_R_EX_for_e=1,k_re_R_EX_fru_e=1,k_re_R_EX_fum_e=1,k_re_R_EX_glc_e=1,k_re_R_EX_gln_L_e=1,k_re_R_EX_glu_L_e=1,k_re_R_EX_lac_D_e=1,k_re_R_EX_mal_L_e=1,k_re_R_EX_pyr_e=1,k_re_R_EX_succ_e=1 stageCD anaerobic AllOn
# anaerobic, AllOff
marciez.sh ecoli_core_2010_A_tmall_meta.andl 4 1000 1000 1000 k_R_EX_h_e=0,k_re_R_EX_h_e=0,k_R_EX_h2o_e=0,k_R_EX_h_e_fix=1,k_re_R_EX_h_e_fix=1,k_R_EX_h2o_e_fix=1,k_re_R_PPS=1,k_re_R_FRUpts2=1,k_re_R_GLCpts=1,k_re_R_PPC=1,k_re_R_EX_o2_e=0,k_re_R_EX_ac_e=0,k_re_R_EX_acald_e=0,k_re_R_EX_akg_e=0,k_re_R_EX_etoh_e=0,k_re_R_EX_for_e=0,k_re_R_EX_fru_e=0,k_re_R_EX_fum_e=0,k_re_R_EX_glc_e=0,k_re_R_EX_gln_L_e=0,k_re_R_EX_glu_L_e=0,k_re_R_EX_lac_D_e=0,k_re_R_EX_mal_L_e=0,k_re_R_EX_pyr_e=0,k_re_R_EX_succ_e=0 stageCD anaerobic AllOff