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FindSim_compositeModel_1.g
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FindSim_compositeModel_1.g
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//genesis
// kkit Version 11 flat dumpfile
// Saved on 100
include kkit {argv 1}
FASTDT = 0.001
SIMDT = 0.001
CONTROLDT = 0.1
PLOTDT = 0.1
MAXTIME = 100
TRANSIENT_TIME = 2
VARIABLE_DT_FLAG = 0
DEFAULT_VOL = 1.03367228389e-15
VERSION = 11.0
setfield /file/modpath value ~/scripts/modules
kparms
//genesis
initdump -version 3 -ignoreorphans 1
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
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simundump geometry /kinetics/geometry[1] 0 1.03367228389e-15 3 sphere "" white black -9163 7276 0
simundump geometry /kinetics/geometry 0 1.75486868722e-21 3 sphere "" white black -9163 7276 0
simundump group /kinetics/AKT_activation 0 blue green x 0 0 "" defaultfile \
defaultfile.g 0 0 0 -9166 7276 0
simundump group /kinetics/TrKB 0 blue green x 0 0 "" defaultfile \
defaultfile.g 0 0 0 -9166 7276 0
simundump group /kinetics/PI3K_activation 0 blue green x 0 0 "" defaultfile \
defaultfile.g 0 0 0 -9166 7276 0
simundump group /kinetics/mTORC1 0 blue green x 0 0 "" defaultfile \
defaultfile.g 0 0 0 -9166 7276 0
simundump group /kinetics/S6Kinase 0 blue green x 0 0 "" defaultfile \
defaultfile.g 0 0 0 -9166 7276 0
simundump group /kinetics/4E_BP 0 blue green x 0 0 "" defaultfile \
defaultfile.g 0 0 0 -9166 7276 0
simundump group /kinetics/43S_complex 0 blue green x 0 0 "" defaultfile \
defaultfile.g 0 0 0 -9166 7276 0
simundump group /kinetics/CaM 0 blue green x 0 0 "" defaultfile \
defaultfile.g 0 0 0 -9166 7276 0
simundump group /kinetics/MAPK 0 blue green x 0 0 "" defaultfile \
defaultfile.g 0 0 0 -9166 7276 0
simundump group /kinetics/Ras 0 blue green x 0 0 "" defaultfile \
defaultfile.g 0 0 0 -9166 7276 0
simundump group /kinetics/Sos 0 blue green x 0 0 "" defaultfile \
defaultfile.g 0 0 0 -9166 7276 0
simundump group /kinetics/PKC 0 blue green x 0 0 "" defaultfile \
defaultfile.g 0 0 0 -9166 7276 0
simundump group /kinetics/protein 0 blue green x 0 0 "" defaultfile \
defaultfile.g 0 0 0 -9166 7276 0
simundump group /kinetics/PLC_g 0 blue green x 0 0 "" defaultfile \
defaultfile.g 0 0 0 -9166 7276 0
simundump group /kinetics/BDNF 0 blue green x 0 0 "" defaultfile \
defaultfile.g 0 0 0 -9166 7276 0
simundump group /kinetics/Phosphatase 0 blue green x 0 0 "" defaultfile \
defaultfile.g 0 0 0 -9166 7276 0
simundump group /kinetics/Ca 0 blue green x 0 0 "" defaultfile \
defaultfile.g 0 0 0 -9166 7276 0
simundump group /kinetics/CaMKIII 0 blue green x 0 0 "" defaultfile \
defaultfile.g 0 0 0 -9166 7276 0
simundump group /kinetics/Translation_initiation 0 blue green x 0 0 "" defaultfile \
defaultfile.g 0 0 0 -9166 7276 0
simundump group /kinetics/Translation_elongation 0 blue green x 0 0 "" defaultfile \
defaultfile.g 0 0 0 -9166 7276 0
simundump group /kinetics/40S 0 blue green x 0 0 "" defaultfile \
defaultfile.g 0 0 0 -9166 7276 0
simundump group /kinetics/TSC1_TSC2 0 blue green x 0 0 "" defaultfile \
defaultfile.g 0 0 0 -9166 7276 0
simundump group /kinetics/PLA2 0 blue green x 0 0 "" defaultfile \
defaultfile.g 0 0 0 -9166 7276 0
simundump group /kinetics/PLCbeta 0 blue green x 0 0 "" defaultfile \
defaultfile.g 0 0 0 -9166 7276 0
simundump group /kinetics/mGluRAntag 0 blue green x 0 0 "" defaultfile \
defaultfile.g 0 0 0 -9166 7276 0
simundump group /kinetics/EGFR 0 blue green x 0 0 "" defaultfile \
defaultfile.g 0 0 0 -9166 7276 0
simundump group /kinetics/CaMKII 0 blue green x 0 0 "" defaultfile \
defaultfile.g 0 0 0 -9166 7276 0
simundump group /kinetics/PP1 0 blue green x 0 0 "" defaultfile \
defaultfile.g 0 0 0 -9166 7276 0
simundump group /kinetics/PP2B 0 blue green x 0 0 "" defaultfile \
defaultfile.g 0 0 0 -9166 7276 0
simundump group /kinetics/PKA 0 blue green x 0 0 "" defaultfile \
defaultfile.g 0 0 0 -9166 7276 0
simundump group /kinetics/AC 0 blue green x 0 0 "" defaultfile \
defaultfile.g 0 0 0 -9166 7276 0
simundump group /kinetics/mGluR 0 blue green x 0 0 "" defaultfile \
defaultfile.g 0 0 0 -9166 7276 0
simundump group /kinetics/Gprotein 0 blue green x 0 0 "" defaultfile \
defaultfile.g 0 0 0 -9166 7276 0
simundump group /kinetics/barr2_signaling 0 blue green x 0 0 "" defaultfile \
defaultfile.g 0 0 0 -9166 7276 0
simundump group /kinetics/HomerPIKE 0 blue green x 0 0 "" defaultfile \
defaultfile.g 0 0 0 -9166 7276 0
simundump kpool /kinetics/BDNF/BDNF 0 0.0 0 0 0 31.1246037909 0 0 622492.075821 4 /kinetics/geometry[1] 44 black -9167 4522 0
simundump kpool /kinetics/PLC_g/PLC_g 0 0.0 0 0 0 62251.2826248 0 0 622492.075821 0 /kinetics/geometry[1] cyan black -3208 1062 0
simundump kpool /kinetics/PLC_g/PLC_g_p 0 0.0 0 0 0 0.0 0 0 622492.075821 0 /kinetics/geometry[1] 25 pink -3294 875 0
simundump kpool /kinetics/PI3K_activation/PIP3 0 0.0 0 0 0 0.0 0 0 622492.075821 0 /kinetics/geometry[1] 43 black -262 2663 0
simundump kpool /kinetics/S6Kinase/PDK1 0 0.0 0 0 0 622512.826248 0 0 622492.075821 0 /kinetics/geometry[1] 37 black 1659 2640 0
simundump kpool /kinetics/Phosphatase/PP2A 0 0.0 0 0 0 93376.9239372 0 0 622492.075821 0 /kinetics/geometry[1] 4 black 2917 854 0
simundump kpool /kinetics/AKT_activation/PIP3_AKT 0 0.0 0 0 0 0.0 0 0 622492.075821 0 /kinetics/geometry[1] 53 yellow 1715 2061 0
simundump kpool /kinetics/AKT_activation/PIP3_PDK1 0 0.0 0 0 0 0.0 0 0 622492.075821 0 /kinetics/geometry[1] 9 yellow 1528 3512 0
simundump kpool /kinetics/AKT_activation/PIP3_PDK2 0 0.0 0 0 0 1867.53847875 0 0 622492.075821 0 /kinetics/geometry[1] 39 yellow 5566 1833 0
simundump kpool /kinetics/AKT_activation/PIP3_AKT_thr308 0 0.0 0 0 0 0.0 0 0 622492.075821 0 /kinetics/geometry[1] 60 yellow 3580 1973 0
simundump kpool /kinetics/AKT_activation/PIP3_AKT_t308_s473 0 0.0 0 0 0 0.0 0 0 622492.075821 0 /kinetics/geometry[1] 25 yellow 4634 1410 0
simundump kpool /kinetics/AKT_activation/AKT 0 0.0 0 0 0 124502.565248 0 0 622492.075821 0 /kinetics/geometry[1] 4 yellow 901 3912 0
simundump kpool /kinetics/TSC1_TSC2/TSC1_TSC2_p 0 0.0 0 0 0 0.0 0 0 622492.075821 0 /kinetics/geometry[1] 40 yellow 6268 2281 0
simundump kpool /kinetics/TrKB/Int_BDNF_TrKB2_p_clx 0 0.0 0 0 0 155628.206562 0 0 622492.075821 4 /kinetics/geometry[1] yellow white -6177 3597 0
simundump kpool /kinetics/TrKB/TrKB 0 0.0 0 0 0 155617.831348 0 0 622492.075821 0 /kinetics/geometry[1] 3 white -7699 4032 0
simundump kpool /kinetics/TrKB/BDNF_TrKB2_clx 0 0.0 0 0 0 0.0 0 0 622492.075821 0 /kinetics/geometry[1] 38 white -6540 2894 0
simundump kpool /kinetics/TrKB/BDNF_TrKB_clx 0 0.0 0 0 0 0.0 0 0 622492.075821 0 /kinetics/geometry[1] 45 white -8156 3332 0
simundump kpool /kinetics/TrKB/BDNF_TrKB2_p_clx 0 0.0 0 0 0 0.0 0 0 622492.075821 0 /kinetics/geometry[1] red white -4570 2776 0
simundump kpool /kinetics/PI3K_activation/SHC_p_Grb2_Gab1_PI3K_clx 0 0.0 0 0 0 0.0 0 0 622492.075821 0 /kinetics/geometry[1] brown white -1677 3444 0
simundump kpool /kinetics/PI3K_activation/PI3K 0 0.0 0 0 0 62249.2075821 0 0 622492.075821 0 /kinetics/geometry[1] cyan brown -2107 2511 0
simundump kpool /kinetics/PI3K_activation/PI3K_basal 0 0.0 0 0 0 0.0 0 0 622492.075821 0 /kinetics/geometry[1] 10 brown -1445 3303 0
simundump kpool /kinetics/PI3K_activation/PIP2 0 0.0 0 0 0 4357589.78373 0 0 622492.075821 4 /kinetics/geometry[1] orange brown -2215 1872 0
simundump kpool /kinetics/Sos/SHC 0 0.0 0 0 0 311256.413124 0 0 622492.075821 0 /kinetics/geometry[1] 5 brown -4382 4465 0
simundump kpool /kinetics/Sos/SHC_p_Grb2_clx 0 0.0 0 0 0 0.0 0 0 622492.075821 0 /kinetics/geometry[1] 42 brown -2889 5850 0
simundump kpool /kinetics/PI3K_activation/Gab1 0 0.0 0 0 0 435758.978373 0 0 622492.075821 0 /kinetics/geometry[1] 44 brown -3065 6336 0
simundump kpool /kinetics/PI3K_activation/SHC_p_Grb2_Gab1_clx 0 0.0 0 0 0 0.0 0 0 622492.075821 0 /kinetics/geometry[1] 50 brown -2509 4542 0
simundump kpool /kinetics/PLC_g/PLCg_basal 0 0.0 0 0 0 435.758978373 0 0 622492.075821 0 /kinetics/geometry[1] 33 black -5419 646 0
simundump kpool /kinetics/TSC1_TSC2/TSC1_TSC2 0 0.0 0 0 0 622512.826248 0 0 622492.075821 0 /kinetics/geometry[1] 51 black 5789 3245 0
simundump kpool /kinetics/Translation_initiation/eIF4E 0 0.0 0 0 0 0.0 0 0 622492.075821 0 /kinetics/geometry[1] 42 black 3289 4014 0
simundump kpool /kinetics/mTORC1/Rheb_GTP 0 0.0 0 0 0 622512.826248 0 0 622492.075821 0 /kinetics/geometry[1] 28 black 4722 4735 0
simundump kpool /kinetics/mTORC1/Rheb_GDP 0 0.0 0 0 0 0.0 0 0 622492.075821 0 /kinetics/geometry[1] 39 black 6009 5018 0
simundump kpool /kinetics/mTORC1/TOR_clx 0 0.0 0 0 0 373507.695748 0 0 622492.075821 0 /kinetics/geometry[1] 25 8 3847 5326 0
simundump kpool /kinetics/mTORC1/TOR_Rheb_GTP_clx 0 0.0 0 0 0 0.0 0 0 622492.075821 0 /kinetics/geometry[1] 44 black 3372 3660 0
simundump kpool /kinetics/S6Kinase/S6K_p 0 0.0 0 0 0 0.0 0 0 622492.075821 0 /kinetics/geometry[1] 46 6 2250 2088 0
simundump kpool /kinetics/S6Kinase/S6K 0 0.0 0 0 0 778141.032809 0 0 622492.075821 0 /kinetics/geometry[1] Pink 6 1872 1839 0
simundump kpool /kinetics/S6Kinase/S6K_thr_412 0 0.0 0 0 0 0.0 0 0 622492.075821 0 /kinetics/geometry[1] 48 6 3445 1898 0
simundump kpool /kinetics/40S/40S_inact 0 0.0 0 0 0 12450.2565248 0 0 622492.075821 4 /kinetics/geometry[1] 3 6 4684 1897 0
simundump kpool /kinetics/4E_BP/4E_BP 0 0.0 0 0 0 0.0 0 0 622492.075821 0 /kinetics/geometry[1] 47 white 3506 2582 0
simundump kpool /kinetics/4E_BP/4E_BP_t37_46_s65 0 0.0 0 0 0 0.0 0 0 622492.075821 0 /kinetics/geometry[1] 59 white 2062 2537 0
simundump kpool /kinetics/4E_BP/eIF4E_BP 0 0.0 0 0 0 124502.565248 0 0 622492.075821 0 /kinetics/geometry[1] 52 white 3654 2418 0
simundump kpool /kinetics/4E_BP/eIF4E_BP_thr37_46 0 0.0 0 0 0 0.0 0 0 622492.075821 0 /kinetics/geometry[1] 56 white 2379 2398 0
simundump kpool /kinetics/4E_BP/eIF4E_BP_t37_46_s65 0 0.0 0 0 0 0.0 0 0 622492.075821 0 /kinetics/geometry[1] 39 white 2075 2340 0
simundump kpool /kinetics/40S/40S 0 0.0 0 0 0 0.0 0 0 622492.075821 0 /kinetics/geometry[1] 7 black 4998 1777 0
simundump kpool /kinetics/Translation_initiation/eIF4G_A_clx 0 0.0 0 0 0 0.0 0 0 622492.075821 0 /kinetics/geometry[1] cyan black 4111 5603 0
simundump kpool /kinetics/Translation_initiation/eIF4A 0 0.0 0 0 0 124502.565248 0 0 622492.075821 0 /kinetics/geometry[1] pink black 4381 7275 0
simundump kpool /kinetics/Translation_initiation/eIF4G 0 0.0 0 0 0 24900.51305 0 0 622492.075821 0 /kinetics/geometry[1] 21 black 4984 7002 0
simundump kpool /kinetics/Translation_initiation/eIF4F 0 0.0 0 0 0 0.0 0 0 622492.075821 0 /kinetics/geometry[1] 6 black 5059 4508 0
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addmsg /kinetics/PKC/PKC_DAG_AA_p /kinetics/PKC/PKC_active SUMTOTAL n nInit
addmsg /kinetics/PKC/PKC_Ca_memb_p /kinetics/PKC/PKC_active SUMTOTAL n nInit
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addmsg /kinetics/PKC/PKC_basal_p /kinetics/PKC/PKC_active SUMTOTAL n nInit
addmsg /kinetics/PKC/PKC_AA_p /kinetics/PKC/PKC_active SUMTOTAL n nInit
addmsg /kinetics/CaMKII/CaMKII_CaM /kinetics/CaMKII/tot_CaM_CaMKII SUMTOTAL n nInit
addmsg /kinetics/CaMKII/CaMKII_thr286_p_CaM /kinetics/CaMKII/tot_CaM_CaMKII SUMTOTAL n nInit
addmsg /kinetics/CaMKII/CaMKII_thr286 /kinetics/CaMKII/tot_autonomous_CaMKII SUMTOTAL n nInit
addmsg /kinetics/CaMKII/CaMKII_p_p_p /kinetics/CaMKII/tot_autonomous_CaMKII SUMTOTAL n nInit
addmsg /kinetics/PP2B/CaMCa4_CaNAB /kinetics/CaM/CaM(Ca)n_CaNAB SUMTOTAL n nInit
addmsg /kinetics/PP2B/CaMCa3_CaNAB /kinetics/CaM/CaM(Ca)n_CaNAB SUMTOTAL n nInit
addmsg /kinetics/PP2B/CaMCa2_CaNAB /kinetics/CaM/CaM(Ca)n_CaNAB SUMTOTAL n nInit
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addmsg /kinetics/PI3K_activation/PIP3 /kinetics/AKT_activation/PIP3_bind_AKT SUBSTRATE n
addmsg /kinetics/AKT_activation/PIP3_bind_AKT /kinetics/PI3K_activation/PIP3 REAC A B
addmsg /kinetics/AKT_activation/AKT /kinetics/AKT_activation/PIP3_bind_AKT SUBSTRATE n
addmsg /kinetics/AKT_activation/PIP3_bind_AKT /kinetics/AKT_activation/AKT REAC A B
addmsg /kinetics/AKT_activation/PIP3_AKT /kinetics/AKT_activation/PIP3_bind_AKT PRODUCT n
addmsg /kinetics/AKT_activation/PIP3_bind_AKT /kinetics/AKT_activation/PIP3_AKT REAC B A
addmsg /kinetics/PI3K_activation/PIP3 /kinetics/AKT_activation/PIP3_bind_PDK1 SUBSTRATE n
addmsg /kinetics/AKT_activation/PIP3_bind_PDK1 /kinetics/PI3K_activation/PIP3 REAC A B
addmsg /kinetics/S6Kinase/PDK1 /kinetics/AKT_activation/PIP3_bind_PDK1 SUBSTRATE n
addmsg /kinetics/AKT_activation/PIP3_bind_PDK1 /kinetics/S6Kinase/PDK1 REAC A B
addmsg /kinetics/AKT_activation/PIP3_PDK1 /kinetics/AKT_activation/PIP3_bind_PDK1 PRODUCT n
addmsg /kinetics/AKT_activation/PIP3_bind_PDK1 /kinetics/AKT_activation/PIP3_PDK1 REAC B A
addmsg /kinetics/TSC1_TSC2/TSC1_TSC2_p /kinetics/TSC1_TSC2/TSC1_TSC2_dephospho SUBSTRATE n
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addmsg /kinetics/TrKB/Ligand_binding /kinetics/TrKB/TrKB REAC A B
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addmsg /kinetics/TrKB/Ligand_binding /kinetics/TrKB/BDNF_TrKB_clx REAC B A
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addmsg /kinetics/PLC_g/PLC_g_p_dephospho /kinetics/PLC_g/PLC_g REAC B A
addmsg /kinetics/TrKB/BDNF_TrKB2_p_clx /kinetics/TrKB/LR_Internalize SUBSTRATE n
addmsg /kinetics/TrKB/LR_Internalize /kinetics/TrKB/BDNF_TrKB2_p_clx REAC A B
addmsg /kinetics/TrKB/Int_BDNF_TrKB2_p_clx /kinetics/TrKB/LR_Internalize PRODUCT n
addmsg /kinetics/TrKB/LR_Internalize /kinetics/TrKB/Int_BDNF_TrKB2_p_clx REAC B A
addmsg /kinetics/TrKB/Int_BDNF_TrKB2_p_clx /kinetics/TrKB/LR_Internalize PRODUCT n
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addmsg /kinetics/Sos/SHC_p_dephospho /kinetics/Sos/SHC REAC B A
addmsg /kinetics/Sos/Grb2 /kinetics/Sos/Grb2_bind_SHC SUBSTRATE n
addmsg /kinetics/Sos/Grb2_bind_SHC /kinetics/Sos/Grb2 REAC A B
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addmsg /kinetics/PI3K_activation/bind_Gab1 /kinetics/Sos/SHC_p_Grb2_clx REAC A B
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addmsg /kinetics/PI3K_activation/bind_Gab1 /kinetics/PI3K_activation/Gab1 REAC A B
addmsg /kinetics/PI3K_activation/SHC_p_Grb2_Gab1_clx /kinetics/PI3K_activation/bind_Gab1 PRODUCT n
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addmsg /kinetics/PI3K_activation/PI3K_act /kinetics/PI3K_activation/PI3K REAC A B
addmsg /kinetics/PI3K_activation/SHC_p_Grb2_Gab1_clx /kinetics/PI3K_activation/PI3K_act SUBSTRATE n
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addmsg /kinetics/PI3K_activation/PI3K_basal /kinetics/PI3K_activation/basal_PI3K_act PRODUCT n
addmsg /kinetics/PI3K_activation/basal_PI3K_act /kinetics/PI3K_activation/PI3K_basal REAC B A
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addmsg /kinetics/mTORC1/TOR_Rheb_GTP_clx /kinetics/mTORC1/Rheb_GTP_bind_TORclx PRODUCT n
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addmsg /kinetics/40S/40S /kinetics/S6Kinase/S6_dephosph SUBSTRATE n
addmsg /kinetics/S6Kinase/S6_dephosph /kinetics/40S/40S REAC A B
addmsg /kinetics/40S/40S_inact /kinetics/S6Kinase/S6_dephosph PRODUCT n
addmsg /kinetics/S6Kinase/S6_dephosph /kinetics/40S/40S_inact REAC B A
addmsg /kinetics/Translation_initiation/eIF4E /kinetics/4E_BP/eIF4E_bind_BP2 SUBSTRATE n
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addmsg /kinetics/4E_BP/eIF4E_bind_BP2 /kinetics/4E_BP/4E_BP REAC A B
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addmsg /kinetics/4E_BP/eIF4E_bind_BP2 /kinetics/4E_BP/eIF4E_BP REAC B A
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addmsg /kinetics/4E_BP/eIF4E_BP2_disso /kinetics/4E_BP/eIF4E_BP_t37_46_s65 REAC A B
addmsg /kinetics/Translation_initiation/eIF4E /kinetics/4E_BP/eIF4E_BP2_disso PRODUCT n
addmsg /kinetics/4E_BP/eIF4E_BP2_disso /kinetics/Translation_initiation/eIF4E REAC B A
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