//genesis
// kkit Version 11 flat dumpfile
// Saved on Fri Nov 24 10:08:23 2006
include kkit {argv 1}
FASTDT = 1e-05
SIMDT = 0.0001
CONTROLDT = 0.1
PLOTDT = 0.1
MAXTIME = 20
TRANSIENT_TIME = 2
VARIABLE_DT_FLAG = 0
DEFAULT_VOL = 2e-16
VERSION = 11.0
setfield /file/modpath value /home2/bhalla/scripts/modules
kparms
//genesis
initdump -version 3 -ignoreorphans 1
simobjdump doqcsinfo filename accessname accesstype transcriber developer \
citation species tissue cellcompartment methodology sources \
model_implementation model_validation x y z
simobjdump table input output alloced step_mode stepsize x y z
simobjdump xtree path script namemode sizescale
simobjdump xcoredraw xmin xmax ymin ymax
simobjdump xtext editable
simobjdump xgraph xmin xmax ymin ymax overlay
simobjdump xplot pixflags script fg ysquish do_slope wy
simobjdump group xtree_fg_req xtree_textfg_req plotfield expanded movealone \
link savename file version md5sum mod_save_flag x y z
simobjdump geometry size dim shape outside xtree_fg_req xtree_textfg_req x y \
z
simobjdump kpool DiffConst CoInit Co n nInit mwt nMin vol slave_enable \
geomname xtree_fg_req xtree_textfg_req x y z
simobjdump kreac kf kb notes xtree_fg_req xtree_textfg_req x y z
simobjdump kenz CoComplexInit CoComplex nComplexInit nComplex vol k1 k2 k3 \
keepconc usecomplex notes xtree_fg_req xtree_textfg_req link x y z
simobjdump stim level1 width1 delay1 level2 width2 delay2 baselevel trig_time \
trig_mode notes xtree_fg_req xtree_textfg_req is_running x y z
simobjdump xtab input output alloced step_mode stepsize notes editfunc \
xtree_fg_req xtree_textfg_req baselevel last_x last_y is_running x y z
simobjdump kchan perm gmax Vm is_active use_nernst notes xtree_fg_req \
xtree_textfg_req x y z
simobjdump transport input output alloced step_mode stepsize dt delay clock \
kf xtree_fg_req xtree_textfg_req x y z
simobjdump proto x y z
simundump geometry /kinetics/geometry 0 2e-16 3 sphere "" white black 20 8 0
simundump group /kinetics/CELLDIV 0 yellow black x 0 1 "" defaultfile \
defaultfile.g 0 0 0 -31 5 0
simundump group /kinetics/CELLDIV/Growth 0 29 black x 0 0 "" Growth \
defaultfile.g 0 0 0 -33 -3 0
simundump kpool /kinetics/CELLDIV/Growth/mass 0 0 1 1 1.2e+05 1.2e+05 0 0 \
1.2e+05 0 /kinetics/geometry blue 29 -34 -8 0
simundump kenz /kinetics/CELLDIV/Growth/mass/k27 0 0 0 0 0 1.2e+05 8.3333e-06 \
8 2 0 1 "" red blue "" -34 -9 0
simundump kpool /kinetics/CELLDIV/Growth/GM 0 0 0 0 0 0 0 0 1.2e+05 0 \
/kinetics/geometry 6 29 -32 -8 0
simundump kenz /kinetics/CELLDIV/Growth/GM/mu 0 0 0 0 0 1.2e+05 5.0833e-06 \
0.488 0.122 0 1 "" red 6 "" -32 -7 0
simundump kpool /kinetics/CELLDIV/Growth/degraded 0 0 0 0 0 0 0 0 1.2e+05 4 \
/kinetics/geometry 59 29 -32 -6 0
simundump kpool /kinetics/CELLDIV/Growth/AminoAcids 0 0 1 1 1.2e+05 1.2e+05 0 \
0 1.2e+05 4 /kinetics/geometry 54 29 -34 -6 0
simundump kreac /kinetics/CELLDIV/Growth/k28 0 0.2 0 "" white 29 -30 -7 0
simundump kpool /kinetics/CELLDIV/Growth/Rb_dup 0 0 2 10 1.2e+06 2.4e+05 0 0 \
1.2e+05 0 /kinetics/geometry 10 29 -32 -14 0
simundump kreac /kinetics/CELLDIV/Growth/H1 0 9.6451e-22 125 "" white 29 -34 \
-13 0
simundump kpool /kinetics/CELLDIV/Growth/Heaviside_mid 0 0 0 0 0 0 0 0 \
1.2e+05 0 /kinetics/geometry blue 29 -32 -12 0
simundump kpool /kinetics/CELLDIV/Growth/Heaviside_dup 0 0 0 1 1.2e+05 0 0 0 \
1.2e+05 0 /kinetics/geometry blue 29 -36 -10 0
simundump kpool /kinetics/CELLDIV/Growth/Heaviside_inh 0 0 1 1 1.2e+05 \
1.2e+05 0 0 1.2e+05 0 /kinetics/geometry 53 29 -36 -14 0
simundump kpool /kinetics/CELLDIV/Rb_P 0 0 0 0 0 0 0 0 1.2e+05 0 \
/kinetics/geometry blue yellow -24 -12 0
simundump group /kinetics/CELLDIV/Rb_grp 0 51 black x 0 0 "" Rb_grp \
defaultfile.g 0 0 0 -22 -3 0
simundump kreac /kinetics/CELLDIV/Rb_grp/k21b 0 10 0 "" white 51 -24 -8 0
simundump kpool /kinetics/CELLDIV/Rb_grp/PP1 0 0 1 1 1.2e+05 1.2e+05 0 0 \
1.2e+05 0 /kinetics/geometry blue 51 -24 -6 0
simundump kenz /kinetics/CELLDIV/Rb_grp/PP1/k19_prime 0 0 0 0 0 1.2e+05 \
4.1667e-08 0.4 0.1 0 1 "" red blue "" -22 -6 0
simundump kpool /kinetics/CELLDIV/Rb_grp/PP1A 0 0 0 0 0 0 0 0 1.2e+05 0 \
/kinetics/geometry 8 51 -24 -10 0
simundump kenz /kinetics/CELLDIV/Rb_grp/PP1A/k19 0 0 0 0 0 1.2e+05 0.00083333 \
8000 2000 0 1 "" red 8 "" -22 -10 0
simundump kpool /kinetics/CELLDIV/Rb 0 0 10 10 1.2e+06 1.2e+06 0 0 1.2e+05 0 \
/kinetics/geometry 22 yellow -20 -12 0
simundump kpool /kinetics/CELLDIV/CycD 0 0 0 0 0 0 0 0 1.2e+05 0 \
/kinetics/geometry blue yellow 2 -1 0
simundump kenz /kinetics/CELLDIV/CycD/k20_lambdaD 0 0 0 0 0 1.2e+05 0.001375 \
13200 3300 0 1 "" red 14 "" -22 -14 0
simundump kenz /kinetics/CELLDIV/CycD/k20_lambdaD[1] 0 0 0 0 0 1.2e+05 \
0.001375 13200 3300 0 1 "" red 14 "" -3 -8 0
simundump kenz /kinetics/CELLDIV/CycD/k20_lambdaD[2] 0 0 0 0 0 1.2e+05 \
0.001375 13200 3300 0 1 "" red 14 "" -19 -8 0
simundump kpool /kinetics/CELLDIV/CycE 0 0 0 0 0 0 0 0 1.2e+05 0 \
/kinetics/geometry 25 black 2 -16 0
simundump kenz /kinetics/CELLDIV/CycE/k20_lambdaE 0 0 0 0 0 1.2e+05 0.0020833 \
20000 5000 0 1 "" red 29 "" -22 -15 0
simundump kenz /kinetics/CELLDIV/CycE/k21_phiE 0 0 0 0 0 1.2e+05 0.010417 \
10000 2500 0 1 "" red 29 "" -27 -7 0
simundump kenz /kinetics/CELLDIV/CycE/Ak6_etaE 0 0 0 0 0 1.2e+05 0.0020833 \
2000 500 0 1 "" red 25 "" 22 -20 0
simundump kenz /kinetics/CELLDIV/CycE/k8_CycE 0 0 0 0 0 1.2e+05 0.00083333 8 \
2 0 1 "" red 25 "" 4 -12 0
simundump kenz /kinetics/CELLDIV/CycE/k6_E_etaE 0 0 0 0 0 1.2e+05 0.0020833 \
2000 500 0 1 "" red 25 "" 4 -21 0
simundump kenz /kinetics/CELLDIV/CycE/k6_D_etaE 0 0 0 0 0 1.2e+05 0.0020833 \
2000 500 0 1 "" red 25 "" 4 -4 0
simundump kenz /kinetics/CELLDIV/CycE/k8_CycE_Kip1 0 0 0 0 0 1.2e+05 \
0.00083333 8 2 0 1 "" red 25 "" 4 -24 0
simundump kenz /kinetics/CELLDIV/CycE/k6_kip1_E 0 0 0 0 0 1.2e+05 0.0020833 \
2000 500 0 1 "" red 25 "" 11 -8 0
simundump kenz /kinetics/CELLDIV/CycE/k20_lambdaE[1] 0 0 0 0 0 1.2e+05 \
0.0020833 20000 5000 0 1 "" red 29 "" -3 -9 0
simundump kenz /kinetics/CELLDIV/CycE/k20_lambdaE[2] 0 0 0 0 0 1.2e+05 \
0.0020833 20000 5000 0 1 "" red 29 "" -19 -9 0
simundump kpool /kinetics/CELLDIV/CycA 0 0 0 0 0 0 0 0 1.2e+05 0 \
/kinetics/geometry 35 black 20 -16 0
simundump kenz /kinetics/CELLDIV/CycA/k20_lambdaA 0 0 0 0 0 1.2e+05 0.00125 \
12000 3000 0 1 "" red 30 "" -22 -17 0
simundump kenz /kinetics/CELLDIV/CycA/k21_phiE_A 0 0 0 0 0 1.2e+05 0.010417 \
10000 2500 0 1 "" red 30 "" -27 -8 0
simundump kenz /kinetics/CELLDIV/CycA/Cdh1_CycA 0 0 0 0 0 1.2e+05 0.05 48 12 \
0 1 "" red 35 "" -12 -23 0
simundump kenz /kinetics/CELLDIV/CycA/A_phosph_E2F 0 0 0 0 0 1.2e+05 \
4.1667e-05 40 10 0 1 "" red 35 "" -9 -8 0
simundump kenz /kinetics/CELLDIV/CycA/A_phosph_E2FA.Rb 0 0 0 0 0 1.2e+05 \
4.1667e-05 40 10 0 1 "" red 35 "" -9 -10 0
simundump kenz /kinetics/CELLDIV/CycA/Ak6_etaA 0 0 0 0 0 1.2e+05 0.0020833 \
2000 500 0 1 "" red 35 "" 22 -22 0
simundump kenz /kinetics/CELLDIV/CycA/k8_CycA 0 0 0 0 0 1.2e+05 0.00083333 8 \
2 0 1 "" red 35 "" 4 -14 0
simundump kenz /kinetics/CELLDIV/CycA/k6_E_etaA 0 0 0 0 0 1.2e+05 0.0020833 \
2000 500 0 1 "" red 35 "" 4 -23 0
simundump kenz /kinetics/CELLDIV/CycA/k6_D_etaA 0 0 0 0 0 1.2e+05 0.0020833 \
2000 500 0 1 "" red 35 "" 4 -6 0
simundump kenz /kinetics/CELLDIV/CycA/k8_CycA_Kip1 0 0 0 0 0 1.2e+05 \
0.00083333 8 2 0 1 "" red 35 "" 4 -26 0
simundump kenz /kinetics/CELLDIV/CycA/k6_kip1_A 0 0 0 0 0 1.2e+05 0.0020833 \
2000 500 0 1 "" red 35 "" 11 -10 0
simundump kenz /kinetics/CELLDIV/CycA/k20_lambdaA[1] 0 0 0 0 0 1.2e+05 \
0.00125 12000 3000 0 1 "" red 30 "" -3 -11 0
simundump kenz /kinetics/CELLDIV/CycA/k20_lambdaA[2] 0 0 0 0 0 1.2e+05 \
0.00125 12000 3000 0 1 "" red 30 "" -19 -11 0
simundump kpool /kinetics/CELLDIV/CycB 0 0 0 0 0 0 0 0 1.2e+05 0 \
/kinetics/geometry 29 black 20 1 0
simundump kenz /kinetics/CELLDIV/CycB/k20_lambdaB 0 0 0 0 0 1.2e+05 0.0020833 \
20000 5000 0 1 "" red 25 "" -22 -16 0
simundump kenz /kinetics/CELLDIV/CycB/k21_phiB 0 0 0 0 0 1.2e+05 0.00083333 \
800 200 0 1 "" red 25 "" -27 -9 0
simundump kenz /kinetics/CELLDIV/CycB/k31 0 0 0 0 0 1.2e+05 0.0029167 2.8 0.7 \
0 1 "" red 29 "" -14 -34 0
simundump kenz /kinetics/CELLDIV/CycB/k11 0 0 0 0 0 1.2e+05 0.000125 12 3 0 1 \
"" red 29 "" -6 -31 0
simundump kenz /kinetics/CELLDIV/CycB/Cdh1_CycB 0 0 0 0 0 1.2e+05 0.16667 160 \
40 0 1 "" red 29 "" -12 -22 0
simundump kenz /kinetics/CELLDIV/CycB/B_phosph_E2FA 0 0 0 0 0 1.2e+05 \
4.1667e-05 40 10 0 1 "" red 29 "" -13 -8 0
simundump kenz /kinetics/CELLDIV/CycB/B_phosph_E2FA.Rb 0 0 0 0 0 1.2e+05 \
4.1667e-05 40 10 0 1 "" red 29 "" -13 -10 0
simundump kenz /kinetics/CELLDIV/CycB/Ak6_etaB 0 0 0 0 0 1.2e+05 0.0041667 \
4000 1000 0 1 "" red 29 "" 22 -21 0
simundump kenz /kinetics/CELLDIV/CycB/k8_CycB 0 0 0 0 0 1.2e+05 4.1667e-05 \
0.4 0.1 0 1 "" red 29 "" 4 -13 0
simundump kenz /kinetics/CELLDIV/CycB/k6_E_etaB 0 0 0 0 0 1.2e+05 0.0041667 \
4000 1000 0 1 "" red 29 "" 4 -22 0
simundump kenz /kinetics/CELLDIV/CycB/k6_D_etaB 0 0 0 0 0 1.2e+05 0.0041667 \
4000 1000 0 1 "" red 29 "" 4 -5 0
simundump kenz /kinetics/CELLDIV/CycB/k8_CycB_Kip1 0 0 0 0 0 1.2e+05 \
4.1667e-05 0.4 0.1 0 1 "" red 29 "" 4 -25 0
simundump kenz /kinetics/CELLDIV/CycB/k6_kip1_B 0 0 0 0 0 1.2e+05 0.0041667 \
4000 1000 0 1 "" red 29 "" 11 -9 0
simundump kenz /kinetics/CELLDIV/CycB/k20_lambdaB[1] 0 0 0 0 0 1.2e+05 \
0.0020833 20000 5000 0 1 "" red 25 "" -3 -10 0
simundump kenz /kinetics/CELLDIV/CycB/k20_lambdaB[2] 0 0 0 0 0 1.2e+05 \
0.0020833 20000 5000 0 1 "" red 25 "" -19 -10 0
simundump group /kinetics/CELLDIV/IE_GRP 0 3 black x 0 0 "" IE_GRP \
defaultfile.g 0 0 0 -16 -27 0
simundump kreac /kinetics/CELLDIV/IE_GRP/k33 0 0.05 0 "" white 3 -16 -30 0
simundump kreac /kinetics/CELLDIV/IE_GRP/k34 0 0.05 0 "" white 3 -12 -30 0
simundump kpool /kinetics/CELLDIV/IE_GRP/IE 0 0 1 1 1.2e+05 1.2e+05 0 0 \
1.2e+05 0 /kinetics/geometry blue 3 -16 -33 0
simundump kpool /kinetics/CELLDIV/IE_GRP/AminoAcids 0 0 1 1 1.2e+05 1.2e+05 0 \
0 1.2e+05 4 /kinetics/geometry 52 3 -18 -31 0
simundump kpool /kinetics/CELLDIV/IE_GRP/degraded 0 0 0 0 0 0 0 0 1.2e+05 4 \
/kinetics/geometry 26 3 -10 -31 0
simundump kpool /kinetics/CELLDIV/IE_GRP/PPX 0 0 1 1 1.2e+05 1.2e+05 0 0 \
1.2e+05 0 /kinetics/geometry blue 3 -14 -31 0
simundump kenz /kinetics/CELLDIV/IE_GRP/PPX/k32 0 0 0 0 0 1.2e+05 0.0075 7.2 \
1.8 0 1 "" red blue "" -14 -32 0
simundump kpool /kinetics/CELLDIV/IEP 0 0 0 0 0 0 0 0 1.2e+05 0 \
/kinetics/geometry 61 black -12 -33 0
simundump kenz /kinetics/CELLDIV/IEP/k13 0 0 0 0 0 1.2e+05 0.041667 20 5 0 1 \
"" red 61 "" -6 -27 0
simundump group /kinetics/CELLDIV/Cdc20_Grp 0 3 black x 0 0 "" Cdc20_Grp \
defaultfile.g 0 0 0 -4 -22 0
simundump kreac /kinetics/CELLDIV/Cdc20_Grp/k11_prime 0 0 0 "" white 3 -2 -31 \
0
simundump kreac /kinetics/CELLDIV/Cdc20_Grp/k12 0 1.5 0 "" white 3 -2 -24 0
simundump kreac /kinetics/CELLDIV/Cdc20_Grp/k12A 0 1.5 0 "" white 3 0 -27 0
simundump kpool /kinetics/CELLDIV/Cdc20_Grp/AminoAcids 0 0 1 1 1.2e+05 \
1.2e+05 0 0 1.2e+05 4 /kinetics/geometry 52 3 -4 -33 0
simundump kpool /kinetics/CELLDIV/Cdc20_Grp/degraded 0 0 0 0 0 0 0 0 1.2e+05 \
4 /kinetics/geometry 26 3 0 -25 0
simundump kpool /kinetics/CELLDIV/Cdc20_Grp/k14_enz 0 0 1 1 1.2e+05 1.2e+05 0 \
0 1.2e+05 4 /kinetics/geometry blue 3 -2 -29 0
simundump kenz /kinetics/CELLDIV/Cdc20_Grp/k14_enz/k14 0 0 0 0 0 1.2e+05 \
0.020833 10 2.5 0 1 "" red blue "" -2 -27 0
simundump kpool /kinetics/CELLDIV/Cdc20_Grp/Cdc20notA 0 0 0 0 0 0 0 0 1.2e+05 \
0 /kinetics/geometry 47 3 -4 -29 0
simundump kpool /kinetics/CELLDIV/Cdc20 0 0 0 0 0 0 0 0 1.2e+05 0 \
/kinetics/geometry blue black -4 -25 0
simundump kenz /kinetics/CELLDIV/Cdc20/k2_prime_prime 0 0 0 0 0 1.2e+05 \
4.1667e-05 400 100 0 1 "" red blue "" 24 -2 0
simundump kenz /kinetics/CELLDIV/Cdc20/Cdc20_deg_CycA 0 0 0 0 0 1.2e+05 \
0.00083333 800 200 0 1 "" red blue "" 22 -14 0
simundump kenz /kinetics/CELLDIV/Cdc20/Cdc20_deg_CycA_Kip1 0 0 0 0 0 1.2e+05 \
0.00083333 800 200 0 1 "" red blue "" 22 -23 0
simundump kenz /kinetics/CELLDIV/Cdc20/Cdh1_Cdc20 0 0 0 0 0 1.2e+05 0.58333 \
560 140 0 1 "" red 51 "" -12 -20 0
simundump group /kinetics/CELLDIV/Cdh1_grp 0 16 black x 0 0 "" Cdh1_grp \
defaultfile.g 0 0 0 -13 -17 0
simundump kpool /kinetics/CELLDIV/Cdh1_grp/Cdh1_i 0 0 1 1 1.2e+05 1.2e+05 0 0 \
1.2e+05 0 /kinetics/geometry 0 16 -14 -21 0
simundump kenz /kinetics/CELLDIV/Cdh1_grp/Cdh1_i/Cdh1_i_k2_prime 0 0 0 0 0 \
1.2e+05 2.0833e-06 20 5 0 1 "" red 0 "" 22 5 0
simundump kpool /kinetics/CELLDIV/Cdh1_grp/Cdh1 0 0 0 0 0 0 0 0 1.2e+05 0 \
/kinetics/geometry 62 16 -10 -21 0
simundump kenz /kinetics/CELLDIV/Cdh1_grp/Cdh1/Cdh1_k2 0 0 0 0 0 1.2e+05 \
0.00083333 8000 2000 0 1 "" red 62 "" 20 -2 0
simundump kpool /kinetics/CELLDIV/Cdh1_grp/k3_prime 0 0 1 1 1.2e+05 1.2e+05 0 \
0 1.2e+05 0 /kinetics/geometry 4 16 -14 -19 0
simundump kenz /kinetics/CELLDIV/Cdh1_grp/k3_prime/k3_prime 0 0 0 0 0 1.2e+05 \
0.03125 30 7.5 0 1 "" red 4 "" -12 -19 0
simundump group /kinetics/CELLDIV/E2F 0 darkblue black x 0 0 "" E2F \
defaultfile.g 0 0 0 -16 -3 0
simundump kreac /kinetics/CELLDIV/E2F/k22_23_prime 0 1 0.005 "" white \
darkblue -11 -5 0
simundump kpool /kinetics/CELLDIV/E2F/E2FA.Rb 0 0 0 0 0 0 0 0 1.2e+05 0 \
/kinetics/geometry 8 darkblue -14 -12 0
simundump kreac /kinetics/CELLDIV/E2F/k22_23_prime.Rb 0 1 0.005 "" white \
darkblue -11 -13 0
simundump kpool /kinetics/CELLDIV/E2F/E2FAP 0 0 0 0 0 0 0 0 1.2e+05 0 \
/kinetics/geometry 46 darkblue -8 -6 0
simundump kpool /kinetics/CELLDIV/E2F/E2FAP.Rb 0 0 0 0 0 0 0 0 1.2e+05 0 \
/kinetics/geometry 52 darkblue -8 -12 0
simundump kreac /kinetics/CELLDIV/E2F/k26 0 8.3333e-05 200 "" white darkblue \
-16 -9 0
simundump kreac /kinetics/CELLDIV/E2F/k26_P 0 8.3333e-05 200 "" white \
darkblue -6 -9 0
simundump kpool /kinetics/CELLDIV/E2FA 0 0 5 5 6e+05 6e+05 0 0 1.2e+05 0 \
/kinetics/geometry 6 black -14 -6 0
simundump kenz /kinetics/CELLDIV/E2FA/k29 0 0 0 0 0 1.2e+05 2.0833e-06 200 50 \
0 1 "" red 6 "" 20 -15 0
simundump kenz /kinetics/CELLDIV/E2FA/k7 0 0 0 0 0 1.2e+05 5e-05 4.8 1.2 0 1 \
"" red 6 "" 2 -15 0
simundump group /kinetics/CELLDIV/CycB_Grp 0 3 black x 0 0 "" CycB_Grp \
defaultfile.g 0 0 0 18 5 0
simundump kreac /kinetics/CELLDIV/CycB_Grp/dimerize 0 8.3333e-05 10 "" white \
3 20 3 0
simundump kpool /kinetics/CELLDIV/CycB_Grp/AminoAcids 0 0 1 1 1.2e+05 1.2e+05 \
0 0 1.2e+05 4 /kinetics/geometry 52 3 16 -1 0
simundump kreac /kinetics/CELLDIV/CycB_Grp/k1_prime 0 0.1 0 "" white 3 18 0 0
simundump kpool /kinetics/CELLDIV/CycB_Grp/degraded 0 0 0 0 0 0 0 0 1.2e+05 0 \
/kinetics/geometry 26 3 24 1 0
simundump kpool /kinetics/CELLDIV/CycB_Grp/CycB_dup 0 0 0 0 0 0 0 0 1.2e+05 0 \
/kinetics/geometry blue 3 22 2 0
simundump kpool /kinetics/CELLDIV/CycB_Grp/CycB_synth 0 0 1 1 1.2e+05 1.2e+05 \
0 0 1.2e+05 4 /kinetics/geometry 6 3 16 1 0
simundump kenz /kinetics/CELLDIV/CycB_Grp/CycB_synth/k1 0 0 0 0 0 1.2e+05 \
0.0025 2.4 0.6 0 1 "" red 6 "" 18 1 0
simundump kpool /kinetics/CELLDIV/CycB_Grp/CycB_dimer 0 0 0 0 0 0 0 0 1.2e+05 \
0 /kinetics/geometry blue 3 16 3 0
simundump kpool /kinetics/CELLDIV/Kip1 0 0 0 0 0 0 0 0 1.2e+05 0 \
/kinetics/geometry 30 black 12 -13 0
simundump group /kinetics/CELLDIV/CycA_Grp 0 3 black x 0 1 "" CycA_Grp \
defaultfile.g 0 0 0 21 -9 0
simundump kreac /kinetics/CELLDIV/CycA_Grp/k_prime6 0 10 0 "" white 3 22 -17 \
0
simundump kreac /kinetics/CELLDIV/CycA_Grp/k25 0 0.0083333 10 "" white 3 18 \
-17 0
simundump kpool /kinetics/CELLDIV/CycA_Grp/CycA_Kip1 0 0 0 0 0 0 0 0 1.2e+05 \
0 /kinetics/geometry 21 3 20 -18 0
simundump kreac /kinetics/CELLDIV/CycA_Grp/k5 0 20 0 "" white 3 14 -11 0
simundump kpool /kinetics/CELLDIV/CycA_Grp/AminoAcids 0 0 1 1 1.2e+05 1.2e+05 \
0 0 1.2e+05 4 /kinetics/geometry 51 3 16 -13 0
simundump kpool /kinetics/CELLDIV/CycA_Grp/degraded 0 0 0 0 0 0 0 0 1.2e+05 4 \
/kinetics/geometry 26 3 24 -16 0
simundump kreac /kinetics/CELLDIV/CycA_Grp/k_prime_6_kip1 0 10 0 "" white 3 \
11 -7 0
simundump kpool /kinetics/CELLDIV/CycA_Grp/degraded_kip 0 0 0 0 0 0 0 0 \
1.2e+05 4 /kinetics/geometry blue 3 18 -5 0
simundump kpool /kinetics/CELLDIV/Mass_dup 0 0 0 1 1.2e+05 0 0 0 1.2e+05 0 \
/kinetics/geometry 53 yellow 16 -16 0
simundump group /kinetics/CELLDIV/CycE_grp 0 8 black x 0 0 "" CycE_grp \
defaultfile.g 0 0 0 0 -10 0
simundump kreac /kinetics/CELLDIV/CycE_grp/k25 0 0.0083333 10 "" white 8 0 \
-17 0
simundump kpool /kinetics/CELLDIV/CycE_grp/CycE_Kip1 0 0 0 0 0 0 0 0 1.2e+05 \
0 /kinetics/geometry 21 8 2 -18 0
simundump kreac /kinetics/CELLDIV/CycE_grp/k_prime7 0 0 0 "" white 8 0 -12 0
simundump kreac /kinetics/CELLDIV/CycE_grp/k_prime6 0 10 0 "" white 8 4 -17 0
simundump kpool /kinetics/CELLDIV/CycE_grp/AminoAcids 0 0 1 1 1.2e+05 1.2e+05 \
0 0 1.2e+05 4 /kinetics/geometry 52 8 -2 -16 0
simundump kpool /kinetics/CELLDIV/CycE_grp/degraded 0 0 0 0 0 0 0 0 1.2e+05 4 \
/kinetics/geometry 26 8 6 -16 0
simundump kreac /kinetics/CELLDIV/CycE_grp/k_prime_8 0 0.1 0 "" white 8 4 -11 \
0
simundump kreac /kinetics/CELLDIV/CycE_grp/k_prime_8_kip1 0 0.1 0 "" white 8 \
4 -27 0
simundump kpool /kinetics/CELLDIV/DRG 0 0 0 0 0 0 0 0 1.2e+05 0 \
/kinetics/geometry 6 black -10 4 0
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addmsg /kinetics/CELLDIV/Cdh1_grp/Cdh1/Cdh1_k2 /kinetics/CELLDIV/CycB REAC sA B
addmsg /kinetics/CELLDIV/Cdh1_grp/Cdh1_i/Cdh1_i_k2_prime /kinetics/CELLDIV/CycB REAC sA B
addmsg /kinetics/CELLDIV/CycB /kinetics/CELLDIV/CycB/k20_lambdaB ENZYME n
addmsg /kinetics/CELLDIV/Rb /kinetics/CELLDIV/CycB/k20_lambdaB SUBSTRATE n
addmsg /kinetics/CELLDIV/CycB /kinetics/CELLDIV/CycB/k21_phiB ENZYME n
addmsg /kinetics/CELLDIV/Rb_grp/PP1A /kinetics/CELLDIV/CycB/k21_phiB SUBSTRATE n
addmsg /kinetics/CELLDIV/CycB /kinetics/CELLDIV/CycB/k31 ENZYME n
addmsg /kinetics/CELLDIV/IE_GRP/IE /kinetics/CELLDIV/CycB/k31 SUBSTRATE n
addmsg /kinetics/CELLDIV/CycB /kinetics/CELLDIV/CycB/k11 ENZYME n
addmsg /kinetics/CELLDIV/Cdc20_Grp/AminoAcids /kinetics/CELLDIV/CycB/k11 SUBSTRATE n
addmsg /kinetics/CELLDIV/CycB /kinetics/CELLDIV/CycB/Cdh1_CycB ENZYME n
addmsg /kinetics/CELLDIV/Cdh1_grp/Cdh1 /kinetics/CELLDIV/CycB/Cdh1_CycB SUBSTRATE n
addmsg /kinetics/CELLDIV/CycB /kinetics/CELLDIV/CycB/B_phosph_E2FA ENZYME n
addmsg /kinetics/CELLDIV/E2FA /kinetics/CELLDIV/CycB/B_phosph_E2FA SUBSTRATE n
addmsg /kinetics/CELLDIV/CycB /kinetics/CELLDIV/CycB/B_phosph_E2FA.Rb ENZYME n
addmsg /kinetics/CELLDIV/E2F/E2FA.Rb /kinetics/CELLDIV/CycB/B_phosph_E2FA.Rb SUBSTRATE n
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addmsg /kinetics/CELLDIV/CycA_Grp/CycA_Kip1 /kinetics/CELLDIV/CycB/Ak6_etaB SUBSTRATE n
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addmsg /kinetics/CELLDIV/CycE /kinetics/CELLDIV/CycB/k8_CycB SUBSTRATE n
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addmsg /kinetics/CELLDIV/CycE_grp/CycE_Kip1 /kinetics/CELLDIV/CycB/k6_E_etaB SUBSTRATE n
addmsg /kinetics/CELLDIV/CycB /kinetics/CELLDIV/CycB/k6_D_etaB ENZYME n
addmsg /kinetics/CELLDIV/CycD_Grp/CycD_Kip1 /kinetics/CELLDIV/CycB/k6_D_etaB SUBSTRATE n
addmsg /kinetics/CELLDIV/CycB /kinetics/CELLDIV/CycB/k8_CycB_Kip1 ENZYME n
addmsg /kinetics/CELLDIV/CycE_grp/CycE_Kip1 /kinetics/CELLDIV/CycB/k8_CycB_Kip1 SUBSTRATE n
addmsg /kinetics/CELLDIV/CycB /kinetics/CELLDIV/CycB/k6_kip1_B ENZYME n
addmsg /kinetics/CELLDIV/Kip1 /kinetics/CELLDIV/CycB/k6_kip1_B SUBSTRATE n
addmsg /kinetics/CELLDIV/CycB /kinetics/CELLDIV/CycB/k20_lambdaB[1] ENZYME n
addmsg /kinetics/CELLDIV/E2F/E2FAP.Rb /kinetics/CELLDIV/CycB/k20_lambdaB[1] SUBSTRATE n
addmsg /kinetics/CELLDIV/CycB /kinetics/CELLDIV/CycB/k20_lambdaB[2] ENZYME n
addmsg /kinetics/CELLDIV/E2F/E2FA.Rb /kinetics/CELLDIV/CycB/k20_lambdaB[2] SUBSTRATE n
addmsg /kinetics/CELLDIV/IE_GRP/AminoAcids /kinetics/CELLDIV/IE_GRP/k33 SUBSTRATE n
addmsg /kinetics/CELLDIV/IE_GRP/PPX /kinetics/CELLDIV/IE_GRP/k33 PRODUCT n
addmsg /kinetics/CELLDIV/IE_GRP/degraded /kinetics/CELLDIV/IE_GRP/k34 PRODUCT n
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addmsg /kinetics/CELLDIV/IE_GRP/PPX /kinetics/CELLDIV/IE_GRP/PPX/k32 ENZYME n
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addmsg /kinetics/CELLDIV/Cdc20_Grp/degraded /kinetics/CELLDIV/Cdc20_Grp/k12 PRODUCT n
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addmsg /kinetics/CELLDIV/Cdc20_Grp/k12A /kinetics/CELLDIV/Cdc20_Grp/degraded REAC B A
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addmsg /kinetics/CELLDIV/Cdc20_Grp/k12A /kinetics/CELLDIV/Cdc20_Grp/Cdc20notA REAC A B
addmsg /kinetics/CELLDIV/CycB/k11 /kinetics/CELLDIV/Cdc20_Grp/Cdc20notA MM_PRD pA
addmsg /kinetics/CELLDIV/Cdc20_Grp/k11_prime /kinetics/CELLDIV/Cdc20_Grp/Cdc20notA REAC B A
addmsg /kinetics/CELLDIV/Cdc20_Grp/k12 /kinetics/CELLDIV/Cdc20 REAC A B
addmsg /kinetics/CELLDIV/IEP/k13 /kinetics/CELLDIV/Cdc20 MM_PRD pA
addmsg /kinetics/CELLDIV/Cdc20_Grp/k14_enz/k14 /kinetics/CELLDIV/Cdc20 REAC sA B
addmsg /kinetics/CELLDIV/Cdc20 /kinetics/CELLDIV/Cdc20/k2_prime_prime ENZYME n
addmsg /kinetics/CELLDIV/CycB /kinetics/CELLDIV/Cdc20/k2_prime_prime SUBSTRATE n
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addmsg /kinetics/CELLDIV/Cdc20 /kinetics/CELLDIV/Cdc20/Cdc20_deg_CycA_Kip1 ENZYME n
addmsg /kinetics/CELLDIV/CycA_Grp/CycA_Kip1 /kinetics/CELLDIV/Cdc20/Cdc20_deg_CycA_Kip1 SUBSTRATE n
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addmsg /kinetics/CELLDIV/Cdc20/Cdh1_Cdc20 /kinetics/CELLDIV/Cdh1_grp/Cdh1_i REAC sA B
addmsg /kinetics/CELLDIV/CycA/Cdh1_CycA /kinetics/CELLDIV/Cdh1_grp/Cdh1_i MM_PRD pA
addmsg /kinetics/CELLDIV/CycB/Cdh1_CycB /kinetics/CELLDIV/Cdh1_grp/Cdh1_i MM_PRD pA
addmsg /kinetics/CELLDIV/Cdh1_grp/Cdh1_i /kinetics/CELLDIV/Cdh1_grp/Cdh1_i/Cdh1_i_k2_prime ENZYME n
addmsg /kinetics/CELLDIV/CycB /kinetics/CELLDIV/Cdh1_grp/Cdh1_i/Cdh1_i_k2_prime SUBSTRATE n
addmsg /kinetics/CELLDIV/Cdh1_grp/k3_prime/k3_prime /kinetics/CELLDIV/Cdh1_grp/Cdh1 MM_PRD pA
addmsg /kinetics/CELLDIV/Cdc20/Cdh1_Cdc20 /kinetics/CELLDIV/Cdh1_grp/Cdh1 MM_PRD pA
addmsg /kinetics/CELLDIV/CycA/Cdh1_CycA /kinetics/CELLDIV/Cdh1_grp/Cdh1 REAC sA B
addmsg /kinetics/CELLDIV/CycB/Cdh1_CycB /kinetics/CELLDIV/Cdh1_grp/Cdh1 REAC sA B
addmsg /kinetics/CELLDIV/Cdh1_grp/Cdh1 /kinetics/CELLDIV/Cdh1_grp/Cdh1/Cdh1_k2 ENZYME n
addmsg /kinetics/CELLDIV/CycB /kinetics/CELLDIV/Cdh1_grp/Cdh1/Cdh1_k2 SUBSTRATE n
addmsg /kinetics/CELLDIV/Cdh1_grp/k3_prime /kinetics/CELLDIV/Cdh1_grp/k3_prime/k3_prime ENZYME n
addmsg /kinetics/CELLDIV/Cdh1_grp/Cdh1_i /kinetics/CELLDIV/Cdh1_grp/k3_prime/k3_prime SUBSTRATE n
addmsg /kinetics/CELLDIV/E2F/E2FAP /kinetics/CELLDIV/E2F/k22_23_prime SUBSTRATE n
addmsg /kinetics/CELLDIV/E2FA /kinetics/CELLDIV/E2F/k22_23_prime PRODUCT n
addmsg /kinetics/CELLDIV/CycB/B_phosph_E2FA.Rb /kinetics/CELLDIV/E2F/E2FA.Rb REAC sA B
addmsg /kinetics/CELLDIV/CycA/A_phosph_E2FA.Rb /kinetics/CELLDIV/E2F/E2FA.Rb REAC sA B
addmsg /kinetics/CELLDIV/E2F/k22_23_prime.Rb /kinetics/CELLDIV/E2F/E2FA.Rb REAC B A
addmsg /kinetics/CELLDIV/E2F/k26 /kinetics/CELLDIV/E2F/E2FA.Rb REAC B A
addmsg /kinetics/CELLDIV/CycA/k20_lambdaA[2] /kinetics/CELLDIV/E2F/E2FA.Rb REAC sA B
addmsg /kinetics/CELLDIV/CycB/k20_lambdaB[2] /kinetics/CELLDIV/E2F/E2FA.Rb REAC sA B
addmsg /kinetics/CELLDIV/CycE/k20_lambdaE[2] /kinetics/CELLDIV/E2F/E2FA.Rb REAC sA B
addmsg /kinetics/CELLDIV/CycD/k20_lambdaD[2] /kinetics/CELLDIV/E2F/E2FA.Rb REAC sA B
addmsg /kinetics/CELLDIV/E2F/E2FAP.Rb /kinetics/CELLDIV/E2F/k22_23_prime.Rb SUBSTRATE n
addmsg /kinetics/CELLDIV/E2F/E2FA.Rb /kinetics/CELLDIV/E2F/k22_23_prime.Rb PRODUCT n
addmsg /kinetics/CELLDIV/E2F/k22_23_prime /kinetics/CELLDIV/E2F/E2FAP REAC A B
addmsg /kinetics/CELLDIV/CycB/B_phosph_E2FA /kinetics/CELLDIV/E2F/E2FAP MM_PRD pA
addmsg /kinetics/CELLDIV/CycA/A_phosph_E2F /kinetics/CELLDIV/E2F/E2FAP MM_PRD pA
addmsg /kinetics/CELLDIV/E2F/k26_P /kinetics/CELLDIV/E2F/E2FAP REAC A B
addmsg /kinetics/CELLDIV/CycA/k20_lambdaA[1] /kinetics/CELLDIV/E2F/E2FAP MM_PRD pA
addmsg /kinetics/CELLDIV/CycB/k20_lambdaB[1] /kinetics/CELLDIV/E2F/E2FAP MM_PRD pA
addmsg /kinetics/CELLDIV/CycE/k20_lambdaE[1] /kinetics/CELLDIV/E2F/E2FAP MM_PRD pA
addmsg /kinetics/CELLDIV/CycD/k20_lambdaD[1] /kinetics/CELLDIV/E2F/E2FAP MM_PRD pA
addmsg /kinetics/CELLDIV/CycB/B_phosph_E2FA.Rb /kinetics/CELLDIV/E2F/E2FAP.Rb MM_PRD pA
addmsg /kinetics/CELLDIV/CycA/A_phosph_E2FA.Rb /kinetics/CELLDIV/E2F/E2FAP.Rb MM_PRD pA
addmsg /kinetics/CELLDIV/E2F/k22_23_prime.Rb /kinetics/CELLDIV/E2F/E2FAP.Rb REAC A B
addmsg /kinetics/CELLDIV/E2F/k26_P /kinetics/CELLDIV/E2F/E2FAP.Rb REAC B A
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addmsg /kinetics/CELLDIV/CycB/k20_lambdaB[1] /kinetics/CELLDIV/E2F/E2FAP.Rb REAC sA B
addmsg /kinetics/CELLDIV/CycE/k20_lambdaE[1] /kinetics/CELLDIV/E2F/E2FAP.Rb REAC sA B
addmsg /kinetics/CELLDIV/CycD/k20_lambdaD[1] /kinetics/CELLDIV/E2F/E2FAP.Rb REAC sA B
addmsg /kinetics/CELLDIV/Rb /kinetics/CELLDIV/E2F/k26 SUBSTRATE n
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addmsg /kinetics/CELLDIV/E2F/E2FA.Rb /kinetics/CELLDIV/E2F/k26 PRODUCT n
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addmsg /kinetics/CELLDIV/E2F/E2FAP /kinetics/CELLDIV/E2F/k26_P SUBSTRATE n
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addmsg /kinetics/CELLDIV/CycA/A_phosph_E2F /kinetics/CELLDIV/E2FA REAC sA B
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addmsg /kinetics/CELLDIV/CycE/k20_lambdaE[2] /kinetics/CELLDIV/E2FA MM_PRD pA
addmsg /kinetics/CELLDIV/CycD/k20_lambdaD[2] /kinetics/CELLDIV/E2FA MM_PRD pA
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addmsg /kinetics/CELLDIV/Cdh1_grp/Cdh1_i/Cdh1_i_k2_prime /kinetics/CELLDIV/CycB_Grp/degraded MM_PRD pA
addmsg /kinetics/CELLDIV/CycB /kinetics/CELLDIV/CycB_Grp/CycB_dup SUMTOTAL n nInit
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addmsg /kinetics/CELLDIV/CycA_Grp/k25 /kinetics/CELLDIV/Kip1 REAC A B
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addmsg /kinetics/CELLDIV/CycE/k8_CycE_Kip1 /kinetics/CELLDIV/Kip1 MM_PRD pA
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addmsg /kinetics/CELLDIV/CycA/k8_CycA_Kip1 /kinetics/CELLDIV/Kip1 MM_PRD pA
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addmsg /kinetics/CELLDIV/CycE_grp/k_prime_8_kip1 /kinetics/CELLDIV/Kip1 REAC B A
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addmsg /kinetics/CELLDIV/CycA_Grp/CycA_Kip1 /kinetics/CELLDIV/CycA_Grp/k25 PRODUCT n
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addmsg /kinetics/CELLDIV/CycA_Grp/k_prime6 /kinetics/CELLDIV/CycA_Grp/CycA_Kip1 REAC A B
addmsg /kinetics/CELLDIV/CycE/Ak6_etaE /kinetics/CELLDIV/CycA_Grp/CycA_Kip1 REAC sA B
addmsg /kinetics/CELLDIV/CycA/Ak6_etaA /kinetics/CELLDIV/CycA_Grp/CycA_Kip1 REAC sA B
addmsg /kinetics/CELLDIV/CycB/Ak6_etaB /kinetics/CELLDIV/CycA_Grp/CycA_Kip1 REAC sA B
addmsg /kinetics/CELLDIV/Cdc20/Cdc20_deg_CycA_Kip1 /kinetics/CELLDIV/CycA_Grp/CycA_Kip1 REAC sA B
addmsg /kinetics/CELLDIV/CycA_Grp/AminoAcids /kinetics/CELLDIV/CycA_Grp/k5 SUBSTRATE n
addmsg /kinetics/CELLDIV/Kip1 /kinetics/CELLDIV/CycA_Grp/k5 PRODUCT n
addmsg /kinetics/CELLDIV/CycA_Grp/k5 /kinetics/CELLDIV/CycA_Grp/AminoAcids REAC A B
addmsg /kinetics/CELLDIV/CycA_Grp/k_prime6 /kinetics/CELLDIV/CycA_Grp/degraded REAC B A
addmsg /kinetics/CELLDIV/CycE/Ak6_etaE /kinetics/CELLDIV/CycA_Grp/degraded MM_PRD pA
addmsg /kinetics/CELLDIV/CycA/Ak6_etaA /kinetics/CELLDIV/CycA_Grp/degraded MM_PRD pA
addmsg /kinetics/CELLDIV/CycB/Ak6_etaB /kinetics/CELLDIV/CycA_Grp/degraded MM_PRD pA
addmsg /kinetics/CELLDIV/Cdc20/Cdc20_deg_CycA /kinetics/CELLDIV/CycA_Grp/degraded MM_PRD pA
addmsg /kinetics/CELLDIV/Cdc20/Cdc20_deg_CycA_Kip1 /kinetics/CELLDIV/CycA_Grp/degraded MM_PRD pA
addmsg /kinetics/CELLDIV/Kip1 /kinetics/CELLDIV/CycA_Grp/k_prime_6_kip1 SUBSTRATE n
addmsg /kinetics/CELLDIV/CycA_Grp/degraded_kip /kinetics/CELLDIV/CycA_Grp/k_prime_6_kip1 PRODUCT n
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addmsg /kinetics/CELLDIV/CycB/k6_kip1_B /kinetics/CELLDIV/CycA_Grp/degraded_kip MM_PRD pA
addmsg /kinetics/CELLDIV/CycE/k6_kip1_E /kinetics/CELLDIV/CycA_Grp/degraded_kip MM_PRD pA
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addmsg /kinetics/CELLDIV/E2FA/k29 /kinetics/CELLDIV/Mass_dup REAC sA B
addmsg /kinetics/CELLDIV/Growth/mass /kinetics/CELLDIV/Mass_dup SUMTOTAL n nInit
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addmsg /kinetics/CELLDIV/CycE /kinetics/CELLDIV/CycE_grp/k25 SUBSTRATE n
addmsg /kinetics/CELLDIV/CycE_grp/CycE_Kip1 /kinetics/CELLDIV/CycE_grp/k25 PRODUCT n
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addmsg /kinetics/CELLDIV/CycE_grp/k_prime_8_kip1 /kinetics/CELLDIV/CycE_grp/degraded REAC B A
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addmsg /kinetics/CELLDIV/Delayed_Response_Genes/DRG_synth/DRG_synth /kinetics/CELLDIV/DRG MM_PRD pA
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addmsg /kinetics/CELLDIV/Early_Response_Genes/k16 /kinetics/CELLDIV/ERG REAC A B
addmsg /kinetics/CELLDIV/Early_Response_Genes/ERG_synth/ERG_synth /kinetics/CELLDIV/ERG MM_PRD pA
addmsg /kinetics/CELLDIV/ERG /kinetics/CELLDIV/ERG/k_prime_17 ENZYME n
addmsg /kinetics/CELLDIV/Early_Response_Genes/AminoAcids /kinetics/CELLDIV/ERG/k_prime_17 SUBSTRATE n
addmsg /kinetics/CELLDIV/Early_Response_Genes/DRG2_bind_ERG_synth /kinetics/CELLDIV/Early_Response_Genes/ERG_synth REAC A B
addmsg /kinetics/CELLDIV/Early_Response_Genes/ERG_synth /kinetics/CELLDIV/Early_Response_Genes/ERG_synth/ERG_synth ENZYME n
addmsg /kinetics/CELLDIV/Early_Response_Genes/AminoAcids /kinetics/CELLDIV/Early_Response_Genes/ERG_synth/ERG_synth SUBSTRATE n
addmsg /kinetics/CELLDIV/ERG /kinetics/CELLDIV/Early_Response_Genes/k16 SUBSTRATE n
addmsg /kinetics/CELLDIV/Early_Response_Genes/degraded /kinetics/CELLDIV/Early_Response_Genes/k16 PRODUCT n
addmsg /kinetics/CELLDIV/Early_Response_Genes/k16 /kinetics/CELLDIV/Early_Response_Genes/degraded REAC B A
addmsg /kinetics/CELLDIV/Early_Response_Genes/DRG2_bind_ERG_synth /kinetics/CELLDIV/Early_Response_Genes/inhib_ERG_synth REAC B A
addmsg /kinetics/CELLDIV/ERG/k_prime_17 /kinetics/CELLDIV/Early_Response_Genes/AminoAcids REAC sA B
addmsg /kinetics/CELLDIV/Early_Response_Genes/ERG_synth/ERG_synth /kinetics/CELLDIV/Early_Response_Genes/AminoAcids REAC sA B
addmsg /kinetics/CELLDIV/Early_Response_Genes/ERG_synth /kinetics/CELLDIV/Early_Response_Genes/DRG2_bind_ERG_synth SUBSTRATE n
addmsg /kinetics/CELLDIV/Early_Response_Genes/inhib_ERG_synth /kinetics/CELLDIV/Early_Response_Genes/DRG2_bind_ERG_synth PRODUCT n
addmsg /kinetics/CELLDIV/Early_Response_Genes/DRG_2B /kinetics/CELLDIV/Early_Response_Genes/DRG2_bind_ERG_synth SUBSTRATE n
addmsg /kinetics/CELLDIV/Delayed_Response_Genes/DRG_2 /kinetics/CELLDIV/Early_Response_Genes/DRG_2B SUMTOTAL n nInit
addmsg /kinetics/CELLDIV/Early_Response_Genes/DRG2_bind_ERG_synth /kinetics/CELLDIV/Early_Response_Genes/DRG_2B REAC A B
addmsg /kinetics/CELLDIV/Delayed_Response_Genes/k18 /kinetics/CELLDIV/Delayed_Response_Genes/degraded REAC B A
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addmsg /kinetics/CELLDIV/Delayed_Response_Genes/DRG_2A /kinetics/CELLDIV/Delayed_Response_Genes/DRG_synth/DRG_synth SUBSTRATE n
addmsg /kinetics/CELLDIV/Delayed_Response_Genes/degraded /kinetics/CELLDIV/Delayed_Response_Genes/k18 PRODUCT n
addmsg /kinetics/CELLDIV/DRG /kinetics/CELLDIV/Delayed_Response_Genes/k18 SUBSTRATE n
addmsg /kinetics/CELLDIV/DRG /kinetics/CELLDIV/Delayed_Response_Genes/DRG_dup SUMTOTAL n nInit
addmsg /kinetics/CELLDIV/Delayed_Response_Genes/DRG_dimerize /kinetics/CELLDIV/Delayed_Response_Genes/DRG_dup REAC A B
addmsg /kinetics/CELLDIV/Delayed_Response_Genes/DRG_dimerize /kinetics/CELLDIV/Delayed_Response_Genes/DRG_dup REAC A B
addmsg /kinetics/CELLDIV/Delayed_Response_Genes/DRG_dimerize /kinetics/CELLDIV/Delayed_Response_Genes/DRG_2 REAC B A
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addmsg /kinetics/CELLDIV/Delayed_Response_Genes/DRG_dup /kinetics/CELLDIV/Delayed_Response_Genes/DRG_dimerize SUBSTRATE n
addmsg /kinetics/CELLDIV/Delayed_Response_Genes/DRG_2 /kinetics/CELLDIV/Delayed_Response_Genes/DRG_dimerize PRODUCT n
addmsg /kinetics/CELLDIV/Delayed_Response_Genes/DRG_2 /kinetics/CELLDIV/Delayed_Response_Genes/DRG_2A SUMTOTAL n nInit
addmsg /kinetics/CELLDIV/Delayed_Response_Genes/DRG_synth/DRG_synth /kinetics/CELLDIV/Delayed_Response_Genes/DRG_2A REAC sA B
addmsg /kinetics/CELLDIV/CycD /kinetics/CELLDIV/CycD_Grp/k10 SUBSTRATE n
addmsg /kinetics/CELLDIV/CycD_Grp/degraded /kinetics/CELLDIV/CycD_Grp/k10 PRODUCT n
addmsg /kinetics/CELLDIV/CycD_Grp/k24 /kinetics/CELLDIV/CycD_Grp/CycD_Kip1 REAC B A
addmsg /kinetics/CELLDIV/CycD_Grp/k_prime6 /kinetics/CELLDIV/CycD_Grp/CycD_Kip1 REAC A B
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addmsg /kinetics/CELLDIV/CycA/k6_D_etaA /kinetics/CELLDIV/CycD_Grp/CycD_Kip1 REAC sA B
addmsg /kinetics/CELLDIV/CycB/k6_D_etaB /kinetics/CELLDIV/CycD_Grp/CycD_Kip1 REAC sA B
addmsg /kinetics/CELLDIV/CycD_Grp/k10_b /kinetics/CELLDIV/CycD_Grp/CycD_Kip1 REAC A B
addmsg /kinetics/CELLDIV/Kip1 /kinetics/CELLDIV/CycD_Grp/k24 SUBSTRATE n
addmsg /kinetics/CELLDIV/CycD /kinetics/CELLDIV/CycD_Grp/k24 SUBSTRATE n
addmsg /kinetics/CELLDIV/CycD_Grp/CycD_Kip1 /kinetics/CELLDIV/CycD_Grp/k24 PRODUCT n
addmsg /kinetics/CELLDIV/CycD_Grp/CycD_Kip1 /kinetics/CELLDIV/CycD_Grp/k_prime6 SUBSTRATE n
addmsg /kinetics/CELLDIV/CycD_Grp/degraded /kinetics/CELLDIV/CycD_Grp/k_prime6 PRODUCT n
addmsg /kinetics/CELLDIV/CycD /kinetics/CELLDIV/CycD_Grp/k_prime6 PRODUCT n
addmsg /kinetics/CELLDIV/CycD_Grp/CycD_Kip1 /kinetics/CELLDIV/CycD_Grp/k10_b SUBSTRATE n
addmsg /kinetics/CELLDIV/CycD_Grp/degraded /kinetics/CELLDIV/CycD_Grp/k10_b PRODUCT n
addmsg /kinetics/CELLDIV/Kip1 /kinetics/CELLDIV/CycD_Grp/k10_b PRODUCT n
addmsg /kinetics/CELLDIV/DRG/k9 /kinetics/CELLDIV/CycD_Grp/AminoAcids REAC sA B
addmsg /kinetics/CELLDIV/CycD_Grp/k10 /kinetics/CELLDIV/CycD_Grp/degraded REAC B A
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addmsg /kinetics/CELLDIV/CycE/k6_D_etaE /kinetics/CELLDIV/CycD_Grp/degraded MM_PRD pA
addmsg /kinetics/CELLDIV/CycA/k6_D_etaA /kinetics/CELLDIV/CycD_Grp/degraded MM_PRD pA
addmsg /kinetics/CELLDIV/CycB/k6_D_etaB /kinetics/CELLDIV/CycD_Grp/degraded MM_PRD pA
addmsg /kinetics/CELLDIV/CycD_Grp/k10_b /kinetics/CELLDIV/CycD_Grp/degraded REAC B A
addmsg /kinetics/CELLDIV/CycE_grp/CycE_Kip1 /kinetics/CELLDIV/Tot_Kip1 SUMTOTAL n nInit
addmsg /kinetics/CELLDIV/Kip1 /kinetics/CELLDIV/Tot_Kip1 SUMTOTAL n nInit
addmsg /kinetics/CELLDIV/CycA_Grp/CycA_Kip1 /kinetics/CELLDIV/Tot_Kip1 SUMTOTAL n nInit
addmsg /kinetics/CELLDIV/CycD_Grp/CycD_Kip1 /kinetics/CELLDIV/Tot_Kip1 SUMTOTAL n nInit
addmsg /kinetics/CELLDIV/ERG /graphs/conc1/ERG.Co PLOT Co *ERG.Co *0
addmsg /kinetics/CELLDIV/DRG /graphs/conc1/DRG.Co PLOT Co *DRG.Co *9
addmsg /kinetics/CELLDIV/CycE /graphs/conc1/CycE.Co PLOT Co *CycE.Co *25
addmsg /kinetics/CELLDIV/CycD /graphs/conc1/CycD.Co PLOT Co *CycD.Co *blue
addmsg /kinetics/CELLDIV/CycB /graphs/conc1/CycB.Co PLOT Co *CycB.Co *29
addmsg /kinetics/CELLDIV/CycA /graphs/conc1/CycA.Co PLOT Co *CycA.Co *35
addmsg /kinetics/CELLDIV/CycB_Grp/CycB_dimer /graphs/conc1/CycB_dimer.Co PLOT Co *CycB_dimer.Co *blue
addmsg /kinetics/CELLDIV/Growth/mass /graphs/conc2/mass.Co PLOT Co *mass.Co *blue
addmsg /kinetics/CELLDIV/Kip1 /graphs/conc2/Kip1.Co PLOT Co *Kip1.Co *30
addmsg /kinetics/CELLDIV/Cdh1_grp/Cdh1 /graphs/conc2/Cdh1.Co PLOT Co *Cdh1.Co *62
addmsg /kinetics/CELLDIV/E2FA /graphs/conc2/E2FA.Co PLOT Co *E2FA.Co *6
addmsg /kinetics/CELLDIV/CycB_Grp/CycB_dimer /graphs/conc2/CycB_dimer.Co PLOT Co *CycB_dimer.Co *blue
addmsg /kinetics/CELLDIV/Tot_Kip1 /graphs/conc2/Tot_Kip1.Co PLOT Co *Tot_Kip1.Co *47
addmsg /kinetics/CELLDIV/Rb /moregraphs/conc3/Rb.Co PLOT Co *Rb.Co *22
addmsg /kinetics/CELLDIV/Cdc20 /moregraphs/conc4/Cdc20.Co PLOT Co *Cdc20.Co *blue
addmsg /kinetics/CELLDIV/Growth/Heaviside_inh /moregraphs/conc4/Heaviside_inh.Co PLOT Co *Heaviside_inh.Co *53
addmsg /kinetics/CELLDIV/IEP /moregraphs/conc4/IEP.Co PLOT Co *IEP.Co *61
addmsg /kinetics/CELLDIV/Cdc20_Grp/Cdc20notA /moregraphs/conc4/Cdc20notA.Co PLOT Co *Cdc20notA.Co *47
addmsg /kinetics/CELLDIV/DRG /moregraphs/conc4/DRG.Co PLOT Co *DRG.Co *6
enddump
// End of dump
call /kinetics/CELLDIV/Growth/mass/k27/notes LOAD \
"Equation 17" \
"" \
"dGM/dt = k27 * mass * Heaviside_out. k27 = 0.2" \
"If k3 << k2, we have ES ~ E.S.k1/k2" \
"and rate = k3 * ES." \
"So we assume k2 = 1, k3 = 0.1, then k1 = 10 * k27 " \
"so k1 = 2." \
"This gives a rather low Km, leading to much complex formation." \
"Let us use MM form, and assume Km >> Heaviside_out." \
"Take Km = 10, then kcat = Km * k27 = 2" \
"" \
""
call /kinetics/CELLDIV/Growth/GM/notes LOAD \
"Stands for General Machinery, presumably for synthesis."
call /kinetics/CELLDIV/Growth/GM/mu/notes LOAD \
"Rate = E.S.kcat/(Km + S)" \
"We want to represent" \
"dmass/dt = epsilon.mu.GM. " \
"Epsilon is 1 for now." \
"mu = 0.061" \
"" \
"S here is AA, buffered to 1. We assign Km = 1 for simplicity." \
"Then kcat = 2 * mu = 0.122" \
""
call /kinetics/CELLDIV/Growth/k28/notes LOAD \
"k28 = 0.2" \
""
call /kinetics/CELLDIV/Growth/H1/notes LOAD \
"This reaction approximates the Heaviside function." \
"What it does is to present a high-order dependence on" \
"Rb_P, such that when Rb_P is about 0.8 of the total" \
"" \
"It is supposed to be 1 if Rb_hypo <= 0.8 Rb_tot." \
"Here we have Rb_P = Rb_tot - Rb_hypo, so we want the" \
"outcome to be 1 if Rb_P > 0.2" \
"We use a 4th order step to get a sharper transition." \
"Use a sumtotal so that Rb_P itself is not affected." \
"" \
"29 March 2005." \
"Now this is part of a 2-step heaviside function, perhaps" \
"more biologically motivated. Also the input is Rb." \
"" \
"18 Apr 2005." \
"Speeded up 10 fold. Also note that the critical amount of" \
"Rb is Rb/Rbtot. Since Rbtot = 10, the Kd should be 8," \
"not 0.8." \
"" \
""
call /kinetics/CELLDIV/Rb_grp/k21b/notes LOAD \
"A dummy back reaction, implicit in the form of equation 19" \
"" \
"18 Apr 2005. Speeded up 10x."
call /kinetics/CELLDIV/Rb_grp/PP1/k19_prime/notes LOAD \
"k19_prime is actually zero, but I do not want NaNs" \
"(numerical errors due to divide-by-zero) so I set" \
"kcat to a very small value." \
"7 Apr 2005. " \
"Same reasoning, now set Km to 10." \
""
call /kinetics/CELLDIV/Rb_grp/PP1A/k19/notes LOAD \
"This is part of Eqn 20. k19 = 20." \
"It is meant to represent a dephosph step of Rb_p." \
"rate is k19*PP1A." \
"rate in MM form is kcat * PP1A * Rb_P / (Km + Rb_P)" \
"Assume Km << Rb_P. To do so, Km = 0.01" \
"Then kcat = k19." \
"7 Apr 2005. Actually should include substrate term. Take" \
"Km = 10 >> sub. Then" \
"kcat = Km * k19 = 200" \
"18 April. Actually substrate levels are near 10. So need" \
"to scale up." \
"Km = 100, kcat = Km * k19 = 2000" \
""
call /kinetics/CELLDIV/Rb/notes LOAD \
"Rbtot = 10, assigned to CoInit"
call /kinetics/CELLDIV/CycD/k20_lambdaD/notes LOAD \
"With a low Km, rate ~ kcat. Here we have" \
"rate = k20 * lambda_d = 10 * 3.3 = 33." \
"7 Apr 2005." \
"Actually should have the substrate term in here." \
"Use the form Km >> substrate, so " \
"rate = kcat * sub * enz / Km" \
"so kcat = Km * k20 * lambda_d = 10 * 10 * 3.3 = 330"
call /kinetics/CELLDIV/CycD/k20_lambdaD[1]/notes LOAD \
"With a low Km, rate ~ kcat. Here we have" \
"rate = k20 * lambda_d = 10 * 3.3 = 33." \
"7 Apr 2005." \
"Actually should have the substrate term in here." \
"Use the form Km >> substrate, so " \
"rate = kcat * sub * enz / Km" \
"so kcat = Km * k20 * lambda_d = 10 * 10 * 3.3 = 330" \
"" \
"The idea here is that these reactions phosphorylate the Rb" \
"protein attached to E2FAP, so that Rb_P is released and" \
"E2FAP is left."
call /kinetics/CELLDIV/CycD/k20_lambdaD[2]/notes LOAD \
"With a low Km, rate ~ kcat. Here we have" \
"rate = k20 * lambda_d = 10 * 3.3 = 33." \
"7 Apr 2005." \
"Actually should have the substrate term in here." \
"Use the form Km >> substrate, so " \
"rate = kcat * sub * enz / Km" \
"so kcat = Km * k20 * lambda_d = 10 * 10 * 3.3 = 330" \
"" \
"The idea here is that these reactions phosphorylate the Rb" \
"protein attached to E2FA, so that Rb_P is released and" \
"E2FA is left."
call /kinetics/CELLDIV/CycE/k20_lambdaE/notes LOAD \
"For Km ~ 0, rate ~ kcat." \
"rate = k20 * lambdaE = 10 * 5" \
"7 Apr 2005." \
"Actually need to put in substrate term too. Let Km = 10 >> sub." \
"Then," \
"rate ~ kcat * sub * prd /Km" \
"so kcat = Km * k20 * lambdaE = 10 * 10 * 5 = 500"
call /kinetics/CELLDIV/CycE/k21_phiE/notes LOAD \
"Rate is just K21 * phiE * [CycE]." \
"K21 = 1, phiE = 25. So rate= 25 * [CycE]" \
"MM rate = kcat * E.S/(Km + S)" \
"Let Km << S, then we get " \
"rate = kcat * E " \
"So if Km = 0.01, " \
"kcat = 25" \
"7 Apr 2005. Actually should include substrate term. So," \
"Km = 10, kcat = Km * K21 * phiE = 250" \
"" \
"18 Apr 2005. Speeded up 10x."
call /kinetics/CELLDIV/CycE/Ak6_etaE/notes LOAD \
"Rate = V6 * [CycD_Kip1]." \
"6 Apr 2005. Rates were k1 = 500, k2 = 10, k3 = 1 in " \
"explicit E.S reaction form. Changed to MM as Km was too low." \
"New values:" \
"Km = 10" \
"kcat = Km * k6 * etaE = 500."
call /kinetics/CELLDIV/CycE/k8_CycE/notes LOAD \
"Autocatalysis step equation 5." \
"Unfortunately cannot exactly represent" \
"the math of Equation 26. Note that we cannot merge this" \
"enzyme with k6_etaE because this is in the explicit form" \
"to get a little closer to the mathematical form." \
""
call /kinetics/CELLDIV/CycE/k6_E_etaE/notes LOAD \
"k6 = 100, etaE = 0.5" \
"Assume a large Km of 1000 so that the conc of the enzyme" \
"is negligible." \
"Then rate is E.S.Vmax/Km." \
"6 April 2006" \
"I had changed it over to an explict form earlier. Those " \
"values were k1 = 500, k2 = 10, k3 = 1. " \
"Cannot use as effective Km is very small so we would end up" \
"with lots of E.S complex. Change back to MM:" \
"Km = 10, kcat = Km * k6 * etaE = 500."
call /kinetics/CELLDIV/CycE/k6_D_etaE/notes LOAD \
"Rate = V6 * [CycD_Kip1]." \
"k3.k1/k2 = rate = k6 * etaE = 50." \
"6 Apr 2005." \
"Old rates in explicit form were k1 = 500, k2 = 10, k3 = 1." \
" Need to go back to MM form because the above" \
"explict rates give a very low Km, ie, lots of E.S complex." \
"k6 = 100, etaE = 0.5," \
"Let Km >> substrate, so Km = 10." \
"Then kcat = Km * k6 * etaE = 500."
call /kinetics/CELLDIV/CycE/k8_CycE_Kip1/notes LOAD \
"Autocatalysis step equation 5." \
"Unfortunately cannot exactly represent" \
"the math of Equation 26. Note that we cannot merge this" \
"enzyme with k6_etaE because this is in the explicit form" \
"to get a little closer to the mathematical form." \
""
call /kinetics/CELLDIV/CycE/k6_kip1_E/notes LOAD \
"Rate = V6 * [CycD_Kip1]." \
"k3.k1/k2 = rate = k6 * etaE = 50." \
"6 Apr 2005." \
"Old rates in explicit form were k1 = 500, k2 = 10, k3 = 1." \
" Need to go back to MM form because the above" \
"explict rates give a very low Km, ie, lots of E.S complex." \
"k6 = 100, etaE = 0.5," \
"Let Km >> substrate, so Km = 10." \
"Then kcat = Km * k6 * etaE = 500."
call /kinetics/CELLDIV/CycE/k20_lambdaE[1]/notes LOAD \
"For Km ~ 0, rate ~ kcat." \
"rate = k20 * lambdaE = 10 * 5" \
"7 Apr 2005." \
"Actually need to put in substrate term too. Let Km = 10 >> sub." \
"Then," \
"rate ~ kcat * sub * prd /Km" \
"so kcat = Km * k20 * lambdaE = 10 * 10 * 5 = 500"
call /kinetics/CELLDIV/CycE/k20_lambdaE[2]/notes LOAD \
"For Km ~ 0, rate ~ kcat." \
"rate = k20 * lambdaE = 10 * 5" \
"7 Apr 2005." \
"Actually need to put in substrate term too. Let Km = 10 >> sub." \
"Then," \
"rate ~ kcat * sub * prd /Km" \
"so kcat = Km * k20 * lambdaE = 10 * 10 * 5 = 500"
call /kinetics/CELLDIV/CycA/notes LOAD \
"rate = k4.Gamma_A * [CycA] * [Cdh1]/(J4 + [Cdh1])" \
"" \
"J4 = 0.01" \
"k4 = kcat = 40" \
""
call /kinetics/CELLDIV/CycA/k20_lambdaA/notes LOAD \
"Km ~ 0, so rate ~ kcat." \
"Here rate = k20 * lambdaA = 10 * 3" \
"7 Apr 2005: Fix it: rate should have substrate term in it." \
"Set Km = 10 >> substrate. Then," \
"kcat = Km * k20 * lambdaA = 10 * 10 * 3 = 300" \
""
call /kinetics/CELLDIV/CycA/k21_phiE_A/notes LOAD \
"phiE is also used for the reaction catalyzed by A." \
"So rates are identical to k21_phiE" \
""
call /kinetics/CELLDIV/CycA/Cdh1_CycA/notes LOAD \
"J4 = Km = 0.01" \
"k4 = 40." \
"GammaA = 0.3" \
"" \
"kcat = k4 * GammaA = 12" \
"" \
""
call /kinetics/CELLDIV/CycA/A_phosph_E2F/notes LOAD \
"Rate equn has form" \
"[CycA].[E2F].k23" \
"k23 = 1" \
"" \
"MM equn has form" \
"[CycA].[E2F].kcat/(Km + E2F)" \
"So, we set" \
"kcat = Km * k23 where Km >> E2F" \
"25 Mar." \
"Better: Use explicit enz form. " \
"rate = k3.k1/k2 if k3 << k2. Let k3 = 1, k2 = 10," \
"so we get k1 = k23 * 10 = 10." \
"6 Apr." \
"Problem with explicit form is that the enz-substrate complex" \
"may affect the levels of the CycA, B etc. Back to MM." \
"" \
""
call /kinetics/CELLDIV/CycA/A_phosph_E2FA.Rb/notes LOAD \
"Rate equn has form" \
"[CycA].[E2F].k23" \
"k23 = 1" \
"" \
"MM equn has form" \
"[CycA].[E2F].kcat/(Km + E2F)" \
"So, we set" \
"kcat = Km * k23 where Km >> E2F" \
"25 March 2005" \
"Use explicit form. rate = k23 = 1 = k3*k1/k2 where k3 << k2" \
"So k3 = 1, k2 = 10, k1 = 10." \
"" \
"6 Apr 2005." \
"Back to MM form because enz complex formation is depleting" \
"CycA, B etc." \
"" \
""
call /kinetics/CELLDIV/CycA/Ak6_etaA/notes LOAD \
"See Ak6_etaE" \
""
call /kinetics/CELLDIV/CycA/k6_E_etaA/notes LOAD \
"See notes for k6_E_etaE." \
"Explicit rates had been k1 = 500, k2 = 10, k3 = 1 but this" \
"gave a very low Km. So, back to MM:" \
"etaA = 0.5 so kcat = 500, Km = 10 as for k6_E_etaE" \
""
call /kinetics/CELLDIV/CycA/k6_D_etaA/notes LOAD \
"k3.k1/k2 = k6.etaA = 100*0.5 = 50" \
"Also k3 << k2. Assume ratio is 10." \
"Let k3 be reasonable, say 1." \
"Then k2 = 10, k1 = 500." \
"6 April 2005: The above rates are bad because they give" \
"a very low Km and too much E.S. complex. So, back to MM:" \
"Km >> substrate, so Km = 10." \
"Then kcat = Km * k6 * etaA = 10 * 100 * 0.5 = 500."
call /kinetics/CELLDIV/CycA/k6_kip1_A/notes LOAD \
"k3.k1/k2 = k6.etaA = 100*0.5 = 50" \
"Also k3 << k2. Assume ratio is 10." \
"Let k3 be reasonable, say 1." \
"Then k2 = 10, k1 = 500." \
"6 April 2005: The above rates are bad because they give" \
"a very low Km and too much E.S. complex. So, back to MM:" \
"Km >> substrate, so Km = 10." \
"Then kcat = Km * k6 * etaA = 10 * 100 * 0.5 = 500."
call /kinetics/CELLDIV/CycA/k20_lambdaA[1]/notes LOAD \
"Km ~ 0, so rate ~ kcat." \
"Here rate = k20 * lambdaA = 10 * 3" \
"7 Apr 2005: Fix it: rate should have substrate term in it." \
"Set Km = 10 >> substrate. Then," \
"kcat = Km * k20 * lambdaA = 10 * 10 * 3 = 300" \
""
call /kinetics/CELLDIV/CycA/k20_lambdaA[2]/notes LOAD \
"Km ~ 0, so rate ~ kcat." \
"Here rate = k20 * lambdaA = 10 * 3" \
"7 Apr 2005: Fix it: rate should have substrate term in it." \
"Set Km = 10 >> substrate. Then," \
"kcat = Km * k20 * lambdaA = 10 * 10 * 3 = 300" \
""
call /kinetics/CELLDIV/CycB/k20_lambdaB/notes LOAD \
"With Km ~ 0, rate ~ kcat." \
"Here rate = k20 * lambdaB = 10 * 5" \
"7 Apr 2005." \
"Changed to include substrate term. Use Km = 10 >> sub, so" \
"kcat = Km * k20 * lambdaB = 10 * 10 * 5 = 500" \
""
call /kinetics/CELLDIV/CycB/k21_phiB/notes LOAD \
"phiB = 2." \
"See calculation for k21_phiE" \
""
call /kinetics/CELLDIV/CycB/k31/notes LOAD \
"Represented as k31.[IE].[CycB]/(J31 + [IE])" \
"k31 = 0.7" \
"J31 = 0.01" \
""
call /kinetics/CELLDIV/CycB/k11/notes LOAD \
"Represented simply as [CycB]*k11, where k11 is 1.5." \
"As AAs are at 1, we get" \
"" \
"rate = [AAs].[CycB].kcat / (Km + [AAs])" \
"So if we set Km = [AAs] = 1, then kcat = 3 gives our desired" \
"equation."
call /kinetics/CELLDIV/CycB/Cdh1_CycB/notes LOAD \
"Eqn 12." \
"J4 = Km = 0.01" \
"k4 = 40" \
"GammaB = 1" \
"kcat = k4 * GammaB = 40" \
"" \
""
call /kinetics/CELLDIV/CycB/B_phosph_E2FA/notes LOAD \
"See A_phosph_E2F. Same rate of k23 = 1 applies." \
""
call /kinetics/CELLDIV/CycB/B_phosph_E2FA.Rb/notes LOAD \
"See A_phosph_E2F. Same rate of k23 = 1 applies." \
""
call /kinetics/CELLDIV/CycB/Ak6_etaB/notes LOAD \
"See Ak6_etaE" \
""
call /kinetics/CELLDIV/CycB/k6_E_etaB/notes LOAD \
"See notes for k6_E_etaE. Here etaB = 1 so kcat = 1000, " \
"Km as before is 10" \
""
call /kinetics/CELLDIV/CycB/k6_D_etaB/notes LOAD \
"6 Apr 2005." \
"Earlier used explicit E.S complex form with k1 = 1000," \
"k2 = 10, k3 = 1. This gave low Km and lots of E.S. complex." \
"So shift to MM form:" \
"k6 = 100, etaB = 1." \
"Let Km = 10 >> substrate. Then " \
"kcat = Km * k6 * etaB = 1000"
call /kinetics/CELLDIV/CycB/k8_CycB_Kip1/notes LOAD \
"k8 = 0.2, psiB = 0.05, so kcat = 0.1." \
"J8 = 0.1"
call /kinetics/CELLDIV/CycB/k6_kip1_B/notes LOAD \
"6 Apr 2005." \
"Using MM form:" \
"k6 = 100" \
"Let Km = 10 >> substrate. Then " \
"kcat = Km * k6 * eta_B = 1000"
call /kinetics/CELLDIV/CycB/k20_lambdaB[1]/notes LOAD \
"With Km ~ 0, rate ~ kcat." \
"Here rate = k20 * lambdaB = 10 * 5" \
"7 Apr 2005." \
"Changed to include substrate term. Use Km = 10 >> sub, so" \
"kcat = Km * k20 * lambdaB = 10 * 10 * 5 = 500" \
""
call /kinetics/CELLDIV/CycB/k20_lambdaB[2]/notes LOAD \
"With Km ~ 0, rate ~ kcat." \
"Here rate = k20 * lambdaB = 10 * 5" \
"7 Apr 2005." \
"Changed to include substrate term. Use Km = 10 >> sub, so" \
"kcat = Km * k20 * lambdaB = 10 * 10 * 5 = 500" \
""
call /kinetics/CELLDIV/IE_GRP/IE/notes LOAD \
"According to the paper:" \
"IE is an intermediary enzyme that creates a time delay" \
"between CycB accumulation and Cdc20 activation." \
"" \
"No initial value for this is given. I assume it is 1."
call /kinetics/CELLDIV/IE_GRP/PPX/notes LOAD \
"From the notes on the equations:" \
"We assuem that the activity of this phosphatase (in the" \
"nucleus, where it opposes the action of CycB/Cdk1) is" \
"proportional to translational efficiency epsilon. Hence," \
"when epsilon drops to 05, both kinase and phosphatase" \
"acting on IE are halved."
call /kinetics/CELLDIV/IE_GRP/PPX/k32/notes LOAD \
"Represented as k32.[PPx].[IEP] / (J32 + [IEP])" \
"" \
"k32 = 1.8" \
"J32 = 0.01" \
"" \
"" \
""
call /kinetics/CELLDIV/IEP/notes LOAD \
"Represented as k13.[IEP].[Cdc20A]/(J13 + [Cdc20A])" \
"in other words, a classical MM form." \
"k13 = 5, J13 = 0.005" \
""
call /kinetics/CELLDIV/IEP/k13/notes LOAD \
"Represented as k13.[IEP].[Cdc20A]/(J13 + [Cdc20A])" \
"which is a classical MM form." \
"k13 = 5, J13 = 0.005" \
""
call /kinetics/CELLDIV/Cdc20_Grp/notes LOAD \
"The CycD is assumed to be bound to Cdk4, which is present" \
"in large excess. Therefore the Cdk4 does not figure in" \
"these equations, nor in the equations of Novak and Tyson."
call /kinetics/CELLDIV/Cdc20_Grp/k11_prime/notes LOAD \
"Kind of a silly reaction, with all terms zero," \
" but it is there in the" \
"Novak and Tyson equations."
call /kinetics/CELLDIV/Cdc20_Grp/k14_enz/k14/notes LOAD \
"Represented as k14.[Cdc20] / (J4 + [Cdc20])" \
"But I suspect it should be J14." \
"k14 = 2.5" \
"J14 = 0.005" \
"If we set enz = 1, Km = J14, kcat = k14, this equation" \
"applies." \
""
call /kinetics/CELLDIV/Cdc20/k2_prime_prime/notes LOAD \
"k2_prime_prime = 1." \
"rate = k2_prime_prime * Cdc20 * CycB" \
"Using MM:" \
"rate = kcat * Cdc20 * CycB / (CycB + Km)" \
"Let Km >> CycB, ie, around 100." \
"Then kcat = k2_prime_prime * Km = 100." \
""
call /kinetics/CELLDIV/Cdc20/Cdc20_deg_CycA/notes LOAD \
"Rate comes in as k30 = 20" \
"" \
"Rate = [Cdc20]*[CycA] * k30. To put in MM form:" \
"" \
"Rate = [Cdc20]*[CycA] * kcat / (Km + [CycA])" \
"where kcat = k30 * Km and Km >> [CycA]." \
"Put Km = 1000, so kcat = 20000" \
"25 March: use explicit enz form. Use" \
"rate = k3*k1/k2 = 20, which works if k2 >> k3." \
"Then let k3 = 1, k2 = 10, k1 becomes 200" \
"7 Apr 2005: Above won't work because of low Km consuming" \
"too much of the Cdc20 in the complex form." \
"So use Km = 10, kcat = 200." \
"" \
"" \
""
call /kinetics/CELLDIV/Cdc20/Cdc20_deg_CycA_Kip1/notes LOAD \
"Rate comes in as k30 = 20" \
"Same rate as for CycA alone." \
"" \
"Rate = [Cdc20]*[CycA_Kip1] * k30. To put in MM form:" \
"" \
"Rate = [Cdc20]*[CycA_Kip1] * kcat / (Km + [CycA_Kip1])" \
"where kcat = k30 * Km and Km >> [CycA_Kip1]." \
"Put Km = 1000, so kcat = 20000" \
"" \
"Similar to CycA alone, we instead get" \
"k2 = 10, k3 = 1, so k1 = 200." \
"19 Apr 2005: Go back to MM form because of low Km." \
"Let Km = 10, then kcat = Km * k30 = 200." \
"" \
""
call /kinetics/CELLDIV/Cdc20/Cdh1_Cdc20/notes LOAD \
"k3 = 140" \
"Km = j3 = 0.01" \
""
call /kinetics/CELLDIV/Cdh1_grp/Cdh1_i/Cdh1_i_k2_prime/notes LOAD \
"k2_prime = 0.05." \
"so actually this reaction is pretty negligible." \
"" \
"rate = k2_prime * Cdh1_i * CycB" \
"From MM kinetics, " \
"rate = kcat * Cdh1_i * CycB / (CycB + Km). " \
"Let Km >>CycB, so Km = 10." \
"Then kcat = k2_prime * Km = 0.5" \
"" \
""
call /kinetics/CELLDIV/Cdh1_grp/Cdh1/Cdh1_k2/notes LOAD \
"k2 = 20" \
"" \
"Let Km = 100, so it is >> substrate." \
"Then kcat = Km * k2 = 2000"
call /kinetics/CELLDIV/Cdh1_grp/k3_prime/notes LOAD \
"the 'conc' is just a scale factor to make the exchange" \
"eqn fit the MM form. Let k3_prime conc 1 and then it works."
call /kinetics/CELLDIV/Cdh1_grp/k3_prime/k3_prime/notes LOAD \
"k3_prime = 7.5" \
"J3 = Km = 0.01" \
"Rate = [k3_prime] * [Cdh1_i]/(J3 + [Cdh1_i])"
call /kinetics/CELLDIV/E2F/notes LOAD \
"This group manages equations 10, 21 and 22 from the Novak" \
"and Tyson 2004 JTB paper. The last two equations are" \
"only approximately represented, expanded out into my" \
"explicit reaction-based interpretation of the equations" \
"and Figure 1." \
""
call /kinetics/CELLDIV/E2F/k22_23_prime/notes LOAD \
"k22 is the forward rate of 1" \
"k23_prime is the backward rate of 0.005" \
""
call /kinetics/CELLDIV/E2F/E2FA.Rb/notes LOAD \
"This is the active form of E2F." \
""
call /kinetics/CELLDIV/E2F/k22_23_prime.Rb/notes LOAD \
"k22 is the forward rate of 1" \
"k23_prime is the backward rate of 0.005" \
""
call /kinetics/CELLDIV/E2F/k26/notes LOAD \
"k26 = 10, k26r =200" \
"Unless k26 = 10000. There is a period in the paper but" \
"it may be a typo." \
"" \
"The form of the equation is complex, but if k26 is large then" \
"there is more E2F:Rb, so that is the forward reaction here."
call /kinetics/CELLDIV/E2F/k26_P/notes LOAD \
"Same as k26, but acting on the phosph form."
call /kinetics/CELLDIV/E2FA/notes LOAD \
"This is the active form of E2F." \
"E2FTot = 5, and this is used for the CoInit."
call /kinetics/CELLDIV/E2FA/k29/notes LOAD \
"Represented as eps*k29*[E2FA]*[mass], where k29 is 0.05" \
"" \
"Split into two steps, this one deals with the E2FA term." \
"" \
"rate = Mass_dup * E2FA * kcat / (Km + Mass_dup)" \
"Note that Mass_dup will not change." \
"Let Km >> Mass_dup and kcat = k29 * Km." \
"then" \
"rate ~ Mass_dup * E2FA * k29 * Km / Km"
call /kinetics/CELLDIV/E2FA/k7/notes LOAD \
"Represented simply as [E2FA]*k7, where k7 is 0.6" \
"As AAs are at 1, we get" \
"" \
"rate = [AAs].[E2FA].kcat / (Km + [AAs])" \
"So if we set Km = [AAs] = 1, then kcat = 1.2 gives our desired" \
"equation."
call /kinetics/CELLDIV/CycB_Grp/notes LOAD \
"The CycD is assumed to be bound to Cdk4, which is present" \
"in large excess. Therefore the Cdk4 does not figure in" \
"these equations, nor in the equations of Novak and Tyson."
call /kinetics/CELLDIV/CycB_Grp/k1_prime/notes LOAD \
"k1_prime = 0.1" \
""
call /kinetics/CELLDIV/CycB_Grp/CycB_synth/k1/notes LOAD \
"k1 = 0.6." \
"J1 = 0.1" \
"rate = k1([CycB]/J1)^2 / (1 + ([cycB]/J1)^2 )" \
"2nd order term comes from dimerization, assume" \
"rate = k1 * dimer. Doing our usual assumption of AA = Km = 1," \
"we get kcat = 2 * k1 = 1.2" \
"7 April. Revisit this. Multiply expression above and below" \
"by J1^2. Then we have standard MM form, with k1 = kcat," \
"and J1^2 = Km." \
"19 Apr 2005. Altered layout so that dimer form is in" \
"substrate, which it should have been all along." \
""
call /kinetics/CELLDIV/CycA_Grp/notes LOAD \
"The CycD is assumed to be bound to Cdk4, which is present" \
"in large excess. Therefore the Cdk4 does not figure in" \
"these equations, nor in the equations of Novak and Tyson."
call /kinetics/CELLDIV/CycE_grp/notes LOAD \
"The CycD is assumed to be bound to Cdk4, which is present" \
"in large excess. Therefore the Cdk4 does not figure in" \
"these equations, nor in the equations of Novak and Tyson."
call /kinetics/CELLDIV/CycE_grp/k_prime7/notes LOAD \
"This is set to zero in the paper, so this reaction" \
"isn't really doing anything." \
""
call /kinetics/CELLDIV/CycE_grp/k_prime_8/notes LOAD \
"k_prime_8 = 0.1" \
""
call /kinetics/CELLDIV/CycE_grp/k_prime_8_kip1/notes LOAD \
"k_prime_8 = 0.1" \
""
call /kinetics/CELLDIV/DRG/k9/notes LOAD \
"Represented simply as [DRG]*k9, where k9 is 2.5." \
"As AAs are at 1, we get" \
"" \
"rate = [AAs].[DRG].kcat / (Km + [AAs])" \
"So if we set Km = [AAs] = 1, then kcat = 5 gives our desired" \
"equation."
call /kinetics/CELLDIV/ERG/notes LOAD \
"Pool of proteins synthesised by Early Response Genes. " \
"Production is inhibited by DRG, the Delayed Response Genes."
call /kinetics/CELLDIV/ERG/k_prime_17/notes LOAD \
"k17_prime = 0.35." \
"rate = epsilon * k17_prime * [ERG]" \
"Assume AA = 1, Km = 1. Then " \
"rate = kcat * AA * ERG / (Km + AA)" \
"gives " \
"kcat = 0.7" \
""
call /kinetics/CELLDIV/Early_Response_Genes/ERG_synth/notes LOAD \
"Enzyme that synthesiszes ERG. Enters into equations only" \
"implicitly. Initial conc set to 1."
call /kinetics/CELLDIV/Early_Response_Genes/ERG_synth/ERG_synth/notes LOAD \
"kcat = 2 * k15 = 0.5" \
"Km = 1" \
"[AA] = 1"
call /kinetics/CELLDIV/Early_Response_Genes/k16/notes LOAD \
"k16 from paper = 0.25, unidirectional degradation step."
call /kinetics/CELLDIV/Early_Response_Genes/degraded/notes LOAD \
"Degraded products of Early Response Genes. Just a place-" \
"filler pool, does not enter elsewhere."
call /kinetics/CELLDIV/Early_Response_Genes/inhib_ERG_synth/notes LOAD \
"Inhibited complex of ERG_synth with 2 DRG. Enters into" \
"equation 1 only implicitly."
call /kinetics/CELLDIV/Early_Response_Genes/AminoAcids/notes LOAD \
"Amino acid pool, Enters into system indirectly as a scaling" \
"factor. Set to 1."
call /kinetics/CELLDIV/Early_Response_Genes/DRG2_bind_ERG_synth/notes LOAD \
"Kd = J15^2 = (0.1)^2 = 0.01" \
""
call /kinetics/CELLDIV/Delayed_Response_Genes/degraded/notes LOAD \
"Degraded products of Early Response Genes. Just a place-" \
"filler pool, does not enter elsewhere."
call /kinetics/CELLDIV/Delayed_Response_Genes/DRG_synth/notes LOAD \
"Enzyme that synthesiszes ERG. Enters into equations only" \
"implicitly. Initial conc set to 1."
call /kinetics/CELLDIV/Delayed_Response_Genes/DRG_synth/DRG_synth/notes LOAD \
"k17 = 10" \
"J17 = 0.3" \
"This enz represents" \
"rate = k17([DRG]/J17)^2 / (1 + ([DRG]/J17)^2 )" \
"Here we assume that the substrate conc = [DRG]^2. Then it" \
"expands into classical MM form:" \
"rate = k17.sub / (J17^2 + sub)" \
"provided [DRG_synth] = 1."
call /kinetics/CELLDIV/Delayed_Response_Genes/k18/notes LOAD \
"k18 = 10"
call /kinetics/CELLDIV/CycD_Grp/notes LOAD \
"The CycD is assumed to be bound to Cdk4, which is present" \
"in large excess. Therefore the Cdk4 does not figure in" \
"these equations, nor in the equations of Novak and Tyson."
call /kinetics/CELLDIV/CycD_Grp/k24/notes LOAD \
"k24 = 1000" \
"k24r = 10"
call /kinetics/CELLDIV/CycD_Grp/k10_b/notes LOAD \
"This is another degradation step for CycD, but it happens" \
"while the CycD is bound to Kip1. Same rate as k10."
call /kinetics/doqcsinfo/notes LOAD \
"This is a fairly complete mass-action reimplementation of the" \
"Novak and Tyson mammalian cell cycle model. It is inexact on two" \
"counts. First, it replaces many rather abstracted equations with" \
"mass action and Michaelis-Menten forms of enzymes. Second, it does" \
"not handle the halving of cellular volume at the division point." \
"Within these limitations, the model does most of what the original" \
"paper shows including oscillation of the relevant molecules."\
" "
complete_loading