begin name
bosdriesz1
end name

begin reactions
vAAsynt1 {1.0}$EXTERNAL = {1.0}aa1
vAAsynt10 {1.0}$EXTERNAL = {1.0}aa10
vAAsynt11 {1.0}$EXTERNAL = {1.0}aa11
vAAsynt12 {1.0}$EXTERNAL = {1.0}aa12
vAAsynt13 {1.0}$EXTERNAL = {1.0}aa13
vAAsynt14 {1.0}$EXTERNAL = {1.0}aa14
vAAsynt15 {1.0}$EXTERNAL = {1.0}aa15
vAAsynt16 {1.0}$EXTERNAL = {1.0}aa16
vAAsynt17 {1.0}$EXTERNAL = {1.0}aa17
vAAsynt18 {1.0}$EXTERNAL = {1.0}aa18
vAAsynt19 {1.0}$EXTERNAL = {1.0}aa19
vAAsynt2 {1.0}$EXTERNAL = {1.0}aa2
vAAsynt20 {1.0}$EXTERNAL = {1.0}aa20
vAAsynt3 {1.0}$EXTERNAL = {1.0}aa3
vAAsynt4 {1.0}$EXTERNAL = {1.0}aa4
vAAsynt5 {1.0}$EXTERNAL = {1.0}aa5
vAAsynt6 {1.0}$EXTERNAL = {1.0}aa6
vAAsynt7 {1.0}$EXTERNAL = {1.0}aa7
vAAsynt8 {1.0}$EXTERNAL = {1.0}aa8
vAAsynt9 {1.0}$EXTERNAL = {1.0}aa9
vRelA {1.0}$EXTERNAL = {1.0}ppGpp
vSpoT {1.0}ppGpp = {1.0}$EXTERNAL
vbiomass {0.05}taa1 + {0.05}taa10 + {0.05}taa11 + {0.05}taa12 + {0.05}taa13 + {0.05}taa14 + {0.05}taa15 + {0.05}taa16 + {0.05}taa17 + {0.05}taa18 + {0.05}taa19 + {0.05}taa2 + {0.05}taa20 + {0.05}taa3 + {0.05}taa4 + {0.05}taa5 + {0.05}taa6 + {0.05}taa7 + {0.05}taa8 + {0.05}taa9 = {1.0}$EXTERNAL
vrdilution {1.0}r = {1.0}$EXTERNAL
vrsynt {1.0}$EXTERNAL = {1.0}r
vtRNAchar1 {1.0}aa1 = {1.0}taa1
vtRNAchar10 {1.0}aa10 = {1.0}taa10
vtRNAchar11 {1.0}aa11 = {1.0}taa11
vtRNAchar12 {1.0}aa12 = {1.0}taa12
vtRNAchar13 {1.0}aa13 = {1.0}taa13
vtRNAchar14 {1.0}aa14 = {1.0}taa14
vtRNAchar15 {1.0}aa15 = {1.0}taa15
vtRNAchar16 {1.0}aa16 = {1.0}taa16
vtRNAchar17 {1.0}aa17 = {1.0}taa17
vtRNAchar18 {1.0}aa18 = {1.0}taa18
vtRNAchar19 {1.0}aa19 = {1.0}taa19
vtRNAchar2 {1.0}aa2 = {1.0}taa2
vtRNAchar20 {1.0}aa20 = {1.0}taa20
vtRNAchar3 {1.0}aa3 = {1.0}taa3
vtRNAchar4 {1.0}aa4 = {1.0}taa4
vtRNAchar5 {1.0}aa5 = {1.0}taa5
vtRNAchar6 {1.0}aa6 = {1.0}taa6
vtRNAchar7 {1.0}aa7 = {1.0}taa7
vtRNAchar8 {1.0}aa8 = {1.0}taa8
vtRNAchar9 {1.0}aa9 = {1.0}taa9
end reactions

begin rate equations
vAAsynt1 = (bm*e1*kn1*step*(1 - r[t]/rmax))/(nAmet*(1 + aa1[t]/kIa1))
vAAsynt10 = (bm*e10*kn10*step*(1 - r[t]/rmax))/(nAmet*(1 + aa10[t]/kIa10))
vAAsynt11 = (bm*e11*kn11*step*(1 - r[t]/rmax))/(nAmet*(1 + aa11[t]/kIa11))
vAAsynt12 = (bm*e12*kn12*step*(1 - r[t]/rmax))/(nAmet*(1 + aa12[t]/kIa12))
vAAsynt13 = (bm*e13*kn13*step*(1 - r[t]/rmax))/(nAmet*(1 + aa13[t]/kIa13))
vAAsynt14 = (bm*e14*kn14*step*(1 - r[t]/rmax))/(nAmet*(1 + aa14[t]/kIa14))
vAAsynt15 = (bm*e15*kn15*step*(1 - r[t]/rmax))/(nAmet*(1 + aa15[t]/kIa15))
vAAsynt16 = (bm*e16*kn16*step*(1 - r[t]/rmax))/(nAmet*(1 + aa16[t]/kIa16))
vAAsynt17 = (bm*e17*kn17*step*(1 - r[t]/rmax))/(nAmet*(1 + aa17[t]/kIa17))
vAAsynt18 = (bm*e18*kn18*step*(1 - r[t]/rmax))/(nAmet*(1 + aa18[t]/kIa18))
vAAsynt19 = (bm*e19*kn19*step*(1 - r[t]/rmax))/(nAmet*(1 + aa19[t]/kIa19))
vAAsynt2 = (bm*e2*kn2*step*(1 - r[t]/rmax))/(nAmet*(1 + aa2[t]/kIa2))
vAAsynt20 = (bm*e20*kn20*step*(1 - r[t]/rmax))/(nAmet*(1 + aa20[t]/kIa20))
vAAsynt3 = (bm*e3*kn3*step*(1 - r[t]/rmax))/(nAmet*(1 + aa3[t]/kIa3))
vAAsynt4 = (bm*e4*kn4*step*(1 - r[t]/rmax))/(nAmet*(1 + aa4[t]/kIa4))
vAAsynt5 = (bm*e5*kn5*step*(1 - r[t]/rmax))/(nAmet*(1 + aa5[t]/kIa5))
vAAsynt6 = (bm*e6*kn6*step*(1 - r[t]/rmax))/(nAmet*(1 + aa6[t]/kIa6))
vAAsynt7 = (bm*e7*kn7*step*(1 - r[t]/rmax))/(nAmet*(1 + aa7[t]/kIa7))
vAAsynt8 = (bm*e8*kn8*step*(1 - r[t]/rmax))/(nAmet*(1 + aa8[t]/kIa8))
vAAsynt9 = (bm*e9*kn9*step*(1 - r[t]/rmax))/(nAmet*(1 + aa9[t]/kIa9))
vRelA = vSpoTSynt + (kRelA*RelAtot)/(1 + (kDRelA*(0.05*kapparta*(kappart + tau1*r[t] - taa1[t])*taa10[t]*taa11[t]*taa12[t]*taa13[t]*taa14[t]*taa15[t]*taa16[t]*taa17[t]*taa18[t]*taa19[t]*taa2[t]*taa20[t]*taa3[t]*taa4[t]*taa5[t]*taa6[t]*taa7[t]*taa8[t]*taa9[t] + taa1[t]*(0.05*kapparta*(kappart + tau10*r[t] - taa10[t])*taa11[t]*taa12[t]*taa13[t]*taa14[t]*taa15[t]*taa16[t]*taa17[t]*taa18[t]*taa19[t]*taa2[t]*taa20[t]*taa3[t]*taa4[t]*taa5[t]*taa6[t]*taa7[t]*taa8[t]*taa9[t] + taa10[t]*(0.05*kapparta*(kappart + tau11*r[t] - taa11[t])*taa12[t]*taa13[t]*taa14[t]*taa15[t]*taa16[t]*taa17[t]*taa18[t]*taa19[t]*taa2[t]*taa20[t]*taa3[t]*taa4[t]*taa5[t]*taa6[t]*taa7[t]*taa8[t]*taa9[t] + taa11[t]*(0.05*kapparta*(kappart + tau12*r[t] - taa12[t])*taa13[t]*taa14[t]*taa15[t]*taa16[t]*taa17[t]*taa18[t]*taa19[t]*taa2[t]*taa20[t]*taa3[t]*taa4[t]*taa5[t]*taa6[t]*taa7[t]*taa8[t]*taa9[t] + taa12[t]*(0.05*kapparta*(kappart + tau13*r[t] - taa13[t])*taa14[t]*taa15[t]*taa16[t]*taa17[t]*taa18[t]*taa19[t]*taa2[t]*taa20[t]*taa3[t]*taa4[t]*taa5[t]*taa6[t]*taa7[t]*taa8[t]*taa9[t] + taa13[t]*(0.05*kapparta*(kappart + tau14*r[t] - taa14[t])*taa15[t]*taa16[t]*taa17[t]*taa18[t]*taa19[t]*taa2[t]*taa20[t]*taa3[t]*taa4[t]*taa5[t]*taa6[t]*taa7[t]*taa8[t]*taa9[t] + taa14[t]*(0.05*kapparta*(kappart + tau15*r[t] - taa15[t])*taa16[t]*taa17[t]*taa18[t]*taa19[t]*taa2[t]*taa20[t]*taa3[t]*taa4[t]*taa5[t]*taa6[t]*taa7[t]*taa8[t]*taa9[t] + taa15[t]*(0.05*kapparta*(kappart + tau16*r[t] - taa16[t])*taa17[t]*taa18[t]*taa19[t]*taa2[t]*taa20[t]*taa3[t]*taa4[t]*taa5[t]*taa6[t]*taa7[t]*taa8[t]*taa9[t] + taa16[t]*(0.05*kapparta*(kappart + tau17*r[t] - taa17[t])*taa18[t]*taa19[t]*taa2[t]*taa20[t]*taa3[t]*taa4[t]*taa5[t]*taa6[t]*taa7[t]*taa8[t]*taa9[t] + taa17[t]*(0.05*kapparta*(kappart + tau18*r[t] - taa18[t])*taa19[t]*taa2[t]*taa20[t]*taa3[t]*taa4[t]*taa5[t]*taa6[t]*taa7[t]*taa8[t]*taa9[t] + taa18[t]*(0.05*kapparta*(kappart + tau19*r[t] - taa19[t])*taa2[t]*taa20[t]*taa3[t]*taa4[t]*taa5[t]*taa6[t]*taa7[t]*taa8[t]*taa9[t] + taa19[t]*(0.05*kapparta*(kappart + tau2*r[t] - taa2[t])*taa20[t]*taa3[t]*taa4[t]*taa5[t]*taa6[t]*taa7[t]*taa8[t]*taa9[t] + taa2[t]*(0.05*kapparta*(kappart + tau20*r[t] - taa20[t])*taa3[t]*taa4[t]*taa5[t]*taa6[t]*taa7[t]*taa8[t]*taa9[t] + taa20[t]*(0.05*kapparta*(kappart + tau3*r[t] - taa3[t])*taa4[t]*taa5[t]*taa6[t]*taa7[t]*taa8[t]*taa9[t] + taa3[t]*(0.05*kapparta*(kappart + tau4*r[t] - taa4[t])*taa5[t]*taa6[t]*taa7[t]*taa8[t]*taa9[t] + taa4[t]*(0.05*kapparta*(kappart + tau5*r[t] - taa5[t])*taa6[t]*taa7[t]*taa8[t]*taa9[t] + taa5[t]*(0.05*kapparta*(kappart + tau6*r[t] - taa6[t])*taa7[t]*taa8[t]*taa9[t] + taa6[t]*(0.05*kapparta*(kappart + tau7*r[t] - taa7[t])*taa8[t]*taa9[t] + taa7[t]*(0.05*kapparta*(kappart + tau8*r[t] - taa8[t])*taa9[t] + taa8[t]*(0.05*kapparta*(kappart + tau9*r[t] - taa9[t]) + kappart*taa9[t])))))))))))))))))))))/(kapparta*r[t]*(0.05*(tau1*r[t] - taa1[t])*taa10[t]*taa11[t]*taa12[t]*taa13[t]*taa14[t]*taa15[t]*taa16[t]*taa17[t]*taa18[t]*taa19[t]*taa2[t]*taa20[t]*taa3[t]*taa4[t]*taa5[t]*taa6[t]*taa7[t]*taa8[t]*taa9[t] + taa1[t]*(0.05*(tau10*r[t] - taa10[t])*taa11[t]*taa12[t]*taa13[t]*taa14[t]*taa15[t]*taa16[t]*taa17[t]*taa18[t]*taa19[t]*taa2[t]*taa20[t]*taa3[t]*taa4[t]*taa5[t]*taa6[t]*taa7[t]*taa8[t]*taa9[t] + taa10[t]*(0.05*(tau11*r[t] - taa11[t])*taa12[t]*taa13[t]*taa14[t]*taa15[t]*taa16[t]*taa17[t]*taa18[t]*taa19[t]*taa2[t]*taa20[t]*taa3[t]*taa4[t]*taa5[t]*taa6[t]*taa7[t]*taa8[t]*taa9[t] + taa11[t]*(0.05*(tau12*r[t] - taa12[t])*taa13[t]*taa14[t]*taa15[t]*taa16[t]*taa17[t]*taa18[t]*taa19[t]*taa2[t]*taa20[t]*taa3[t]*taa4[t]*taa5[t]*taa6[t]*taa7[t]*taa8[t]*taa9[t] + taa12[t]*(0.05*(tau13*r[t] - taa13[t])*taa14[t]*taa15[t]*taa16[t]*taa17[t]*taa18[t]*taa19[t]*taa2[t]*taa20[t]*taa3[t]*taa4[t]*taa5[t]*taa6[t]*taa7[t]*taa8[t]*taa9[t] + taa13[t]*(0.05*(tau14*r[t] - taa14[t])*taa15[t]*taa16[t]*taa17[t]*taa18[t]*taa19[t]*taa2[t]*taa20[t]*taa3[t]*taa4[t]*taa5[t]*taa6[t]*taa7[t]*taa8[t]*taa9[t] + taa14[t]*(0.05*(tau15*r[t] - taa15[t])*taa16[t]*taa17[t]*taa18[t]*taa19[t]*taa2[t]*taa20[t]*taa3[t]*taa4[t]*taa5[t]*taa6[t]*taa7[t]*taa8[t]*taa9[t] + taa15[t]*(0.05*(tau16*r[t] - taa16[t])*taa17[t]*taa18[t]*taa19[t]*taa2[t]*taa20[t]*taa3[t]*taa4[t]*taa5[t]*taa6[t]*taa7[t]*taa8[t]*taa9[t] + taa16[t]*(0.05*(tau17*r[t] - taa17[t])*taa18[t]*taa19[t]*taa2[t]*taa20[t]*taa3[t]*taa4[t]*taa5[t]*taa6[t]*taa7[t]*taa8[t]*taa9[t] + taa17[t]*(0.05*(tau18*r[t] - taa18[t])*taa19[t]*taa2[t]*taa20[t]*taa3[t]*taa4[t]*taa5[t]*taa6[t]*taa7[t]*taa8[t]*taa9[t] + taa18[t]*(0.05*(tau19*r[t] - taa19[t])*taa2[t]*taa20[t]*taa3[t]*taa4[t]*taa5[t]*taa6[t]*taa7[t]*taa8[t]*taa9[t] + taa19[t]*(0.05*(tau2*r[t] - taa2[t])*taa20[t]*taa3[t]*taa4[t]*taa5[t]*taa6[t]*taa7[t]*taa8[t]*taa9[t] + taa2[t]*(0.05*(tau20*r[t] - taa20[t])*taa3[t]*taa4[t]*taa5[t]*taa6[t]*taa7[t]*taa8[t]*taa9[t] + taa20[t]*(0.05*(tau3*r[t] - taa3[t])*taa4[t]*taa5[t]*taa6[t]*taa7[t]*taa8[t]*taa9[t] + taa3[t]*(0.05*(tau4*r[t] - taa4[t])*taa5[t]*taa6[t]*taa7[t]*taa8[t]*taa9[t] + taa4[t]*(0.05*(tau5*r[t] - taa5[t])*taa6[t]*taa7[t]*taa8[t]*taa9[t] + taa5[t]*(0.05*(tau6*r[t] - taa6[t])*taa7[t]*taa8[t]*taa9[t] + taa6[t]*(0.05*taa7[t]*taa8[t]*(tau9*r[t] - taa9[t]) + 0.05*taa7[t]*(tau8*r[t] - taa8[t])*taa9[t] + 0.05*(tau7*r[t] - taa7[t])*taa8[t]*taa9[t]))))))))))))))))))))
vSpoT = kSpoTdeg*ppGpp[t]
vbiomass = (krib*r[t])/(1 + (0.05*kapparta*(kappart + tau1*r[t] - taa1[t]))/(kappart*taa1[t]) + (0.05*kapparta*(kappart + tau10*r[t] - taa10[t]))/(kappart*taa10[t]) + (0.05*kapparta)/taa11[t] + (0.05*kapparta*(tau11*r[t] - taa11[t]))/(kappart*taa11[t]) + (0.05*kapparta)/taa12[t] + (0.05*kapparta*(tau12*r[t] - taa12[t]))/(kappart*taa12[t]) + (0.05*kapparta)/taa13[t] + (0.05*kapparta*(tau13*r[t] - taa13[t]))/(kappart*taa13[t]) + (0.05*kapparta)/taa14[t] + (0.05*kapparta*(tau14*r[t] - taa14[t]))/(kappart*taa14[t]) + (0.05*kapparta)/taa15[t] + (0.05*kapparta*(tau15*r[t] - taa15[t]))/(kappart*taa15[t]) + (0.05*kapparta)/taa16[t] + (0.05*kapparta*(tau16*r[t] - taa16[t]))/(kappart*taa16[t]) + (0.05*kapparta)/taa17[t] + (0.05*kapparta*(tau17*r[t] - taa17[t]))/(kappart*taa17[t]) + (0.05*kapparta)/taa18[t] + (0.05*kapparta*(tau18*r[t] - taa18[t]))/(kappart*taa18[t]) + (0.05*kapparta)/taa19[t] + (0.05*kapparta*(tau19*r[t] - taa19[t]))/(kappart*taa19[t]) + (0.05*kapparta)/taa2[t] + (0.05*kapparta*(tau2*r[t] - taa2[t]))/(kappart*taa2[t]) + (0.05*kapparta)/taa20[t] + (0.05*kapparta*(tau20*r[t] - taa20[t]))/(kappart*taa20[t]) + (0.05*kapparta)/taa3[t] + (0.05*kapparta*(tau3*r[t] - taa3[t]))/(kappart*taa3[t]) + (0.05*kapparta)/taa4[t] + (0.05*kapparta*(tau4*r[t] - taa4[t]))/(kappart*taa4[t]) + (0.05*kapparta)/taa5[t] + (0.05*kapparta*(tau5*r[t] - taa5[t]))/(kappart*taa5[t]) + (0.05*kapparta)/taa6[t] + (0.05*kapparta*(tau6*r[t] - taa6[t]))/(kappart*taa6[t]) + (0.05*kapparta)/taa7[t] + (0.05*kapparta*(tau7*r[t] - taa7[t]))/(kappart*taa7[t]) + (0.05*kapparta)/taa8[t] + (0.05*kapparta*(tau8*r[t] - taa8[t]))/(kappart*taa8[t]) + (0.05*kapparta)/taa9[t] + (0.05*kapparta*(tau9*r[t] - taa9[t]))/(kappart*taa9[t]))
vrdilution = (krib*r[t]^2)/(bm*(1 + (0.05*kapparta*(kappart + tau1*r[t] - taa1[t]))/(kappart*taa1[t]) + (0.05*kapparta*(kappart + tau10*r[t] - taa10[t]))/(kappart*taa10[t]) + (0.05*kapparta)/taa11[t] + (0.05*kapparta*(tau11*r[t] - taa11[t]))/(kappart*taa11[t]) + (0.05*kapparta)/taa12[t] + (0.05*kapparta*(tau12*r[t] - taa12[t]))/(kappart*taa12[t]) + (0.05*kapparta)/taa13[t] + (0.05*kapparta*(tau13*r[t] - taa13[t]))/(kappart*taa13[t]) + (0.05*kapparta)/taa14[t] + (0.05*kapparta*(tau14*r[t] - taa14[t]))/(kappart*taa14[t]) + (0.05*kapparta)/taa15[t] + (0.05*kapparta*(tau15*r[t] - taa15[t]))/(kappart*taa15[t]) + (0.05*kapparta)/taa16[t] + (0.05*kapparta*(tau16*r[t] - taa16[t]))/(kappart*taa16[t]) + (0.05*kapparta)/taa17[t] + (0.05*kapparta*(tau17*r[t] - taa17[t]))/(kappart*taa17[t]) + (0.05*kapparta)/taa18[t] + (0.05*kapparta*(tau18*r[t] - taa18[t]))/(kappart*taa18[t]) + (0.05*kapparta)/taa19[t] + (0.05*kapparta*(tau19*r[t] - taa19[t]))/(kappart*taa19[t]) + (0.05*kapparta)/taa2[t] + (0.05*kapparta*(tau2*r[t] - taa2[t]))/(kappart*taa2[t]) + (0.05*kapparta)/taa20[t] + (0.05*kapparta*(tau20*r[t] - taa20[t]))/(kappart*taa20[t]) + (0.05*kapparta)/taa3[t] + (0.05*kapparta*(tau3*r[t] - taa3[t]))/(kappart*taa3[t]) + (0.05*kapparta)/taa4[t] + (0.05*kapparta*(tau4*r[t] - taa4[t]))/(kappart*taa4[t]) + (0.05*kapparta)/taa5[t] + (0.05*kapparta*(tau5*r[t] - taa5[t]))/(kappart*taa5[t]) + (0.05*kapparta)/taa6[t] + (0.05*kapparta*(tau6*r[t] - taa6[t]))/(kappart*taa6[t]) + (0.05*kapparta)/taa7[t] + (0.05*kapparta*(tau7*r[t] - taa7[t]))/(kappart*taa7[t]) + (0.05*kapparta)/taa8[t] + (0.05*kapparta*(tau8*r[t] - taa8[t]))/(kappart*taa8[t]) + (0.05*kapparta)/taa9[t] + (0.05*kapparta*(tau9*r[t] - taa9[t]))/(kappart*taa9[t])))
vrsynt = min[(0.000666666666666667*rnapF*vInitMax)/((kMrrn + rnapF)*(1 + (ppGpp[t]/kIppGpp)^nppGpp)), (gammamax*krib*r[t])/(nARib*(1 + (0.05*kapparta*(kappart + tau1*r[t] - taa1[t]))/(kappart*taa1[t]) + (0.05*kapparta*(kappart + tau10*r[t] - taa10[t]))/(kappart*taa10[t]) + (0.05*kapparta)/taa11[t] + (0.05*kapparta*(tau11*r[t] - taa11[t]))/(kappart*taa11[t]) + (0.05*kapparta)/taa12[t] + (0.05*kapparta*(tau12*r[t] - taa12[t]))/(kappart*taa12[t]) + (0.05*kapparta)/taa13[t] + (0.05*kapparta*(tau13*r[t] - taa13[t]))/(kappart*taa13[t]) + (0.05*kapparta)/taa14[t] + (0.05*kapparta*(tau14*r[t] - taa14[t]))/(kappart*taa14[t]) + (0.05*kapparta)/taa15[t] + (0.05*kapparta*(tau15*r[t] - taa15[t]))/(kappart*taa15[t]) + (0.05*kapparta)/taa16[t] + (0.05*kapparta*(tau16*r[t] - taa16[t]))/(kappart*taa16[t]) + (0.05*kapparta)/taa17[t] + (0.05*kapparta*(tau17*r[t] - taa17[t]))/(kappart*taa17[t]) + (0.05*kapparta)/taa18[t] + (0.05*kapparta*(tau18*r[t] - taa18[t]))/(kappart*taa18[t]) + (0.05*kapparta)/taa19[t] + (0.05*kapparta*(tau19*r[t] - taa19[t]))/(kappart*taa19[t]) + (0.05*kapparta)/taa2[t] + (0.05*kapparta*(tau2*r[t] - taa2[t]))/(kappart*taa2[t]) + (0.05*kapparta)/taa20[t] + (0.05*kapparta*(tau20*r[t] - taa20[t]))/(kappart*taa20[t]) + (0.05*kapparta)/taa3[t] + (0.05*kapparta*(tau3*r[t] - taa3[t]))/(kappart*taa3[t]) + (0.05*kapparta)/taa4[t] + (0.05*kapparta*(tau4*r[t] - taa4[t]))/(kappart*taa4[t]) + (0.05*kapparta)/taa5[t] + (0.05*kapparta*(tau5*r[t] - taa5[t]))/(kappart*taa5[t]) + (0.05*kapparta)/taa6[t] + (0.05*kapparta*(tau6*r[t] - taa6[t]))/(kappart*taa6[t]) + (0.05*kapparta)/taa7[t] + (0.05*kapparta*(tau7*r[t] - taa7[t]))/(kappart*taa7[t]) + (0.05*kapparta)/taa8[t] + (0.05*kapparta*(tau8*r[t] - taa8[t]))/(kappart*taa8[t]) + (0.05*kapparta)/taa9[t] + (0.05*kapparta*(tau9*r[t] - taa9[t]))/(kappart*taa9[t])))]
vtRNAchar1 = (ks1*sTot1*aa1[t]*(tau1*r[t] - taa1[t]))/(kMaa1*kMtf1*(aa1[t]/kMaa1 + (tau1*r[t] - taa1[t])/kMtf1 + (aa1[t]*(tau1*r[t] - taa1[t]))/(kMaa1*kMtf1)))
vtRNAchar10 = (ks10*sTot10*aa10[t]*(tau10*r[t] - taa10[t]))/(kMaa10*kMtf10*(aa10[t]/kMaa10 + (tau10*r[t] - taa10[t])/kMtf10 + (aa10[t]*(tau10*r[t] - taa10[t]))/(kMaa10*kMtf10)))
vtRNAchar11 = (ks11*sTot11*aa11[t]*(tau11*r[t] - taa11[t]))/(kMaa11*kMtf11*(aa11[t]/kMaa11 + (tau11*r[t] - taa11[t])/kMtf11 + (aa11[t]*(tau11*r[t] - taa11[t]))/(kMaa11*kMtf11)))
vtRNAchar12 = (ks12*sTot12*aa12[t]*(tau12*r[t] - taa12[t]))/(kMaa12*kMtf12*(aa12[t]/kMaa12 + (tau12*r[t] - taa12[t])/kMtf12 + (aa12[t]*(tau12*r[t] - taa12[t]))/(kMaa12*kMtf12)))
vtRNAchar13 = (ks13*sTot13*aa13[t]*(tau13*r[t] - taa13[t]))/(kMaa13*kMtf13*(aa13[t]/kMaa13 + (tau13*r[t] - taa13[t])/kMtf13 + (aa13[t]*(tau13*r[t] - taa13[t]))/(kMaa13*kMtf13)))
vtRNAchar14 = (ks14*sTot14*aa14[t]*(tau14*r[t] - taa14[t]))/(kMaa14*kMtf14*(aa14[t]/kMaa14 + (tau14*r[t] - taa14[t])/kMtf14 + (aa14[t]*(tau14*r[t] - taa14[t]))/(kMaa14*kMtf14)))
vtRNAchar15 = (ks15*sTot15*aa15[t]*(tau15*r[t] - taa15[t]))/(kMaa15*kMtf15*(aa15[t]/kMaa15 + (tau15*r[t] - taa15[t])/kMtf15 + (aa15[t]*(tau15*r[t] - taa15[t]))/(kMaa15*kMtf15)))
vtRNAchar16 = (ks16*sTot16*aa16[t]*(tau16*r[t] - taa16[t]))/(kMaa16*kMtf16*(aa16[t]/kMaa16 + (tau16*r[t] - taa16[t])/kMtf16 + (aa16[t]*(tau16*r[t] - taa16[t]))/(kMaa16*kMtf16)))
vtRNAchar17 = (ks17*sTot17*aa17[t]*(tau17*r[t] - taa17[t]))/(kMaa17*kMtf17*(aa17[t]/kMaa17 + (tau17*r[t] - taa17[t])/kMtf17 + (aa17[t]*(tau17*r[t] - taa17[t]))/(kMaa17*kMtf17)))
vtRNAchar18 = (ks18*sTot18*aa18[t]*(tau18*r[t] - taa18[t]))/(kMaa18*kMtf18*(aa18[t]/kMaa18 + (tau18*r[t] - taa18[t])/kMtf18 + (aa18[t]*(tau18*r[t] - taa18[t]))/(kMaa18*kMtf18)))
vtRNAchar19 = (ks19*sTot19*aa19[t]*(tau19*r[t] - taa19[t]))/(kMaa19*kMtf19*(aa19[t]/kMaa19 + (tau19*r[t] - taa19[t])/kMtf19 + (aa19[t]*(tau19*r[t] - taa19[t]))/(kMaa19*kMtf19)))
vtRNAchar2 = (ks2*sTot2*aa2[t]*(tau2*r[t] - taa2[t]))/(kMaa2*kMtf2*(aa2[t]/kMaa2 + (tau2*r[t] - taa2[t])/kMtf2 + (aa2[t]*(tau2*r[t] - taa2[t]))/(kMaa2*kMtf2)))
vtRNAchar20 = (ks20*sTot20*aa20[t]*(tau20*r[t] - taa20[t]))/(kMaa20*kMtf20*(aa20[t]/kMaa20 + (tau20*r[t] - taa20[t])/kMtf20 + (aa20[t]*(tau20*r[t] - taa20[t]))/(kMaa20*kMtf20)))
vtRNAchar3 = (ks3*sTot3*aa3[t]*(tau3*r[t] - taa3[t]))/(kMaa3*kMtf3*(aa3[t]/kMaa3 + (tau3*r[t] - taa3[t])/kMtf3 + (aa3[t]*(tau3*r[t] - taa3[t]))/(kMaa3*kMtf3)))
vtRNAchar4 = (ks4*sTot4*aa4[t]*(tau4*r[t] - taa4[t]))/(kMaa4*kMtf4*(aa4[t]/kMaa4 + (tau4*r[t] - taa4[t])/kMtf4 + (aa4[t]*(tau4*r[t] - taa4[t]))/(kMaa4*kMtf4)))
vtRNAchar5 = (ks5*sTot5*aa5[t]*(tau5*r[t] - taa5[t]))/(kMaa5*kMtf5*(aa5[t]/kMaa5 + (tau5*r[t] - taa5[t])/kMtf5 + (aa5[t]*(tau5*r[t] - taa5[t]))/(kMaa5*kMtf5)))
vtRNAchar6 = (ks6*sTot6*aa6[t]*(tau6*r[t] - taa6[t]))/(kMaa6*kMtf6*(aa6[t]/kMaa6 + (tau6*r[t] - taa6[t])/kMtf6 + (aa6[t]*(tau6*r[t] - taa6[t]))/(kMaa6*kMtf6)))
vtRNAchar7 = (ks7*sTot7*aa7[t]*(tau7*r[t] - taa7[t]))/(kMaa7*kMtf7*(aa7[t]/kMaa7 + (tau7*r[t] - taa7[t])/kMtf7 + (aa7[t]*(tau7*r[t] - taa7[t]))/(kMaa7*kMtf7)))
vtRNAchar8 = (ks8*sTot8*aa8[t]*(tau8*r[t] - taa8[t]))/(kMaa8*kMtf8*(aa8[t]/kMaa8 + (tau8*r[t] - taa8[t])/kMtf8 + (aa8[t]*(tau8*r[t] - taa8[t]))/(kMaa8*kMtf8)))
vtRNAchar9 = (ks9*sTot9*aa9[t]*(tau9*r[t] - taa9[t]))/(kMaa9*kMtf9*(aa9[t]/kMaa9 + (tau9*r[t] - taa9[t])/kMtf9 + (aa9[t]*(tau9*r[t] - taa9[t]))/(kMaa9*kMtf9)))
end rate equations

begin parameters
EXTERNAL = 1.0
RelAtot = 0.0666666666667
bm = 1000000.0
e1 = 0.05
e10 = 0.05
e11 = 0.05
e12 = 0.05
e13 = 0.05
e14 = 0.05
e15 = 0.05
e16 = 0.05
e17 = 0.05
e18 = 0.05
e19 = 0.05
e2 = 0.05
e20 = 0.05
e3 = 0.05
e4 = 0.05
e5 = 0.05
e6 = 0.05
e7 = 0.05
e8 = 0.05
e9 = 0.05
gammamax = 1.0
kDRelA = 0.26
kIa1 = 100.0
kIa10 = 100.0
kIa11 = 100.0
kIa12 = 100.0
kIa13 = 100.0
kIa14 = 100.0
kIa15 = 100.0
kIa16 = 100.0
kIa17 = 100.0
kIa18 = 100.0
kIa19 = 100.0
kIa2 = 100.0
kIa20 = 100.0
kIa3 = 100.0
kIa4 = 100.0
kIa5 = 100.0
kIa6 = 100.0
kIa7 = 100.0
kIa8 = 100.0
kIa9 = 100.0
kIppGpp = 1.0
kMaa1 = 100.0
kMaa10 = 100.0
kMaa11 = 100.0
kMaa12 = 100.0
kMaa13 = 100.0
kMaa14 = 100.0
kMaa15 = 100.0
kMaa16 = 100.0
kMaa17 = 100.0
kMaa18 = 100.0
kMaa19 = 100.0
kMaa2 = 100.0
kMaa20 = 100.0
kMaa3 = 100.0
kMaa4 = 100.0
kMaa5 = 100.0
kMaa6 = 100.0
kMaa7 = 100.0
kMaa8 = 100.0
kMaa9 = 100.0
kMrrn = 20.0
kMtf1 = 1.0
kMtf10 = 1.0
kMtf11 = 1.0
kMtf12 = 1.0
kMtf13 = 1.0
kMtf14 = 1.0
kMtf15 = 1.0
kMtf16 = 1.0
kMtf17 = 1.0
kMtf18 = 1.0
kMtf19 = 1.0
kMtf2 = 1.0
kMtf20 = 1.0
kMtf3 = 1.0
kMtf4 = 1.0
kMtf5 = 1.0
kMtf6 = 1.0
kMtf7 = 1.0
kMtf8 = 1.0
kMtf9 = 1.0
kRelA = 75.0
kSpoTdeg = 0.0231049060187
kappart = 500.0
kapparta = 1.0
kn1 = 0.176694097633
kn10 = 0.175155965973
kn11 = 0.218930812944
kn12 = 0.189250477437
kn13 = 0.182501157889
kn14 = 0.168797176257
kn15 = 0.17817281343
kn16 = 0.163557478413
kn17 = 0.240562151147
kn18 = 0.234708428287
kn19 = 0.23885732482
kn2 = 0.170472469931
kn20 = 0.192552580536
kn3 = 0.21501492449
kn4 = 0.160529780205
kn5 = 0.154007815603
kn6 = 0.232252087628
kn7 = 0.188971693283
kn8 = 0.202409099613
kn9 = 0.221447303291
krib = 20.0
ks1 = 100.0
ks10 = 100.0
ks11 = 100.0
ks12 = 100.0
ks13 = 100.0
ks14 = 100.0
ks15 = 100.0
ks16 = 100.0
ks17 = 100.0
ks18 = 100.0
ks19 = 100.0
ks2 = 100.0
ks20 = 100.0
ks3 = 100.0
ks4 = 100.0
ks5 = 100.0
ks6 = 100.0
ks7 = 100.0
ks8 = 100.0
ks9 = 100.0
nARib = 12307.35
nAmet = 300.0
nRRNRib = 4567.0
nppGpp = 1.0
rmax = 81.2522598285
rnapF = 1.0
sTot1 = 1.0
sTot10 = 1.0
sTot11 = 1.0
sTot12 = 1.0
sTot13 = 1.0
sTot14 = 1.0
sTot15 = 1.0
sTot16 = 1.0
sTot17 = 1.0
sTot18 = 1.0
sTot19 = 1.0
sTot2 = 1.0
sTot20 = 1.0
sTot3 = 1.0
sTot4 = 1.0
sTot5 = 1.0
sTot6 = 1.0
sTot7 = 1.0
sTot8 = 1.0
sTot9 = 1.0
step = 1.375
tau1 = 0.5
tau10 = 0.5
tau11 = 0.5
tau12 = 0.5
tau13 = 0.5
tau14 = 0.5
tau15 = 0.5
tau16 = 0.5
tau17 = 0.5
tau18 = 0.5
tau19 = 0.5
tau2 = 0.5
tau20 = 0.5
tau3 = 0.5
tau4 = 0.5
tau5 = 0.5
tau6 = 0.5
tau7 = 0.5
tau8 = 0.5
tau9 = 0.5
vInitMax = 2000.0
vSpoTSynt = 0.001
default = 1.0
end parameters

begin initial conditions
aa1[0] = aa1i
aa10[0] = aa10i
aa11[0] = aa11i
aa12[0] = aa12i
aa13[0] = aa13i
aa14[0] = aa14i
aa15[0] = aa15i
aa16[0] = aa16i
aa17[0] = aa17i
aa18[0] = aa18i
aa19[0] = aa19i
aa2[0] = aa2i
aa20[0] = aa20i
aa3[0] = aa3i
aa4[0] = aa4i
aa5[0] = aa5i
aa6[0] = aa6i
aa7[0] = aa7i
aa8[0] = aa8i
aa9[0] = aa9i
ppGpp[0] = ppGppi
r[0] = ri
taa1[0] = taa1i
taa10[0] = taa10i
taa11[0] = taa11i
taa12[0] = taa12i
taa13[0] = taa13i
taa14[0] = taa14i
taa15[0] = taa15i
taa16[0] = taa16i
taa17[0] = taa17i
taa18[0] = taa18i
taa19[0] = taa19i
taa2[0] = taa2i
taa20[0] = taa20i
taa3[0] = taa3i
taa4[0] = taa4i
taa5[0] = taa5i
taa6[0] = taa6i
taa7[0] = taa7i
taa8[0] = taa8i
taa9[0] = taa9i
end initial conditions

begin initial values
aa1i = 1.0
aa10i = 1.0
aa11i = 1.0
aa12i = 1.0
aa13i = 1.0
aa14i = 1.0
aa15i = 1.0
aa16i = 1.0
aa17i = 1.0
aa18i = 1.0
aa19i = 1.0
aa2i = 1.0
aa20i = 1.0
aa3i = 1.0
aa4i = 1.0
aa5i = 1.0
aa6i = 1.0
aa7i = 1.0
aa8i = 1.0
aa9i = 1.0
ppGppi = 1.0
ri = 24.3757
taa1i = 7.3127
taa10i = 7.3127
taa11i = 7.3127
taa12i = 7.3127
taa13i = 7.3127
taa14i = 7.3127
taa15i = 7.3127
taa16i = 7.3127
taa17i = 7.3127
taa18i = 7.3127
taa19i = 7.3127
taa2i = 7.3127
taa20i = 7.3127
taa3i = 7.3127
taa4i = 7.3127
taa5i = 7.3127
taa6i = 7.3127
taa7i = 7.3127
taa8i = 7.3127
taa9i = 7.3127
end initial values

begin assignment rules
end assignment rules

begin function definitions
min[a_,b_] := Piecewise[{{a, a < b}}, b]
end function definitions

begin events
upshift = (t > 10000, {step -> 1.375}, 0)
downshift = (t > 5000, {step -> 0.75}, 0)
end events

begin process annotations
end process annotations

begin species annotations
end species annotations

begin units
end units