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get_shadow_prices.gms
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********************************************************************************************
*script to generate all FBA data for the 15 trials which will be used by the ED model which
*will be the input to makeKopticInputs.pl which will finally be the KOPTIC inputs
*By: Wheaton Schroeder
*Research Group: PI: Rajib Saha SSBIO University of Nebraska-Lincoln
*Latest Version: 11/21/2019
********************************************************************************************
$INLINECOM /* */
$EOLCOM !!
$onlisting
$offdigit
$onempty
options limrow = 1000
optCR = 1E-9
optCA = 1E-9
iterlim = 1000000
decimals = 8
reslim = 1000000
work = 50000000
lp = cplex;
SETS
jED Reactions of k-ath model
$include "rxns.txt"
iED Metabolites of k-ath model
$include "mets.txt"
reg_off(jED) Reactions turned off (regulated)
$include "reg_rxns.txt"
irrev_f(jED) Reactions that are irreversible, forwards
$include "irrev_rxns_f.txt"
irrev_b(jED) reactions that are irreversible, backwards
$include "irrev_rxns_b.txt"
;
PARAMETERS
UBED(jED) UB on rxns of ED
LBED(jED) LB on rxns of ED
rxntype_ED(jED) Reaction type for rxns of ED
$include "rxntype.txt"
trial_count
trial_count_temp
conc(iED) /*metabolite concentration*/
epsilon /*a very small number*/
;
epsilon = 1E-7;
trial_count = 1;
trial_count_temp = 1;
****************** Set the values of LB and UB ******************
SCALAR Vmax /10000/;
SCALAR BigM /9900/;
*** Set the experimental conditions
* irreversible reactions forward (rxntype = 1)
UBED(jED)$(rxntype_ED(jED) = 1) = Vmax;
LBED(jED)$(rxntype_ED(jED) = 1) = 0;
* For reversible reactions (rxntype = 0)
UBED(jED)$(rxntype_ED(jED) = 0) = Vmax;
LBED(jED)$(rxntype_ED(jED) = 0) = -Vmax;
* irreversible reactions backwards (rxntype = -1)
UBED(jED)$(rxntype_ED(jED) = -1) = 0;
LBED(jED)$(rxntype_ED(jED) = -1) = -Vmax;
**********************************************trial 1************************************************
* carbon limited, sucrose as only carbon source, LB(R003ex) = -0.25 *
*****************************************************************************************************
*** Set the experimental conditions
* irreversible reactions forward (rxntype = 1)
UBED(jED)$(rxntype_ED(jED) = 1) = Vmax;
LBED(jED)$(rxntype_ED(jED) = 1) = 0;
* For reversible reactions (rxntype = 0)
UBED(jED)$(rxntype_ED(jED) = 0) = Vmax;
LBED(jED)$(rxntype_ED(jED) = 0) = -Vmax;
* irreversible reactions backwards (rxntype = -1)
UBED(jED)$(rxntype_ED(jED) = -1) = 0;
LBED(jED)$(rxntype_ED(jED) = -1) = -Vmax;
LBED('R001ex')=-Vmax; !!water
LBED('R002ex')=-Vmax; !!phosphate
LBED('R003ex')=-0.25; !!sucrose
LBED('R004ex')=-Vmax; !!ammonia
LBED('R005ex')=-Vmax; !!sulfate
LBED('R006ex')=-Vmax; !!H+
LBED('R007ex')=0; !!Carbon dioxide
LBED('R008ex')=-Vmax; !!oxygen
LBED('R009ex')=0; !!ethanol
LBED('R010ex')=0; !!acetate
LBED('R011ex')=0; !!glucose
LBED('R012ex')=0; !!urate
UBED('R001ex')=Vmax; !!water
UBED('R002ex')=0; !!phosphate
UBED('R003ex')=0; !!sucrose
UBED('R004ex')=0; !!ammonia
UBED('R005ex')=0; !!sulfate
UBED('R006ex')=Vmax; !!H+
UBED('R007ex')=Vmax; !!Carbon dioxide
UBED('R008ex')=0; !!oxygen
UBED('R009ex')=Vmax; !!ethanol
UBED('R010ex')=0; !!acetate
UBED('R011ex')=0; !!glucose
UBED('R012ex')=Vmax; !!urate
* Reactions turned off
UBED(jED)$reg_off(jED) = 0;
LBED(jED)$reg_off(jED) = 0;
****************stoichiometry*****************
PARAMETERS
SED(iED,jED) Stoichiometric matrix for ED
$include "Sij.txt"
;
PARAMETERS
C(jED)
max(jED)
min(jED);
alias (j1ED, jED);
*set objective as the biomass function
c(jED) = 0;
c('biomass_si') = 1;
VARIABLES
zprimal_ED primal objective function (rxn fluxes in each loop) for ED
zdual_ED primal objective function (rxn fluxes in each loop) for ED
vED(jED) Flux of ED rxns
lambda(iED) dual variable associated with the mass balance
POSITIVE VARIABLES
muLB(jED) dual variable associated with the lower bound constraint
muUB(jED) dual variable associated with the upper bound constraint
;
vED.lo(jED)=LBED(jED);
vED.up(jED)=UBED(jED);
*********************EQUATIONS NAMES**************************
EQUATIONS
primalobj_ED primal problem objective function (rxn fluxes in each loop) for ED
massbalance_ED(iED) Mass balance for ED
dual_obj dual problem objective
dual_const_1(jED) dual constraint 1
dual_const_2(jED) dual constraint 2
strong_duality enforces strong duality
;
****************************** Primal Equations*******************************
primalobj_ED.. zprimal_ED =e= sum(jED$(C(jED) eq 1),vED(jED));
massbalance_ED(iED).. sum(jED,SED(iED,jED)*vED(jED)) =e= 0;
******************************************************************************
****************************** Dual Equations*********************************
dual_obj.. zdual_ED =e= sum(iED, 0 * lambda(iED)) + sum(jED, - LBED(jED) * muLB(jED)) + sum(jED, UBED(jED) * muUB(jED));
dual_const_1(jED)$(c(jED) = 0).. sum(iED, SED(iED,jED) * lambda(iED)) - muLB(jED) + muUB(jED) =e= 0;
dual_const_2(jED)$(c(jED) = 1).. sum(iED, SED(iED,jED) * lambda(iED)) - muLB(jED) + muUB(jED) =e= 1;
******************************************************************************
strong_duality.. zdual_ED =e= zprimal_ED;
model PRIMALED
/
primalobj_ED
massbalance_ED
/
;
model DUALED
/
dual_obj
dual_const_1
dual_const_2
/
;
model STRONGED
/
primalobj_ED
massbalance_ED
dual_obj
dual_const_1
dual_const_2
strong_duality
/
;
*no optimization file
PRIMALED.optfile=1;
DUALED.optfile=1;
STRONGED.optfile=1;
*solve this scenario for maximum biomass
SOLVE STRONGED USING LP MAXIMIZING zprimal_ED;
*print output for the flux rates
FILE RXNOUT /rxn_rates_out.csv/;
PUT RXNOUT;
RXNOUT.lw = 25;
RXNOUT.pc = 5;
PUT "trial";
LOOP(jED,
PUT jED.tl;
);
PUT /;
PUT trial_count;
LOOP(jED,
PUT vED.l(jED):0:8/;
);
PUTCLOSE;
*file for shadow prices
FILE SHADOW /shadow_price.csv/;
PUT SHADOW;
SHADOW.pc = 5;
SHADOW.lw = 25;
SHADOW.pw = 30000;
*write the header
PUT "Trial number","trial code";
PUT "growth rate";
PUT "X00001[c]";
PUT "C04033[c]";
PUT "C00779[c]";
PUT "C01173[c]";
PUT "C01624[c]";
PUT "C00083[c]";
PUT "C17937DHN[e]";
PUT "C05578[e]";
PUT "C05579[e]";
PUT "C01693[e]";
PUT "C05604[e]";
PUT "C00355[c]";
PUT "C00822[c]";
PUT "C00082[c]";
PUT "C17937Eu[e]";
PUT "C00544[c]";
PUT "X00002[c]";
PUT "C01179[c]";
PUT "C17937Pyo[e]";
PUT "C00353[c]";
PUT "C03427[c]";
PUT "C05421[c]";
PUT "C05414[c]";
PUT "C05430[c]";
PUT "C05431[c]";
PUT "C05432[c]";
PUT "C05435[c]";
PUT "C15867[c]";
PUT "C08613[c]";
PUT "C02094[c]";
PUT "C19892[c]";
PUT "C08607[c]";
PUT "C00097[c]";
PUT "Model Status"/;
*print the shadow price of just the pigments
PUT trial_count,"SCL";
PUT vED.l('biomass_wt_37'):0:8;
PUT lambda.l('X00001[c]'):0:8;
PUT lambda.l('C04033[c]'):0:8;
PUT lambda.l('C00779[c]'):0:8;
PUT lambda.l('C01173[c]'):0:8;
PUT lambda.l('C01624[c]'):0:8;
PUT lambda.l('C00083[c]'):0:8;
PUT lambda.l('C17937DHN[e]'):0:8;
PUT lambda.l('C05578[e]'):0:8;
PUT lambda.l('C05579[e]'):0:8;
PUT lambda.l('C01693[e]'):0:8;
PUT lambda.l('C05604[e]'):0:8;
PUT lambda.l('C00355[c]'):0:8;
PUT lambda.l('C00822[c]'):0:8;
PUT lambda.l('C00082[c]'):0:8;
PUT lambda.l('C17937Eu[e]'):0:8;
PUT lambda.l('C00544[c]'):0:8;
PUT lambda.l('X00002[c]'):0:8;
PUT lambda.l('C01179[c]'):0:8;
PUT lambda.l('C17937Pyo[e]'):0:8;
PUT lambda.l('C00353[c]'):0:8;
PUT lambda.l('C03427[c]'):0:8;
PUT lambda.l('C05421[c]'):0:8;
PUT lambda.l('C05414[c]'):0:8;
PUT lambda.l('C05430[c]'):0:8;
PUT lambda.l('C05431[c]'):0:8;
PUT lambda.l('C05432[c]'):0:8;
PUT lambda.l('C05435[c]'):0:8;
PUT lambda.l('C15867[c]'):0:8;
PUT lambda.l('C08613[c]'):0:8;
PUT lambda.l('C02094[c]'):0:8;
PUT lambda.l('C19892[c]'):0:8;
PUT lambda.l('C08607[c]'):0:8;
PUT lambda.l('C00097[c]'):0:8;
PUT STRONGED.ModelStat/;
PUTCLOSE;
*file for shadow prices related to malonyl-CoA
FILE SHADOWMCoA /shadow_price_MCoA.csv/;
PUT SHADOWMCoA;
SHADOWMCoA.pc = 5;
SHADOWMCoA.lw = 25;
SHADOWMCoA.pw = 30000;
*write the header
PUT "Trial number","trial code";
PUT "growth rate";
PUT "C00083[c]";
PUT "C00002[c]";
PUT "C00024[c]";
PUT "C00033[c]";
PUT "C00010[c]";
PUT "C00882[c]";
PUT "C01134[c]";
PUT "C04352[c]";
PUT "C00097[c]";
PUT "C03492[c]";
PUT "C00288[c]";
PUT "C00008[c]";
PUT "C00020[c]";
PUT "C00009[c]";
PUT "C00013[c]";
PUT "C00001[c]";
PUT "C00011[c]";
PUT "C00063[c]";
PUT "C00055[c]";
PUT "Model Status"/;
PUT trial_count,"SCL";
PUT vED.l('biomass_wt_37'):0:8;
PUT lambda.l('C00083[c]'):0:8;
PUT lambda.l('C00002[c]'):0:8;
PUT lambda.l('C00024[c]'):0:8;
PUT lambda.l('C00033[c]'):0:8;
PUT lambda.l('C00010[c]'):0:8;
PUT lambda.l('C00882[c]'):0:8;
PUT lambda.l('C01134[c]'):0:8;
PUT lambda.l('C04352[c]'):0:8;
PUT lambda.l('C00097[c]'):0:8;
PUT lambda.l('C03492[c]'):0:8;
PUT lambda.l('C00288[c]'):0:8;
PUT lambda.l('C00008[c]'):0:8;
PUT lambda.l('C00020[c]'):0:8;
PUT lambda.l('C00009[c]'):0:8;
PUT lambda.l('C00013[c]'):0:8;
PUT lambda.l('C00001[c]'):0:8;
PUT lambda.l('C00011[c]'):0:8;
PUT lambda.l('C00063[c]'):0:8;
PUT lambda.l('C00055[c]'):0:8;
PUT STRONGED.ModelStat/;
PUTCLOSE;
*file for shadow prices related to malonyl-CoA
FILE SHADOWBIO /shadow_price_biomass.csv/;
PUT SHADOWBIO;
SHADOWBIO.pc = 5;
SHADOWBIO.lw = 25;
SHADOWBIO.pw = 30000;
*make header
PUT "C00049[c]";
PUT "C00025[c]";
PUT "C00041[c]";
PUT "C00037[c]";
PUT "C00064[c]";
PUT "C00152[c]";
PUT "C00148[c]";
PUT "C00097[c]";
PUT "C00062[c]";
PUT "C00073[c]";
PUT "C00065[c]";
PUT "C00078[c]";
PUT "C00188[c]";
PUT "C00135[c]";
PUT "C00079[c]";
PUT "C00082[c]";
PUT "C00183[c]";
PUT "C00123[c]";
PUT "C00407[c]";
PUT "C00047[c]";
PUT "C00017[c]";
PUT "C00249[im]";
PUT "C01530[im]";
PUT "C06425[im]";
PUT "C00712[im]";
PUT "C01595[im]";
PUT "C01356[im]";
PUT "C00075[c]";
PUT "C00044[c]";
PUT "C00182[c]";
PUT "C00116[c]";
PUT "C00422[c]";
PUT "C00350[c]";
PUT "C02737[c]";
PUT "C00063[c]";
PUT "C01356[c]";
PUT "C00017[c";
PUT "C00286[c]";
PUT "C00131[c]";
PUT "C00458[c]";
PUT "C00459[c]";
PUT "cell[c]";
PUT "C00965[e]";
PUT "C01356[e]";
PUT "C17937DHN[e]";
PUT "C17937Eu[e]";
PUT "C17937Pyo[e]";
PUT "C00017[e]";
PUT "C00140[e]";
PUT "C00461[e]";
PUT "cell_wall[e]";
PUT "C02094[c]";
PUT "C19892[c]";
PUT "C08607[c]";
PUT "C00097[c]";
PUT "carotenoids[c]";
PUT "biomass"/;
PUT lambda.l('C00049[c]'):0:8;
PUT lambda.l('C00025[c]'):0:8;
PUT lambda.l('C00041[c]'):0:8;
PUT lambda.l('C00037[c]'):0:8;
PUT lambda.l('C00064[c]'):0:8;
PUT lambda.l('C00152[c]'):0:8;
PUT lambda.l('C00148[c]'):0:8;
PUT lambda.l('C00097[c]'):0:8;
PUT lambda.l('C00062[c]'):0:8;
PUT lambda.l('C00073[c]'):0:8;
PUT lambda.l('C00065[c]'):0:8;
PUT lambda.l('C00078[c]'):0:8;
PUT lambda.l('C00188[c]'):0:8;
PUT lambda.l('C00135[c]'):0:8;
PUT lambda.l('C00079[c]'):0:8;
PUT lambda.l('C00082[c]'):0:8;
PUT lambda.l('C00183[c]'):0:8;
PUT lambda.l('C00123[c]'):0:8;
PUT lambda.l('C00407[c]'):0:8;
PUT lambda.l('C00047[c]'):0:8;
PUT lambda.l('C00017[c]'):0:8;
PUT lambda.l('C00249[im]'):0:8;
PUT lambda.l('C01530[im]'):0:8;
PUT lambda.l('C06425[im]'):0:8;
PUT lambda.l('C00712[im]'):0:8;
PUT lambda.l('C01595[im]'):0:8;
PUT lambda.l('C01356[im]'):0:8;
PUT lambda.l('C00075[c]'):0:8;
PUT lambda.l('C00044[c]'):0:8;
PUT lambda.l('C00182[c]'):0:8;
PUT lambda.l('C00116[c]'):0:8;
PUT lambda.l('C00422[c]'):0:8;
PUT lambda.l('C00350[c]'):0:8;
PUT lambda.l('C02737[c]'):0:8;
PUT lambda.l('C00063[c]'):0:8;
PUT lambda.l('C01356[c]'):0:8;
PUT lambda.l('C00017[c]'):0:8;
PUT lambda.l('C00286[c]'):0:8;
PUT lambda.l('C00131[c]'):0:8;
PUT lambda.l('C00458[c]'):0:8;
PUT lambda.l('C00459[c]'):0:8;
PUT lambda.l('cell[c]'):0:8;
PUT lambda.l('C00965[e]'):0:8;
PUT lambda.l('C01356[e]'):0:8;
PUT lambda.l('C17937DHN[e]'):0:8;
PUT lambda.l('C17937Eu[e]'):0:8;
PUT lambda.l('C17937Pyo[e]'):0:8;
PUT lambda.l('C00017[e]'):0:8;
PUT lambda.l('C00140[e]'):0:8;
PUT lambda.l('C00461[e]'):0:8;
PUT lambda.l('cell_wall[e]'):0:8;
PUT lambda.l('C02094[c]'):0:8;
PUT lambda.l('C19892[c]'):0:8;
PUT lambda.l('C08607[c]'):0:8;
PUT lambda.l('C00097[c]'):0:8;
PUT lambda.l('carotenoids[c]'):0:8;
PUT lambda.l('biomass'):0:8/;
PUTCLOSE;
*update the trial counter
trial_count_temp = trial_count + 1;
trial_count = trial_count_temp;
**********************************************trial 2************************************************
* carbon limited, sucrose as only carbon source, LB(R003ex) = -0.5 *
*****************************************************************************************************
LBED('R001ex')=-Vmax; !!water
LBED('R002ex')=-Vmax; !!phosphate
LBED('R003ex')=-0.5; !!sucrose
LBED('R004ex')=-Vmax; !!ammonia
LBED('R005ex')=-Vmax; !!sulfate
LBED('R006ex')=-Vmax; !!H+
LBED('R007ex')=0; !!Carbon dioxide
LBED('R008ex')=-Vmax; !!oxygen
LBED('R009ex')=0; !!ethanol
LBED('R010ex')=0; !!acetate
LBED('R011ex')=0; !!glucose
LBED('R012ex')=0; !!urate
UBED('R001ex')=Vmax; !!water
UBED('R002ex')=0; !!phosphate
UBED('R003ex')=0; !!sucrose
UBED('R004ex')=0; !!ammonia
UBED('R005ex')=0; !!sulfate
UBED('R006ex')=Vmax; !!H+
UBED('R007ex')=Vmax; !!Carbon dioxide
UBED('R008ex')=0; !!oxygen
UBED('R009ex')=Vmax; !!ethanol
UBED('R010ex')=0; !!acetate
UBED('R011ex')=0; !!glucose
UBED('R012ex')=Vmax; !!urate
vED.lo(jED)=LBED(jED);
vED.up(jED)=UBED(jED);
SOLVE STRONGED USING LP MAXIMIZING zprimal_ED;
RXNOUT.ap = 1;
PUT RXNOUT;
RXNOUT.pc = 5;
RXNOUT.lw = 25;
PUT trial_count;
LOOP(jED,
PUT vED.l(jED):0:8;
);
PUT /;
PUTCLOSE;
SHADOW.ap = 1;
PUT SHADOW;
SHADOW.pc = 5;
SHADOW.lw = 25;
SHADOW.pw = 30000;
SHADOW.pw = 30000;
*print the shadow price of just the pigments and precursors
PUT trial_count,"SCM";
PUT vED.l('biomass_wt_37'):0:8;
PUT lambda.l('X00001[c]'):0:8;
PUT lambda.l('C04033[c]'):0:8;
PUT lambda.l('C00779[c]'):0:8;
PUT lambda.l('C01173[c]'):0:8;
PUT lambda.l('C01624[c]'):0:8;
PUT lambda.l('C00083[c]'):0:8;
PUT lambda.l('C17937DHN[e]'):0:8;
PUT lambda.l('C05578[e]'):0:8;
PUT lambda.l('C05579[e]'):0:8;
PUT lambda.l('C01693[e]'):0:8;
PUT lambda.l('C05604[e]'):0:8;
PUT lambda.l('C00355[c]'):0:8;
PUT lambda.l('C00822[c]'):0:8;
PUT lambda.l('C00082[c]'):0:8;
PUT lambda.l('C17937Eu[e]'):0:8;
PUT lambda.l('C00544[c]'):0:8;
PUT lambda.l('X00002[c]'):0:8;
PUT lambda.l('C01179[c]'):0:8;
PUT lambda.l('C17937Pyo[e]'):0:8;
PUT lambda.l('C00353[c]'):0:8;
PUT lambda.l('C03427[c]'):0:8;
PUT lambda.l('C05421[c]'):0:8;
PUT lambda.l('C05414[c]'):0:8;
PUT lambda.l('C05430[c]'):0:8;
PUT lambda.l('C05431[c]'):0:8;
PUT lambda.l('C05432[c]'):0:8;
PUT lambda.l('C05435[c]'):0:8;
PUT lambda.l('C15867[c]'):0:8;
PUT lambda.l('C08613[c]'):0:8;
PUT lambda.l('C02094[c]'):0:8;
PUT lambda.l('C19892[c]'):0:8;
PUT lambda.l('C08607[c]'):0:8;
PUT lambda.l('C00097[c]'):0:8;
PUT STRONGED.ModelStat/;
PUTCLOSE;
SHADOWMCoA.ap = 1;
PUT SHADOWMCoA;
SHADOWMCoA.pc = 5;
SHADOWMCoA.lw = 25;
SHADOWMCoA.pw = 30000;
SHADOWMCoA.pw = 30000;
PUT trial_count,"SCM";
PUT vED.l('biomass_wt_37'):0:8;
PUT lambda.l('C00083[c]'):0:8;
PUT lambda.l('C00002[c]'):0:8;
PUT lambda.l('C00024[c]'):0:8;
PUT lambda.l('C00033[c]'):0:8;
PUT lambda.l('C00010[c]'):0:8;
PUT lambda.l('C00882[c]'):0:8;
PUT lambda.l('C01134[c]'):0:8;
PUT lambda.l('C04352[c]'):0:8;
PUT lambda.l('C00097[c]'):0:8;
PUT lambda.l('C03492[c]'):0:8;
PUT lambda.l('C00288[c]'):0:8;
PUT lambda.l('C00008[c]'):0:8;
PUT lambda.l('C00020[c]'):0:8;
PUT lambda.l('C00009[c]'):0:8;
PUT lambda.l('C00013[c]'):0:8;
PUT lambda.l('C00001[c]'):0:8;
PUT lambda.l('C00011[c]'):0:8;
PUT lambda.l('C00063[c]'):0:8;
PUT lambda.l('C00055[c]'):0:8;
PUT STRONGED.ModelStat/;
PUTCLOSE;
SHADOWBIO.ap = 1;
PUT SHADOWBIO;
SHADOWBIO.pc = 5;
SHADOWBIO.lw = 25;
SHADOWBIO.pw = 30000;
SHADOWBIO.pw = 30000;
PUT lambda.l('C00049[c]'):0:8;
PUT lambda.l('C00025[c]'):0:8;
PUT lambda.l('C00041[c]'):0:8;
PUT lambda.l('C00037[c]'):0:8;
PUT lambda.l('C00064[c]'):0:8;
PUT lambda.l('C00152[c]'):0:8;
PUT lambda.l('C00148[c]'):0:8;
PUT lambda.l('C00097[c]'):0:8;
PUT lambda.l('C00062[c]'):0:8;
PUT lambda.l('C00073[c]'):0:8;
PUT lambda.l('C00065[c]'):0:8;
PUT lambda.l('C00078[c]'):0:8;
PUT lambda.l('C00188[c]'):0:8;
PUT lambda.l('C00135[c]'):0:8;
PUT lambda.l('C00079[c]'):0:8;
PUT lambda.l('C00082[c]'):0:8;
PUT lambda.l('C00183[c]'):0:8;
PUT lambda.l('C00123[c]'):0:8;
PUT lambda.l('C00407[c]'):0:8;
PUT lambda.l('C00047[c]'):0:8;
PUT lambda.l('C00017[c]'):0:8;
PUT lambda.l('C00249[im]'):0:8;
PUT lambda.l('C01530[im]'):0:8;
PUT lambda.l('C06425[im]'):0:8;
PUT lambda.l('C00712[im]'):0:8;
PUT lambda.l('C01595[im]'):0:8;
PUT lambda.l('C01356[im]'):0:8;
PUT lambda.l('C00075[c]'):0:8;
PUT lambda.l('C00044[c]'):0:8;
PUT lambda.l('C00182[c]'):0:8;
PUT lambda.l('C00116[c]'):0:8;
PUT lambda.l('C00422[c]'):0:8;
PUT lambda.l('C00350[c]'):0:8;
PUT lambda.l('C02737[c]'):0:8;
PUT lambda.l('C00063[c]'):0:8;
PUT lambda.l('C01356[c]'):0:8;
PUT lambda.l('C00017[c]'):0:8;
PUT lambda.l('C00286[c]'):0:8;
PUT lambda.l('C00131[c]'):0:8;
PUT lambda.l('C00458[c]'):0:8;
PUT lambda.l('C00459[c]'):0:8;
PUT lambda.l('cell[c]'):0:8;
PUT lambda.l('C00965[e]'):0:8;
PUT lambda.l('C01356[e]'):0:8;
PUT lambda.l('C17937DHN[e]'):0:8;
PUT lambda.l('C17937Eu[e]'):0:8;
PUT lambda.l('C17937Pyo[e]'):0:8;
PUT lambda.l('C00017[e]'):0:8;
PUT lambda.l('C00140[e]'):0:8;
PUT lambda.l('C00461[e]'):0:8;
PUT lambda.l('cell_wall[e]'):0:8;
PUT lambda.l('C02094[c]'):0:8;
PUT lambda.l('C19892[c]'):0:8;
PUT lambda.l('C08607[c]'):0:8;
PUT lambda.l('C00097[c]'):0:8;
PUT lambda.l('carotenoids[c]'):0:8;
PUT lambda.l('biomass'):0:8/;
PUTCLOSE;
*update the trial counter
trial_count_temp = trial_count + 1;
trial_count = trial_count_temp;
**********************************************trial 3************************************************
* carbon limited, sucrose as only carbon source, LB(R003ex) = -1 *
*****************************************************************************************************
LBED('R001ex')=-Vmax; !!water
LBED('R002ex')=-Vmax; !!phosphate
LBED('R003ex')=-1; !!sucrose
LBED('R004ex')=-Vmax; !!ammonia
LBED('R005ex')=-Vmax; !!sulfate
LBED('R006ex')=-Vmax; !!H+
LBED('R007ex')=0; !!Carbon dioxide
LBED('R008ex')=-Vmax; !!oxygen
LBED('R009ex')=0; !!ethanol
LBED('R010ex')=0; !!acetate
LBED('R011ex')=0; !!glucose
LBED('R012ex')=0; !!urate
UBED('R001ex')=Vmax; !!water
UBED('R002ex')=0; !!phosphate
UBED('R003ex')=0; !!sucrose
UBED('R004ex')=0; !!ammonia
UBED('R005ex')=0; !!sulfate
UBED('R006ex')=Vmax; !!H+
UBED('R007ex')=Vmax; !!Carbon dioxide
UBED('R008ex')=0; !!oxygen
UBED('R009ex')=Vmax; !!ethanol
UBED('R010ex')=0; !!acetate
UBED('R011ex')=0; !!glucose
UBED('R012ex')=Vmax; !!urate
vED.lo(jED)=LBED(jED);
vED.up(jED)=UBED(jED);
vED.lo(jED)=LBED(jED);
vED.up(jED)=UBED(jED);
SOLVE STRONGED USING LP MAXIMIZING zprimal_ED;
RXNOUT.ap = 1;
PUT RXNOUT;
RXNOUT.pc = 5;
RXNOUT.lw = 25;
PUT trial_count;
LOOP(jED,
PUT vED.l(jED):0:8;
);
PUT /;
PUTCLOSE;
SHADOW.ap = 1;
PUT SHADOW;
SHADOW.pc = 5;
SHADOW.lw = 25;
SHADOW.pw = 30000;
*print the shadow price of just the pigments
PUT trial_count,"SCH";
PUT vED.l('biomass_wt_37'):0:8;
PUT lambda.l('X00001[c]'):0:8;
PUT lambda.l('C04033[c]'):0:8;
PUT lambda.l('C00779[c]'):0:8;
PUT lambda.l('C01173[c]'):0:8;
PUT lambda.l('C01624[c]'):0:8;
PUT lambda.l('C00083[c]'):0:8;
PUT lambda.l('C17937DHN[e]'):0:8;
PUT lambda.l('C05578[e]'):0:8;
PUT lambda.l('C05579[e]'):0:8;
PUT lambda.l('C01693[e]'):0:8;
PUT lambda.l('C05604[e]'):0:8;
PUT lambda.l('C00355[c]'):0:8;
PUT lambda.l('C00822[c]'):0:8;
PUT lambda.l('C00082[c]'):0:8;
PUT lambda.l('C17937Eu[e]'):0:8;
PUT lambda.l('C00544[c]'):0:8;
PUT lambda.l('X00002[c]'):0:8;
PUT lambda.l('C01179[c]'):0:8;
PUT lambda.l('C17937Pyo[e]'):0:8;
PUT lambda.l('C00353[c]'):0:8;
PUT lambda.l('C03427[c]'):0:8;
PUT lambda.l('C05421[c]'):0:8;
PUT lambda.l('C05414[c]'):0:8;
PUT lambda.l('C05430[c]'):0:8;
PUT lambda.l('C05431[c]'):0:8;
PUT lambda.l('C05432[c]'):0:8;
PUT lambda.l('C05435[c]'):0:8;
PUT lambda.l('C15867[c]'):0:8;
PUT lambda.l('C08613[c]'):0:8;
PUT lambda.l('C02094[c]'):0:8;
PUT lambda.l('C19892[c]'):0:8;
PUT lambda.l('C08607[c]'):0:8;
PUT lambda.l('C00097[c]'):0:8;
PUT STRONGED.ModelStat/;
PUTCLOSE;
SHADOWMCoA.ap = 1;
PUT SHADOWMCoA;
SHADOWMCoA.pc = 5;
SHADOWMCoA.lw = 25;
SHADOWMCoA.pw = 30000;
SHADOWMCoA.pw = 30000;
PUT trial_count,"SCH";
PUT vED.l('biomass_wt_37'):0:8;
PUT lambda.l('C00083[c]'):0:8;
PUT lambda.l('C00002[c]'):0:8;
PUT lambda.l('C00024[c]'):0:8;
PUT lambda.l('C00033[c]'):0:8;
PUT lambda.l('C00010[c]'):0:8;
PUT lambda.l('C00882[c]'):0:8;
PUT lambda.l('C01134[c]'):0:8;
PUT lambda.l('C04352[c]'):0:8;
PUT lambda.l('C00097[c]'):0:8;
PUT lambda.l('C03492[c]'):0:8;
PUT lambda.l('C00288[c]'):0:8;
PUT lambda.l('C00008[c]'):0:8;
PUT lambda.l('C00020[c]'):0:8;
PUT lambda.l('C00009[c]'):0:8;
PUT lambda.l('C00013[c]'):0:8;
PUT lambda.l('C00001[c]'):0:8;
PUT lambda.l('C00011[c]'):0:8;
PUT lambda.l('C00063[c]'):0:8;
PUT lambda.l('C00055[c]'):0:8;
PUT STRONGED.ModelStat/;
PUTCLOSE;
SHADOWBIO.ap = 1;
PUT SHADOWBIO;
SHADOWBIO.pc = 5;
SHADOWBIO.lw = 25;
SHADOWBIO.pw = 30000;
SHADOWBIO.pw = 30000;
PUT lambda.l('C00049[c]'):0:8;
PUT lambda.l('C00025[c]'):0:8;
PUT lambda.l('C00041[c]'):0:8;
PUT lambda.l('C00037[c]'):0:8;
PUT lambda.l('C00064[c]'):0:8;
PUT lambda.l('C00152[c]'):0:8;
PUT lambda.l('C00148[c]'):0:8;
PUT lambda.l('C00097[c]'):0:8;
PUT lambda.l('C00062[c]'):0:8;
PUT lambda.l('C00073[c]'):0:8;
PUT lambda.l('C00065[c]'):0:8;
PUT lambda.l('C00078[c]'):0:8;
PUT lambda.l('C00188[c]'):0:8;
PUT lambda.l('C00135[c]'):0:8;
PUT lambda.l('C00079[c]'):0:8;
PUT lambda.l('C00082[c]'):0:8;
PUT lambda.l('C00183[c]'):0:8;
PUT lambda.l('C00123[c]'):0:8;
PUT lambda.l('C00407[c]'):0:8;
PUT lambda.l('C00047[c]'):0:8;
PUT lambda.l('C00017[c]'):0:8;
PUT lambda.l('C00249[im]'):0:8;
PUT lambda.l('C01530[im]'):0:8;
PUT lambda.l('C06425[im]'):0:8;
PUT lambda.l('C00712[im]'):0:8;
PUT lambda.l('C01595[im]'):0:8;
PUT lambda.l('C01356[im]'):0:8;
PUT lambda.l('C00075[c]'):0:8;
PUT lambda.l('C00044[c]'):0:8;
PUT lambda.l('C00182[c]'):0:8;
PUT lambda.l('C00116[c]'):0:8;
PUT lambda.l('C00422[c]'):0:8;
PUT lambda.l('C00350[c]'):0:8;
PUT lambda.l('C02737[c]'):0:8;
PUT lambda.l('C00063[c]'):0:8;
PUT lambda.l('C01356[c]'):0:8;
PUT lambda.l('C00017[c]'):0:8;
PUT lambda.l('C00286[c]'):0:8;
PUT lambda.l('C00131[c]'):0:8;
PUT lambda.l('C00458[c]'):0:8;
PUT lambda.l('C00459[c]'):0:8;
PUT lambda.l('cell[c]'):0:8;
PUT lambda.l('C00965[e]'):0:8;
PUT lambda.l('C01356[e]'):0:8;
PUT lambda.l('C17937DHN[e]'):0:8;
PUT lambda.l('C17937Eu[e]'):0:8;
PUT lambda.l('C17937Pyo[e]'):0:8;
PUT lambda.l('C00017[e]'):0:8;
PUT lambda.l('C00140[e]'):0:8;
PUT lambda.l('C00461[e]'):0:8;
PUT lambda.l('cell_wall[e]'):0:8;
PUT lambda.l('C02094[c]'):0:8;
PUT lambda.l('C19892[c]'):0:8;
PUT lambda.l('C08607[c]'):0:8;
PUT lambda.l('C00097[c]'):0:8;
PUT lambda.l('carotenoids[c]'):0:8;
PUT lambda.l('biomass'):0:8/;
PUTCLOSE;
*update the trial counter
trial_count_temp = trial_count + 1;
trial_count = trial_count_temp;
**********************************************trial 4************************************************
* carbon limited, ethanol as only carbon source, LB(R009ex) = -1.5 *
*****************************************************************************************************
LBED('R001ex')=-Vmax; !!water
LBED('R002ex')=-Vmax; !!phosphate
LBED('R003ex')=0; !!sucrose
LBED('R004ex')=-Vmax; !!ammonia
LBED('R005ex')=-Vmax; !!sulfate
LBED('R006ex')=-Vmax; !!H+
LBED('R007ex')=0; !!Carbon dioxide
LBED('R008ex')=-Vmax; !!oxygen
LBED('R009ex')=-1.5; !!ethanol
LBED('R010ex')=0; !!acetate
LBED('R011ex')=0; !!glucose
LBED('R012ex')=0; !!urate
UBED('R001ex')=Vmax; !!water
UBED('R002ex')=0; !!phosphate
UBED('R003ex')=0; !!sucrose
UBED('R004ex')=0; !!ammonia
UBED('R005ex')=0; !!sulfate
UBED('R006ex')=Vmax; !!H+
UBED('R007ex')=Vmax; !!Carbon dioxide
UBED('R008ex')=0; !!oxygen
UBED('R009ex')=Vmax; !!ethanol
UBED('R010ex')=0; !!acetate
UBED('R011ex')=0; !!glucose
UBED('R012ex')=Vmax; !!glucose
vED.lo(jED)=LBED(jED);
vED.up(jED)=UBED(jED);
SOLVE STRONGED USING LP MAXIMIZING zprimal_ED;
RXNOUT.ap = 1;
PUT RXNOUT;
RXNOUT.pc = 5;
RXNOUT.lw = 25;
PUT trial_count;
LOOP(jED,
PUT vED.l(jED):0:8;
);
PUT /;
PUTCLOSE;
SHADOW.ap = 1;
PUT SHADOW;
SHADOW.pc = 5;
SHADOW.lw = 25;
SHADOW.pw = 30000;
*print the shadow price of just the pigments
PUT trial_count,"ECL";
PUT vED.l('biomass_wt_37'):0:8;
PUT lambda.l('X00001[c]'):0:8;
PUT lambda.l('C04033[c]'):0:8;
PUT lambda.l('C00779[c]'):0:8;
PUT lambda.l('C01173[c]'):0:8;
PUT lambda.l('C01624[c]'):0:8;
PUT lambda.l('C00083[c]'):0:8;
PUT lambda.l('C17937DHN[e]'):0:8;
PUT lambda.l('C05578[e]'):0:8;
PUT lambda.l('C05579[e]'):0:8;
PUT lambda.l('C01693[e]'):0:8;
PUT lambda.l('C05604[e]'):0:8;
PUT lambda.l('C00355[c]'):0:8;
PUT lambda.l('C00822[c]'):0:8;
PUT lambda.l('C00082[c]'):0:8;
PUT lambda.l('C17937Eu[e]'):0:8;
PUT lambda.l('C00544[c]'):0:8;
PUT lambda.l('X00002[c]'):0:8;
PUT lambda.l('C01179[c]'):0:8;
PUT lambda.l('C17937Pyo[e]'):0:8;
PUT lambda.l('C00353[c]'):0:8;
PUT lambda.l('C03427[c]'):0:8;
PUT lambda.l('C05421[c]'):0:8;
PUT lambda.l('C05414[c]'):0:8;
PUT lambda.l('C05430[c]'):0:8;