## Set file for C:\cygwin\home\kathy\files\budding_yeast\ICtest\report_for_TAR12_17_IC\TAR12.ode on Mon Nov 17 19:58:36 2003 48 Number of equations and auxiliaries 151 Number of parameters # Numerical stuff 1 nout 40 nullcline mesh 7 BackEul 500 total 0.1 DeltaT 0 T0 0 Transient 2000 Bound 1e-012 DtMin 1 DtMax 1e-005 Tolerance 0 Max Delay 100 Eigenvector iterates 0.001 Eigenvector tolerance 0.001 Newton tolerance 0 Poincare plane 1e-005 Boundary value tolerance 1e-005 Boundary value epsilon 20 Boundary value iterates 0 Poincare None 1 Poincare variable 1 Poincare sign 0 Stop on Section 0 Delay flag 500 Current time 500 Last Time 0 MyStart 1 INFLAG # Delays 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 # Bndry conds 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # Old ICs 1.212595105171204 MASS 0.06160590425133705 CLN2 0.1463514417409897 CLB2 0.05336679145693779 CLB5 0.0224220622330904 SIC1 0.1065565720200539 CDC6 0.2355565875768662 C2 0.07044374197721481 C5 0.2333101183176041 F2 7.30368701624684e-005 F5 0.006754010915756226 SIC1P 0.02513346634805203 C2P 0.007269222289323807 C5P 0.01626908965408802 CDC6P 0.0287732295691967 F2P 8.398712452617474e-006 F5P 0.9746344089508057 SWI5T 0.9530601501464844 SWI5 0.1031579822301865 IEP 1.915212273597717 CDC20T 0.4455196857452393 CDC20 1 CDH1T 0.9031444191932678 CDH1 2 CDC14T 0.4156905114650726 CDC14 2.799999952316284 NET1T 0.02745954133570194 NET1 1.145977735519409 RENT 0.8588392734527588 TEM1 0.649145245552063 CDC15 0.1245575398206711 PPX 0.02615203335881233 PDS1 0.2967464327812195 ESP1 0.0002092957147397101 ORI 0.01568104699254036 BUD 0.05497833341360092 SPN 0.6562694907188416 TARGET 0.009999999776482582 VI20 0.1000000014901161 LTE1 0.2000000029802322 BUB2 0.8718729615211487 PRET # Ending ICs 2.505102040400841 MASS 0.1350976123876209 CLN2 1.226243833998367 CLB2 0.2074304889681429 CLB5 0.001529028201131343 SIC1 0.006810646794702837 CDC6 0.03800073403775228 C2 0.006631637401895887 C5 0.03937045576940156 F2 5.378924557060161e-006 F5 0.008372986453164569 SIC1P 0.07386322885275824 C2P 0.01331099743719258 C5P 0.02135507090844824 CDC6P 0.08631997413738081 F2P 1.208175996005617e-005 F5P 0.9390439974810306 SWI5T 0.7641360533408727 SWI5 0.2992132219402954 IEP 1.995961013965142 CDC20T 0.5124179175696627 CDC20 1 CDH1T 0.02539796769663136 CDH1 2 CDC14T 0.139749170252221 CDC14 2.799999999999874 NET1T 0.1085945020746706 NET1 1.388967544787674 RENT 0.9778336096873994 TEM1 0.6617052107434359 CDC15 0.3462662472112426 PPX 0.1889152665674551 PDS1 0.05934961919514939 ESP1 24.48598750329769 ORI 1.991268386734307 BUD 1.239962870511987 SPN 0.01447224761857417 TARGET 0.01 VI20 1 LTE1 0.2 BUB2 95.09732352719647 PRET # Parameters 0.054 BCK0 0.4 CLN3MAX 1 Dn3 6 Jn3 0 ksn2' 0.15 ksn2" 0.12 kdn2 2 esbfn2 10 esbfn3 2 esbfb5 0.38 kasbf 0.6 kisbf' 8 kisbf" 0.01 Jasbf 0.01 Jisbf 0.001 ksb2' 0.04 ksb2" 0.003 kdb2' 0.4 kdb2" 0.15 kdb2p 1 kamcm 0.15 kimcm 0.1 Jamcm 0.1 Jimcm 0.0008 ksb5' 0.005 ksb5" 0.01 kdb5' 0.16 kdb5" 0.012 ksc1' 0.12 ksc1" 0.01 kd1c1 1 kd2c1 0.05 Jd2c1 0.03 ec1k2 0.06 ec1n2 0.1 ec1b5 0.45 ec1b2 0.3 ec1n3 50 kasb2 0.05 kdib2 50 kasb5 0.06 kdib5 1 kd3c1 4 kppc1 0.024 ksf6' 0.12 ksf6" 0.004 ksf6"' 0.01 kd1f6 1 kd2f6 0.05 Jd2f6 0.03 ef6k2 0.06 ef6n2 0.1 ef6b5 0.55 ef6b2 0.3 ef6n3 15 kasf2 0.5 kdif2 0.01 kasf5 0.01 kdif5 1 kd3f6 4 kppf6 0.005 ksswi' 0.08 ksswi" 0.08 kdswi 2 kaswi 0.05 kiswi 0.1 kaiep 0.15 kiiep 0.1 Jaiep 0.1 Jiiep 0.006 ks20' 0.6 ks20" 0.3 kd20 0.05 ka20' 0.2 ka20" 0.01 ki20' 8 ki20" 0.01 kscdh 0.01 kdcdh 0.01 kacdh' 0.8 kacdh" 0.03 Jicdh 0.03 Jacdh 0.001 kicdh' 0.08 kicdh" 0.4 eicdhn2 0.25 eicdhn3 8 eicdhb5 1.2 eicdhb2 0.2 ks14 0.1 kd14 0.08400000000000001 ksnet 0.03 kdnet 160 kasrent 1 kasrentp 1 kdirent 2 kdirentp 0.05 kppnet' 3 kppnet" 0.01 kkpnet' 0.6 kkpnet" 0 kspds' 0.03 ks1pds" 0.055 ks2pds" 0.01 kd1pds' 0.2 kd2pds" 0.04 kd3pds" 50 kasesp 0.5 kdiesp 1 ESP1T 0.1 ksppx 0.04 kmpds 0.17 kdppx' 2 kdppx" 0.15 eps20ppx 2 ksori 0.06 kdori 0.9 eorib5 0.45 eorib2 0.2 ksbud 0.06 kdbud 0.25 ebudn2 0.05 ebudn3 1 ebudb5 0.1 ksspn 0.06 kdspn 0.14 Jspn 0.1 lte1l 1 lte1h 0.2 Bub2l 1 Bub2h 1 TEM1T 0.1 jatem 0.1 Jitem 1 Cdc15T 0.002 ka15' 1 ka15" 0.001 ka15p 0.5 ki15 0.3 KEZ 90 mdt 1 MorD 0.2 kez2 0.02 katar' 1 katar" 0.01 kitar' 0.53 kitar" 0.05 Jatar 0.05 Jitar 0.4 keztar 0 mintval # Graphics 0.7071097251469876 rm -0.4999999999826661 rm 0.4999958366025516 rm 0.7071038372138505 rm 0.5000041633974484 rm -0.4999999999826661 rm 0 rm 0.7071038372138505 rm 0.7071097251469876 rm 0 1 2 1 0 0 42 2 1 2 0 43 2 1 6 0 44 2 1 9 0 23 2 1 10 0 21 2 1 3 0 25 2 1 8 0 32 2 1 11 0 30 2 1 0 0 37 2 1 4 -1000 1000 0 0 3DFlag 1 Timeflag 0 Colorflag 0 Type 1 color scale 0 minscale 500 xmax 0 xmin 3 ymax 0 ymin 12 zmax -12 zmin 250 0.004 1.5 0.6666666666666666 0 0.08333333333333333 45 Theta 45 Phi 0 xshft 0 yshft 0 zshft 0 xlo 0 ylo 0 0 500 xhi 3 yhi 500 3 RHS etc ... dMASS/dT= MU*MASS*(1-MASS/MAXMASS) dCLN2/dT= (KSN2'+KSN2"*SBF)*MASS-KDN2*CLN2 dCLB2/dT=(KSB2'+KSB2"*MCM1)*MASS+(KD3C1*C2P+KD3F6*F2P)+(KDIB2*C2+KDIF2*F2) - dCLB5/dT= (KSB5'+KSB5"*SBF)*MASS+(KD3C1*C5P+KD3F6*F5P)+(KDIB5*C5+KDIF5*F5) - dSIC1/dT=(KSC1'+KSC1"*SWI5)+(VDB2*C2+VDB5*C5)+(KDIB2*C2+KDIB5*C5)+VPPC1*SIC1P dCDC6/dT=(KSF6'+KSF6"*SWI5+KSF6"'*SBF)+(VDB2*F2+VDB5*F5)+(KDIF2*F2+KDIF5*F5)+VPPF6*CDC6 dC2/dT= KASB2*CLB2*SIC1+VPPC1*C2P-(KDIB2+VDB2+VKPC1)*C2 dC5/dT= KASB5*CLB5*SIC1+VPPC1*C5P-(KDIB5+VDB5+VKPC1)*C5 dF2/dT= KASF2*CLB2*CDC6+VPPF6*F2P-(KDIF2+VDB2+VKPF6)*F2 dF5/dT= KASF5*CLB5*CDC6+VPPF6*F5P-(KDIF5+VDB5+VKPF6)*F5 dSIC1P/dT=VKPC1*SIC1-(VPPC1+KD3C1)*SIC1P+VDB2*C2P+VDB5*C5P dC2P/dT=VKPC1*C2-(VPPC1+KD3C1+VDB2)*C2P dC5P/dT=VKPC1*C5-(VPPC1+KD3C1+VDB5)*C5P dCDC6P/dT=VKPF6*CDC6-(VPPF6+KD3F6)*CDC6P+VDB2*F2P+VDB5*F5P dF2P/dT=VKPF6*F2-(VPPF6+KD3F6+VDB2)*F2P dF5P/dT=VKPF6*F5-(VPPF6+KD3F6+VDB5)*F5P dSWI5T/dT= KSSWI'+KSSWI"*MCM1-KDSWI*SWI5T dSWI5/dT= KSSWI'+KSSWI"*MCM1+KASWI*CDC14*(SWI5T-SWI5)-(KISWI*CLB2+KDSWI)*SWI5 dIEP/dT= VAIEP*(1-IEP)/(JAIEP+1-IEP)-KIIEP*IEP/(JIIEP+IEP) dCDC20T/dT= (KS20'+KS20"*MCM1)-KD20*CDC20T dCDC20/dT= (KA20'+KA20"*IEP)*(CDC20T-CDC20)-(VI20+KD20)*CDC20 dCDH1T/dT= KSCDH - KDCDH*CDH1T dCDH1/dT=KSCDH-KDCDH*CDH1+VACDH*(CDH1T-CDH1)/(JACDH+CDH1T-CDH1) -VICDH*CDH1/ dCDC14T/dT=KS14 - KD14*CDC14T dCDC14/dT=(KDIRENT*RENT+KDIRENTP*RENTP) -(KASRENT*NET1+KASRENTP*NET1P)*CDC14 dNET1T/dT= KSNET - KDNET*NET1T dNET1/dT= KDIRENT*RENT-KASRENT*NET1*CDC14+VPPNET*NET1P-VKPNET*NET1 +KSNET-K dRENT/dT=-KDIRENT*RENT+KASRENT*NET1*CDC14+VPPNET*RENTP-VKPNET*RENT -(KD14+K dTEM1/dT= LTE1*(TEM1T-TEM1)/(JATEM+TEM1T-TEM1)-BUB2*TEM1/(JITEM+TEM1) dCDC15/dT= (KA15'*(TEM1T-TEM1)+KA15"*TEM1+KA15P*CDC14)*(CDC15T-CDC15)-KI15*CDC15 dPPX/dT= KSPPX-VDPPX*PPX dPDS1/dT= (KSPDS'+KS1PDS"*SBF+KS2PDS"*MCM1)+KDIESP*PE-(VDPDS+KASESP*ESP1)*PDS1 dESP1/dT= -KASESP*PDS1*ESP1+(KDIESP+VDPDS)*PE dORI/dT= KSORI*(EORIB5*CLB5+EORIB2*CLB2)-KDORI*ORI dBUD/dT= KSBUD*(EBUDN2*CLN2+EBUDN3*CLN3+EBUDB5*CLB5)-KDBUD*BUD dSPN/dT= KSSPN*CLB2/(JSPN+CLB2)-KDSPN*SPN dTARGET/dT=(KATAR'+KATAR"*CDC14)*(1-TARGET)/(JATAR+1-TARGET) -(KITAR'+KITAR"*C dVI20/dT= 0 dLTE1/dT= 0 dBUB2/dT= 0 dPRET/dT= 1 CLB2T=CLB2+C2+F2+C2P+F2P CLB5T=CLB5+C5+F5+C5P+F5P CKIT=SIC1T+CDC6T SIC1T=SIC1T CDC6T=CDC6T SBF=SBF MALLOW=MALLOW where ... BCK2 = BCK0*MASS CLN3 = CLN3MAX*DN3*MASS/(JN3+DN3*MASS) SIC1T = SIC1+C2+C5+SIC1P+C2P+C5P CDC6T = CDC6+F2+F5+CDC6P+F2P+F5P RENTP = CDC14T-RENT-CDC14 NET1P = NET1T-NET1-CDC14T+CDC14 PE = ESP1T-ESP1 VASBF = KASBF*(ESBFN2*CLN2+ESBFN3*(CLN3+BCK2)+ESBFB5*CLB5) VDB2 = KDB2'+KDB2"*CDH1+KDB2P*CDC20 VDB5 = KDB5'+KDB5"*CDC20 VKPC1 = KD1C1+KD2C1*(EC1N3*CLN3+EC1K2*BCK2+EC1N2*CLN2+EC1B2*CLB2+EC1B5*CLB5)/(JD2C1+SIC1T) VPPC1 = KPPC1*CDC14 VKPF6 = KD1F6+KD2F6*(EF6N3*CLN3+EF6K2*BCK2+EF6N2*CLN2+EF6B2*CLB2+EF6B5*CLB5)/(JD2F6+CDC6T) VPPF6 = KPPF6*CDC14 VAIEP = KAIEP*CLB2 VACDH = KACDH'+KACDH"*CDC14 VICDH = KICDH'+KICDH"*(EICDHN3*CLN3+EICDHN2*CLN2+EICDHB5*CLB5+EICDHB2*CLB2) VPPNET = KPPNET'+KPPNET"*PPX VKPNET = (KKPNET'+KKPNET"*CDC15)*MASS VDPDS = KD1PDS'+KD2PDS"*CDC20+KD3PDS"*CDH1 VDPPX = KDPPX'+KDPPX"*(EPS20PPX+CDC20)*KMPDS/(KMPDS+PDS1) SBF = GK(VASBF, KISBF'+KISBF"*CLB2, JASBF, JISBF) MCM1 = GK(KAMCM*CLB2, KIMCM, JAMCM, JIMCM) MALLOW = HEAV(PRET-MINTVAL) User-defined functions: BB(VA,VI,JA,JI) = VI-VA+JA*VI+JI*VA GK(VA,VI,JA,JI) = 2*JI*VA/(BB(VA,VI,JA,JI)+SQRT(BB(VA,VI,JA,JI)^2-4*(VI-VA)*JI*VA))