## Set file for C:\cygwin\home\Administrator\files\budding_yeast\apc_del\David\apc-del.ode on Mon May 10 08:40:24 2004 45 Number of equations and auxiliaries 156 Number of parameters # Numerical stuff 1 nout 40 nullcline mesh 9 Stiff 1000 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 2000 Current time 2000 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 0.7434539198875427 MASS 0.08342601358890533 CLN2 0.1147801578044891 CLB2 0.08410494029521942 CLB5 0.01803707145154476 SIC1 0.114388071000576 CDC6 0.1739573329687119 C2 0.09688682109117508 C5 0.2167218327522278 F2 0.0001311646337853745 F5 0.003010560292750597 SIC1P 0.01348251756280661 C2P 0.007275680545717478 C5P 0.00837775319814682 CDC6P 0.01413857843726873 F2P 8.055226317082997e-006 F5P 0.7103575468063355 SWI5T 0.7024384140968323 SWI5 0.08511807024478912 IEP 1.855605721473694 CDC20T 0.4204259514808655 CDC20 1 CDH1T 0.994186282157898 CDH1 2 CDC14T 0.5468657612800598 CDC14 2.799999952316284 NET1T 0.009161100722849369 NET1 0.9802321195602417 RENT 0.8777932524681091 TEM1 0.6525858640670776 CDC15 0.08033313602209091 PPX 0.002407065592706204 PDS1 0.8274482488632202 ESP1 0.001062883646227419 ORI 0.02198665030300617 BUD 0.04054306820034981 SPN 0.009999999776482582 VI20 0.1000000014901161 LTE1 0.2000000029802322 BUB2 # Ending ICs 0.8178950003963158 MASS 0.02007893137079867 CLN2 1.18987542796082e-005 CLB2 0.0002087564013775358 CLB5 0.9990698237384444 SIC1 1.388038790376951 CDC6 0.001370086887858302 C2 0.1176511562031183 C5 0.0002738297054210552 F2 0.0001179877650387045 F5 0.02245362954442605 SIC1P 2.337603889793013e-005 C2P 0.002651204953741123 C5P 0.02763631356726589 CDC6P 4.07215990635772e-006 F2P 2.393465119499459e-006 F5P 0.1820331343171932 SWI5T 0.1820223829599187 SWI5 7.273772983790719e-007 IEP 0.02326629320109423 CDC20T 0.004943577859765599 CDC20 1 CDH1T 0.9955038989098559 CDH1 2 CDC14T 0.01244609702349925 CDC14 2.799999999999885 NET1T 0.5366471621653636 NET1 1.929540431949801 RENT 0.08219566694674779 TEM1 0.14485980182562 CDC15 0.2067447494875466 PPX 0.0001711951796375019 PDS1 0.9840558123165142 ESP1 0.0520647985042867 ORI 0.0416090168594342 BUD 0.0212666679105564 SPN 0.01 VI20 0.1 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 0.00075 ksb2' 0.05 ksb2" 0.006 kdb2' 0.38 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 0.5 ec1b5 0.38 ec1b2 0.3 ec1n3 50 kasb2 0.05 kdib2 50 kasb5 0.06 kdib5 1 kd3c1 6 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 6 kppf6 0.005 ksswi' 0.06 ksswi" 0.08 kdswi 2.2 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 0.5 kdirent 2 kdirentp 0.05 kppnet' 2.5 kppnet" 0.01 kkpnet' 0.6 kkpnet" 0 kspds' 0.03 ks1pds" 0.055 ks2pds" 0.01 kd1pds' 0.8 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 0.3 ebudn2 0.06 ebudn3 1.2 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 150 mdt 1 MorD 0.2 kez2 30 MAXMASS 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 1000 xmax 0 xmin 3 ymax 0 ymin 12 zmax -12 zmin 500 0.002 1.5 0.6666666666666666 0 0.08333333333333333 45 Theta 45 Phi 0 xshft 0 yshft 0 zshft 0 xlo 0 ylo 0 0 1000 xhi 3 yhi 500 3 RHS etc ... dMASS/dT= KG*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 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))