(* Generated by JWS Online *)

(* This is an experimental feature of JWS Online. Please report any mistakes.*)

(* Note that the following notable SBML entities or features are not supported in notebook outputyet: *)
    (* Events *)
    (* Constraints *)
    (* Units and UnitDefinitions *)
    (* AlgebraicRules *)
    (* conversionFactors *)

variables = {
aa1[t], aa10[t], aa11[t], aa12[t], aa13[t], aa14[t], aa15[t], aa16[t], aa17[t], aa18[t], aa19[t], aa2[t], aa20[t], aa3[t], aa4[t], aa5[t], aa6[t], aa7[t], aa8[t], aa9[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]
};

initialValues = {
aa1[0] == 1.0, aa10[0] == 1.0, aa11[0] == 1.0, aa12[0] == 1.0, aa13[0] == 1.0, aa14[0] == 1.0, aa15[0] == 1.0, aa16[0] == 1.0, aa17[0] == 1.0, aa18[0] == 1.0, aa19[0] == 1.0, aa2[0] == 1.0, aa20[0] == 1.0, aa3[0] == 1.0, aa4[0] == 1.0, aa5[0] == 1.0, aa6[0] == 1.0, aa7[0] == 1.0, aa8[0] == 1.0, aa9[0] == 1.0, taa1[0] == 7.3127, taa10[0] == 7.3127, taa11[0] == 7.3127, taa12[0] == 7.3127, taa13[0] == 7.3127, taa14[0] == 7.3127, taa15[0] == 7.3127, taa16[0] == 7.3127, taa17[0] == 7.3127, taa18[0] == 7.3127, taa19[0] == 7.3127, taa2[0] == 7.3127, taa20[0] == 7.3127, taa3[0] == 7.3127, taa4[0] == 7.3127, taa5[0] == 7.3127, taa6[0] == 7.3127, taa7[0] == 7.3127, taa8[0] == 7.3127, taa9[0] == 7.3127
};

rates = {
vAAsynt1, vAAsynt10, vAAsynt11, vAAsynt12, vAAsynt13, vAAsynt14, vAAsynt15, vAAsynt16, vAAsynt17, vAAsynt18, vAAsynt19, vAAsynt2, vAAsynt20, vAAsynt3, vAAsynt4, vAAsynt5, vAAsynt6, vAAsynt7, vAAsynt8, vAAsynt9, vbiomass, vtRNAchar1, vtRNAchar10, vtRNAchar11, vtRNAchar12, vtRNAchar13, vtRNAchar14, vtRNAchar15, vtRNAchar16, vtRNAchar17, vtRNAchar18, vtRNAchar19, vtRNAchar2, vtRNAchar20, vtRNAchar3, vtRNAchar4, vtRNAchar5, vtRNAchar6, vtRNAchar7, vtRNAchar8, vtRNAchar9
};

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

parameters = {
EXTERNAL -> 1.0, 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, 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, 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, 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, kappart -> 500.0, kapparta -> 1.0, kn1 -> 0.176694097633303, kn10 -> 0.175155965973061, kn11 -> 0.21893081294363, kn12 -> 0.189250477436635, kn13 -> 0.182501157889419, kn14 -> 0.168797176256554, kn15 -> 0.178172813430161, kn16 -> 0.163557478413, kn17 -> 0.240562151147302, kn18 -> 0.234708428287117, kn19 -> 0.238857324820486, kn2 -> 0.170472469931078, kn20 -> 0.192552580536003, kn3 -> 0.215014924490181, kn4 -> 0.160529780205187, kn5 -> 0.154007815602573, kn6 -> 0.232252087628394, kn7 -> 0.188971693282943, kn8 -> 0.202409099613367, kn9 -> 0.221447303290898, 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, nAmet -> 300.0, rmax -> 81.2522598284765, 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, 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, r -> 24.3757, default -> 1.0
};

assignments = {

};

events = {

};

speciesAnnotations = {

};

reactionAnnotations = {

};

units = {
{"time" -> "", "metabolite" -> "", "extent" -> ""}
};

(* Time evolution *)
odes = {
aa1'[t] == 1.0*vAAsynt1 -1.0*vtRNAchar1, aa10'[t] == 1.0*vAAsynt10 -1.0*vtRNAchar10, aa11'[t] == 1.0*vAAsynt11 -1.0*vtRNAchar11, aa12'[t] == 1.0*vAAsynt12 -1.0*vtRNAchar12, aa13'[t] == 1.0*vAAsynt13 -1.0*vtRNAchar13, aa14'[t] == 1.0*vAAsynt14 -1.0*vtRNAchar14, aa15'[t] == 1.0*vAAsynt15 -1.0*vtRNAchar15, aa16'[t] == 1.0*vAAsynt16 -1.0*vtRNAchar16, aa17'[t] == 1.0*vAAsynt17 -1.0*vtRNAchar17, aa18'[t] == 1.0*vAAsynt18 -1.0*vtRNAchar18, aa19'[t] == 1.0*vAAsynt19 -1.0*vtRNAchar19, aa2'[t] == 1.0*vAAsynt2 -1.0*vtRNAchar2, aa20'[t] == 1.0*vAAsynt20 -1.0*vtRNAchar20, aa3'[t] == 1.0*vAAsynt3 -1.0*vtRNAchar3, aa4'[t] == 1.0*vAAsynt4 -1.0*vtRNAchar4, aa5'[t] == 1.0*vAAsynt5 -1.0*vtRNAchar5, aa6'[t] == 1.0*vAAsynt6 -1.0*vtRNAchar6, aa7'[t] == 1.0*vAAsynt7 -1.0*vtRNAchar7, aa8'[t] == 1.0*vAAsynt8 -1.0*vtRNAchar8, aa9'[t] == 1.0*vAAsynt9 -1.0*vtRNAchar9, taa1'[t] == 1.0*vtRNAchar1 -0.05*vbiomass, taa10'[t] == 1.0*vtRNAchar10 -0.05*vbiomass, taa11'[t] == 1.0*vtRNAchar11 -0.05*vbiomass, taa12'[t] == 1.0*vtRNAchar12 -0.05*vbiomass, taa13'[t] == 1.0*vtRNAchar13 -0.05*vbiomass, taa14'[t] == 1.0*vtRNAchar14 -0.05*vbiomass, taa15'[t] == 1.0*vtRNAchar15 -0.05*vbiomass, taa16'[t] == 1.0*vtRNAchar16 -0.05*vbiomass, taa17'[t] == 1.0*vtRNAchar17 -0.05*vbiomass, taa18'[t] == 1.0*vtRNAchar18 -0.05*vbiomass, taa19'[t] == 1.0*vtRNAchar19 -0.05*vbiomass, taa2'[t] == 1.0*vtRNAchar2 -0.05*vbiomass, taa20'[t] == 1.0*vtRNAchar20 -0.05*vbiomass, taa3'[t] == 1.0*vtRNAchar3 -0.05*vbiomass, taa4'[t] == 1.0*vtRNAchar4 -0.05*vbiomass, taa5'[t] == 1.0*vtRNAchar5 -0.05*vbiomass, taa6'[t] == 1.0*vtRNAchar6 -0.05*vbiomass, taa7'[t] == 1.0*vtRNAchar7 -0.05*vbiomass, taa8'[t] == 1.0*vtRNAchar8 -0.05*vbiomass, taa9'[t] == 1.0*vtRNAchar9 -0.05*vbiomass
};
timeCourse = NDSolve[Join[odes, initialValues]//.rateEquations//.assignments//.parameters, variables, {t, 0, 100}];

(* Steady-state solution initialized with result of time evolution *)
findRootEquations = odes /.D[_[t],t]->0;
findRootVariables = Partition[Flatten[{#, #/.timeCourse/.t->100} &/@variables],2];
steadyStateVariables = FindRoot[findRootEquations//.rateEquations//.assignments//.parameters, findRootVariables, MaxIterations->100]
fluxes = #//.assignments//.parameters/.steadyStateVariables&/@rateEquations

(* Plot the time evolution of the variables *)
plotTable=Table[Plot[variables[[i]]/.parameters/.timeCourse,{t,0,100},PlotLegends->variables[[i]],PlotRange->Full],{i,Length[variables]}]