$offlisting

Parameters genestatus(genes),reactionstatus(j);
reactionstatus(j)=0;
genestatus(genes)=0;

loop(select_condition, genestatus(genes)=ExpressionData(genes,select_condition));


********************************************************************************
**********Change Reaction Status to 0 When Genes Needed Aren't Expressed********
********************************************************************************
reactionstatus('ICL')=genestatus('aceA');
reactionstatus('MALS')=genestatus('aceB');
reactionstatus('ACKr')=genestatus('ackA');
reactionstatus('ADHEr')=genestatus('adhE');
reactionstatus('ADK1')=genestatus('adk');
reactionstatus('FUMt2_2')=genestatus('dctA');
reactionstatus('SUCCt2_2')=genestatus('dctA');
reactionstatus('SUCCt2b')=genestatus('dcuC');
reactionstatus('ENO')=genestatus('eno');
reactionstatus('FBA')=genestatus('fba');
reactionstatus('FBP')=genestatus('fbp');
reactionstatus('FORt')=genestatus('focA');
reactionstatus('GAPD')=genestatus('gapA');
reactionstatus('CS')=genestatus('gltA');
reactionstatus('GND')=genestatus('gnd');
reactionstatus('ICDHyr')=genestatus('icdA');
reactionstatus('LDH_D')=genestatus('ldhA');
reactionstatus('ME2')=genestatus('maeB');
reactionstatus('MDH')=genestatus('mdh');
reactionstatus('PPCK')=genestatus('pckA');
reactionstatus('PGI')=genestatus('pgi');
reactionstatus('PGK')=genestatus('pgk');
reactionstatus('PGL')=genestatus('pgl');
reactionstatus('PGM')=genestatus('pgm');
reactionstatus('PPC')=genestatus('ppc');
reactionstatus('PPS')=genestatus('ppsA');
reactionstatus('PTAr')=genestatus('pta');
reactionstatus('RPE')=genestatus('rpe');
reactionstatus('RPI')=genestatus('rpi');
reactionstatus('ME1')=genestatus('sfcA');
reactionstatus('TALA')=genestatus('talA');
reactionstatus('TPI')=genestatus('tpi');
reactionstatus('G6PDH2r')=genestatus('zwf');

*These reactions have isozymes so if at least one is present the reaction can occur
reactionstatus('ACONT')=max(genestatus('acnA'),genestatus('acnB'));
reactionstatus('FUM')=max(genestatus('fumA'),genestatus('fumB'),genestatus('fumC'));
reactionstatus('PFK')=max(genestatus('pfkA'),genestatus('pfkB'));
reactionstatus('PFL')=max(min(genestatus('pflA'),genestatus('pflB')),min(genestatus('pflC'),genestatus('pflD')));
reactionstatus('PYK')=max(genestatus('pykA'),genestatus('pykF'));
reactionstatus('TKT1')=max(genestatus('tktA'),genestatus('tktB'));
reactionstatus('TKT2')=max(genestatus('tktA'),genestatus('tktB'));
reactionstatus('PIt')=max(genestatus('pitA'),genestatus('pitB'));

*These reactions are carried out by multiple gene products, all have to be expressed for the reaction to occur
reactionstatus('SUCOAS')=min(genestatus('sucC'),genestatus('sucD'));
reactionstatus('AKGDH')=min(genestatus('sucA'),genestatus('sucB'),genestatus('lpdA'));
reactionstatus('PDH')=min(genestatus('aceE'),genestatus('aceF'),genestatus('lpdA'));
reactionstatus('NADTRHD')=min(genestatus('pntA'),genestatus('pntB'));
reactionstatus('THD2')=min(genestatus('pntA'),genestatus('pntB'));
reactionstatus('SUCD1i')=min(genestatus('sdhA'),genestatus('sdhB'),genestatus('sdhC'),genestatus('sdhD'));
reactionstatus('SUCD4')=min(genestatus('sdhA'),genestatus('sdhB'),genestatus('sdhC'),genestatus('sdhD'));
reactionstatus('FRD')=min(genestatus('frdA'),genestatus('frdB'),genestatus('frdC'),genestatus('frdD'));
reactionstatus('NADH11')=min(genestatus('nuoA'),genestatus('nuoB'),genestatus('nuoE'),genestatus('nuoF'),genestatus('nuoG'),genestatus('nuoH'),genestatus('nuoI'),genestatus('nuoJ'),genestatus('nuoK'),genestatus('nuoL'),genestatus('nuoM'),genestatus('nuoN'));
reactionstatus('GLCpts')=min(genestatus('ptsG'),genestatus('ptsH'),genestatus('ptsI'),genestatus('crr'));
reactionstatus('ATPS4r')=min(genestatus('atpA'),genestatus('atpB'),genestatus('atpC'),genestatus('atpD'),genestatus('atpE'),genestatus('atpF'),genestatus('atpG'),genestatus('atpH'),genestatus('atpI'));
reactionstatus('CYTBD')=min(genestatus('cydA'),genestatus('cydB'));

*These reactions have no genes associated with them
set NoGPR(j) /EX_ac_e,EX_akg_e,EX_co2_e,EX_etoh_e,EX_for_e,EX_fum_e,EX_glc_e,EX_h_e,EX_h2o_e,EX_lac_D_e,EX_o2_e,EX_pi_e,EX_pyr_e,EX_succ_e
ACt2r,AKGt2r,ATPM,Biomass,CO2t,D_LACt2,ETOHt2r,H2Ot,O2t,PYRt2r/;
reactionstatus(NoGPR)=(high_cutoff+low_cutoff)/2;

sets Rhigh(j),Rmed(j),Rlow(j);
Rhigh(j)=no;Rmed(j)=no;Rlow(j)=no;
loop(j, if ( reactionstatus(j)>high_cutoff, 
		Rhigh(j)=yes;
            elseif (reactionstatus(j)<low_cutoff), 
		Rlow(j)=yes;
            else
		 Rmed(j)=yes; );
	);

display Rhigh, Rmed, Rlow;