## Set file for C:\cygwin\home\Administrator\files\budding_yeast\cell03\cell033.ode on Fri Jul 18 10:11:51 2003 45 Number of equations and auxiliaries 155 Number of parameters # Numerical stuff 1 nout 40 nullcline mesh 9 Stiff 500 total 0.1 DeltaT 0 T0 0 Transient 2000 Bound 1e-012 DtMin 1 DtMax 1e-005 Tolerance 0.001 Abs. 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 # 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 # Old ICs 1.206019401550293 MASS 0.0652511790394783 CLN2 0.1469227224588394 CLB2 0.05180418863892555 CLB5 0.02287768945097923 SIC1 0.1075804308056831 CDC6 0.2384047210216522 C2 0.07008149474859238 C5 0.2360586225986481 F2 7.245147571666166e-005 F5 0.006410160101950169 SIC1P 0.02403404749929905 C2P 0.006878305226564407 C5P 0.01548638287931681 CDC6P 0.02739384770393372 F2P 7.90633202996105e-006 F5P 0.9764602780342102 SWI5T 0.9561624526977539 SWI5 0.1015391126275063 IEP 1.916339993476868 CDC20T 0.4442965388298035 CDC20 1 CDH1T 0.930499255657196 CDH1 2 CDC14T 0.46834397315979 CDC14 2.799999952316284 NET1T 0.01864561997354031 NET1 1.049547672271729 RENT 0.9038969278335571 TEM1 0.6565329432487488 CDC15 0.1231788992881775 PPX 0.02561234869062901 PDS1 0.3013133406639099 ESP1 0.0009094525594264269 ORI 0.008473447524011135 BUD 0.03056218847632408 SPN 0.009999999776482582 VI20 0.1000000014901161 LTE1 0.2000000029802322 BUB2 # Ending ICs 2.509396495117448 MASS 0.1149634381854938 CLN2 1.172797608923446 CLB2 0.1830774030149369 CLB5 0.001681527030491935 SIC1 0.007554871179139756 CDC6 0.04445569075337426 C2 0.007171980489170029 C5 0.0457315387990989 F2 5.850982067966126e-006 F5 0.008130024871667753 SIC1P 0.07434352432013963 C2P 0.01234983739338646 C5P 0.02070080237021405 CDC6P 0.08625019866998906 F2P 1.124648390033782e-005 F5P 0.9498686741902963 SWI5T 0.7841727683606932 SWI5 0.2908133069243452 IEP 1.995520461868337 CDC20T 0.5146974104769589 CDC20 1 CDH1T 0.03798913473829101 CDH1 2 CDC14T 0.1715238357856944 CDC14 2.799999999999867 NET1T 0.06860863171398124 NET1 1.338567381619038 RENT 0.9778336096873994 TEM1 0.6617104596004815 CDC15 0.2960788189010626 PPX 0.1292014410572146 PDS1 0.08349544631330499 ESP1 24.30484963700435 ORI 1.880035843581905 BUD 1.25858519100649 SPN 0.01 VI20 1 LTE1 0.2 BUB2 # Parameters 0.054 B0 0.4 C0 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 200 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 Jpds 0.17 kdppx' 2 kdppx" 0.15 J20ppx 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 0.12 galcln2 0.12 galclb2 0.012 galclb5 0.12 galsic1 0.12 galcdc6 6 galcdc20 20 galcln3 20 galtem1 20 galcdc15 0.005 net1ts_f 0.04 tab61_f 0.075 clb2db_f # 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 40 2 1 2 0 41 2 1 6 0 42 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 2 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= KG*MASS 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 dVI20/dT= 0 dLTE1/dT= 0 dBUB2/dT= 0 CLB2T=CLB2+C2+F2+C2P+F2P CLB5T=CLB5+C5+F5+C5P+F5P CKIT=SIC1T+CDC6T SIC1T=SIC1T MCM1=MCM1 SBF=SBF where ... BCK2 = B0*MASS CLN3 = C0*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"*(J20PPX+CDC20)*JPDS/(JPDS+PDS1) SBF = GK(VASBF, KISBF'+KISBF"*CLB2, JASBF, JISBF) MCM1 = GK(KAMCM*CLB2, KIMCM, JAMCM, JIMCM) 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))