//genesis // kkit Version 11 flat dumpfile // Saved on Mon Mar 2 11:09:44 2009 include kkit {argv 1} FASTDT = 2e-06 SIMDT = 0.001 CONTROLDT = 1 PLOTDT = 10 MAXTIME = 1000 TRANSIENT_TIME = 2 VARIABLE_DT_FLAG = 1 DEFAULT_VOL = 1e-15 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 simobjdump text str simundump geometry /kinetics/geometry 0 9.9997e-16 3 sphere "" white black 0 \ 0 0 simundump kpool /kinetics/BDNF 0 0 5e-05 5e-05 29.999 29.999 0 0 5.9998e+05 4 \ /kinetics/geometry 44 black -13 33 0 simundump kpool /kinetics/PLC_g 0 0 0.1 0.1 60000 60000 0 0 6e+05 0 \ /kinetics/geometry cyan black -4 13 0 simundump kpool /kinetics/PLC_g* 0 0 0 0 0 0 0 0 6e+05 0 /kinetics/geometry \ "hot pink" black 2 16 0 simundump kpool /kinetics/PIP3 0 0 0 0 0 0 0 0 5.9998e+05 0 \ /kinetics/geometry 43 black 10 -11 0 simundump group /kinetics/TrKB_mod 0 15 black x 0 0 "" TrKB_mod defaultfile.g \ 0 0 0 1 8 0 simundump kpool /kinetics/TrKB_mod/Int_BDNF_TrKB2*_clx 0 0 0.25 0.25 1.5e+05 \ 1.5e+05 0 0 6e+05 4 /kinetics/geometry yellow 15 -13 -10 0 simundump kpool /kinetics/TrKB_mod/TrKB 0 0 0.25 0.25 1.4999e+05 1.4999e+05 0 \ 0 5.9996e+05 0 /kinetics/geometry 3 15 -13 9 0 simundump kpool /kinetics/TrKB_mod/BDNF_TrkB2_clx 0 0 0 0 0 0 0 0 5.9998e+05 \ 0 /kinetics/geometry 38 15 -8 1 0 simundump kreac /kinetics/TrKB_mod/Autophos_TrKB 0 0.02 0 "" white 15 -5 9 0 simundump kreac /kinetics/TrKB_mod/Dimeriz_TrKB 0 1.6667e-06 0.02 "" white 15 \ -8 9 0 simundump kpool /kinetics/TrKB_mod/BDNF_TrkB_clx 0 0 0 0 0 0 0 0 5.9996e+05 0 \ /kinetics/geometry 45 15 -8 24 0 simundump kreac /kinetics/TrKB_mod/Ligand_binding 0 1.6668e-06 0.05 "" white \ 15 -13 24 0 simundump kpool /kinetics/TrKB_mod/BDNF_TrkB2*_clx 0 0 0 0 0 0 0 0 5.9998e+05 \ 0 /kinetics/geometry red 15 -3 2 0 simundump kenz /kinetics/TrKB_mod/BDNF_TrkB2*_clx/PLC_g_phospho 0 0 0 0 0 \ 5.9998e+05 1.3889e-05 2 0.5 0 0 "" red red "" -2 7 0 simundump kenz /kinetics/TrKB_mod/BDNF_TrkB2*_clx/Shc_phospho 0 0 0 0 0 \ 5.9998e+05 3.0002e-06 1.2 0.3 0 0 "" red red "" -3 -2 0 simundump kreac /kinetics/TrKB_mod/PLC_g*_dephospho 0 0.07 0 "" white 15 -1 \ 14 0 simundump kpool /kinetics/TrKB_mod/Shc*_Grb2-Gab1_PI3K_clx 0 0 0 0 0 0 0 0 \ 5.9998e+05 0 /kinetics/geometry brown 15 2 -3 0 simundump kenz /kinetics/TrKB_mod/Shc*_Grb2-Gab1_PI3K_clx/Phospho 0 0 0 0 0 \ 5.9998e+05 8.3336e-06 16 4 0 0 "" red brown "" 2 -4 0 simundump kreac /kinetics/TrKB_mod/LR_Internalize 0 0.01 0 "" white 15 -9 -11 \ 0 simundump kreac /kinetics/TrKB_mod/LR_cycling 0 0.001 0.001 "" white 15 -13 0 \ 0 simundump group /kinetics/PI3K_mod 0 brown black x 0 0 "" PI3K_mod \ defaultfile.g 0 0 0 -9 -15 0 simundump kpool /kinetics/PI3K_mod/PI3K 0 0 0.1 0.1 59998 59998 0 0 \ 5.9998e+05 0 /kinetics/geometry cyan brown 4 -18 0 simundump kpool /kinetics/PI3K_mod/PI3K_basal 0 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry 10 brown -5 -15 0 simundump kenz /kinetics/PI3K_mod/PI3K_basal/basal_phosp 0 0 0 0 0 6e+05 \ 8.3333e-06 16 4 0 0 "" red 10 "" -5 -11 0 simundump kpool /kinetics/PI3K_mod/PIP2 0 0 7 7 4.2e+06 4.2e+06 0 0 6e+05 4 \ /kinetics/geometry orange brown 1 -11 0 simundump kpool /kinetics/PI3K_mod/Shc 0 0 0.5 0.5 3e+05 3e+05 0 0 6e+05 0 \ /kinetics/geometry 5 brown -5 -9 0 simundump kreac /kinetics/PI3K_mod/Shc*_dephospho 0 0.2 0 "" white brown -2 \ -9 0 simundump kreac /kinetics/PI3K_mod/Grb2_bind_Shc 0 1.6667e-06 1 "" white \ brown 0 -4 0 simundump kpool /kinetics/PI3K_mod/Shc*_Grb2_clx 0 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry 42 brown 2 -7 0 simundump kpool /kinetics/PI3K_mod/Gab1 0 0 0.7 0.7 4.2e+05 4.2e+05 0 0 6e+05 \ 0 /kinetics/geometry 44 brown 2 -5 0 simundump kreac /kinetics/PI3K_mod/bind_Gab1 0 5e-07 1 "" white brown 11 11 0 simundump kpool /kinetics/PI3K_mod/Shc*_Grb2-Gab1_clx 0 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry 50 brown 10 -3 0 simundump kreac /kinetics/PI3K_mod/PI3K_act 0 8.3336e-06 0.08 "" white brown \ 5 -13 0 simundump kreac /kinetics/PI3K_mod/basal_PI3K_act 0 0.00068 0.45 "" white \ brown 1 -19 0 simundump kpool /kinetics/PLCg_basal 0 0 0.0007 0.0007 420 420 0 0 6e+05 0 \ /kinetics/geometry 33 black -2 27 0 simundump kenz /kinetics/PLCg_basal/PLC_g_phospho 0 0 0 0 0 6e+05 1.3889e-05 \ 2 0.5 0 0 "" red 33 "" -3 23 0 simundump kpool /kinetics/Grb2 1 0 1 1 6e+05 6e+05 0 0 6e+05 0 \ /kinetics/geometry orange yellow 3 3 0 simundump kpool /kinetics/Shc* 1 0 0 0 0 0 0 0 6e+05 0 /kinetics/geometry \ orange yellow 0 -7 0 simundump kpool /kinetics/PTEN 0 0 0.27 0.27 1.62e+05 1.62e+05 0 0 6e+05 0 \ /kinetics/geometry 37 black 1 -16 0 simundump kenz /kinetics/PTEN/PIP3_dephosp 0 0 0 0 0 6e+05 0.00057292 22 5.5 \ 0 0 "" red 37 "" 9 -18 0 simundump kpool /kinetics/Ras-GTP_PI3K 0 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry 31 black -4 -23 0 simundump kenz /kinetics/Ras-GTP_PI3K/PIP2_phospho_Ras-GTP 0 0 0 0 0 6e+05 \ 8.3333e-06 16 4 0 0 "" red 31 "" -4 -22 0 simundump kreac /kinetics/PI3K_bind_Ras-GTP 0 3e-06 5 "" white black 13 -24 0 simundump doqcsinfo /kinetics/doqcsinfo 0 BDNF_Receptor.g BDNF_Receptor \ Pathway "Pragati Jain, NCBS" "Pragati Jain, NCBS" "citation here" \ "General Mammalian" "NIH 3T3 Expression" "Surface, Cytosol" Qualitative \ "Jain P, and Bhalla, U.S. PLoS Comput Biol. 2009 Feb;5(2). ( Peer-reviewed publication )" \ "Exact GENESIS implementation" "Approximates original data " 0 0 0 simundump xgraph /graphs/conc1 0 0 10070 0 0.88766 0 simundump xgraph /graphs/conc2 0 0 7890 0 0.47175 0 simundump xplot /graphs/conc2/BDNF_TrkB2*_clx.Co 3 524288 \ "delete_plot.w ; edit_plot.D " red 0 0 1 simundump xplot /graphs/conc2/BDNF_TrkB_clx.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 45 0 0 1 simundump xgraph /moregraphs/conc3 0 0 12000 0 0.25 0 simundump xgraph /moregraphs/conc4 0 0 12000 0 0.71395 0 simundump xplot /moregraphs/conc3/Shc*.Co 3 524288 \ "delete_plot.w ; edit_plot.D " orange 0 0 1 simundump xplot /moregraphs/conc3/PIP3.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 43 0 0 1 simundump xplot /moregraphs/conc3/Shc*_Grb2-Gab1_PI3K_clx.Co 3 524288 \ "delete_plot.w ; edit_plot.D " brown 0 0 1 simundump xplot /moregraphs/conc3/PI3K_basal.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 10 0 0 1 simundump xplot /moregraphs/conc3/Shc*_Grb2_clx.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 42 0 0 1 simundump xplot /moregraphs/conc3/TrKB.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 3 0 0 1 simundump xplot /moregraphs/conc3/Shc*_Grb2-Gab1_clx.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 50 0 0 1 simundump xplot /moregraphs/conc3/Ras-GTP_PI3K.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 31 0 0 1 simundump xcoredraw /edit/draw 0 -15 15 -26 35 simundump xtree /edit/draw/tree 0 \ /kinetics/#[],/kinetics/#[]/#[],/kinetics/#[]/#[]/#[][TYPE!=proto],/kinetics/#[]/#[]/#[][TYPE!=linkinfo]/##[] \ "edit_elm.D ; drag_from_edit.w " auto 0.6 simundump xtext /file/notes 0 1 xtextload /file/notes \ "" \ " " addmsg /kinetics/TrKB_mod/Ligand_binding /kinetics/BDNF REAC A B addmsg /kinetics/TrKB_mod/BDNF_TrkB2*_clx/PLC_g_phospho /kinetics/PLC_g REAC sA B addmsg /kinetics/TrKB_mod/PLC_g*_dephospho /kinetics/PLC_g REAC B A addmsg /kinetics/PLCg_basal/PLC_g_phospho /kinetics/PLC_g REAC sA B addmsg /kinetics/TrKB_mod/BDNF_TrkB2*_clx/PLC_g_phospho /kinetics/PLC_g* MM_PRD pA addmsg /kinetics/TrKB_mod/PLC_g*_dephospho /kinetics/PLC_g* REAC A B addmsg /kinetics/PLCg_basal/PLC_g_phospho /kinetics/PLC_g* MM_PRD pA addmsg /kinetics/TrKB_mod/Shc*_Grb2-Gab1_PI3K_clx/Phospho /kinetics/PIP3 MM_PRD pA addmsg /kinetics/PI3K_mod/PI3K_basal/basal_phosp /kinetics/PIP3 MM_PRD pA addmsg /kinetics/PTEN/PIP3_dephosp /kinetics/PIP3 REAC sA B addmsg /kinetics/Ras-GTP_PI3K/PIP2_phospho_Ras-GTP /kinetics/PIP3 MM_PRD pA addmsg /kinetics/TrKB_mod/LR_Internalize /kinetics/TrKB_mod/Int_BDNF_TrKB2*_clx REAC B A addmsg /kinetics/TrKB_mod/LR_cycling /kinetics/TrKB_mod/Int_BDNF_TrKB2*_clx REAC A B addmsg /kinetics/TrKB_mod/LR_Internalize /kinetics/TrKB_mod/Int_BDNF_TrKB2*_clx REAC B A addmsg /kinetics/TrKB_mod/Ligand_binding /kinetics/TrKB_mod/TrKB REAC A B addmsg /kinetics/TrKB_mod/Dimeriz_TrKB /kinetics/TrKB_mod/TrKB REAC A B addmsg /kinetics/TrKB_mod/LR_cycling /kinetics/TrKB_mod/TrKB REAC B A addmsg /kinetics/TrKB_mod/Dimeriz_TrKB /kinetics/TrKB_mod/BDNF_TrkB2_clx REAC B A addmsg /kinetics/TrKB_mod/Autophos_TrKB /kinetics/TrKB_mod/BDNF_TrkB2_clx REAC A B addmsg /kinetics/TrKB_mod/BDNF_TrkB2*_clx /kinetics/TrKB_mod/Autophos_TrKB PRODUCT n addmsg /kinetics/TrKB_mod/BDNF_TrkB2_clx /kinetics/TrKB_mod/Autophos_TrKB SUBSTRATE n addmsg /kinetics/TrKB_mod/BDNF_TrkB2_clx /kinetics/TrKB_mod/Dimeriz_TrKB PRODUCT n addmsg /kinetics/TrKB_mod/BDNF_TrkB_clx /kinetics/TrKB_mod/Dimeriz_TrKB SUBSTRATE n addmsg /kinetics/TrKB_mod/TrKB /kinetics/TrKB_mod/Dimeriz_TrKB SUBSTRATE n addmsg /kinetics/TrKB_mod/Ligand_binding /kinetics/TrKB_mod/BDNF_TrkB_clx REAC B A addmsg /kinetics/TrKB_mod/Dimeriz_TrKB /kinetics/TrKB_mod/BDNF_TrkB_clx REAC A B addmsg /kinetics/TrKB_mod/TrKB /kinetics/TrKB_mod/Ligand_binding SUBSTRATE n addmsg /kinetics/BDNF /kinetics/TrKB_mod/Ligand_binding SUBSTRATE n addmsg /kinetics/TrKB_mod/BDNF_TrkB_clx /kinetics/TrKB_mod/Ligand_binding PRODUCT n addmsg /kinetics/TrKB_mod/Autophos_TrKB /kinetics/TrKB_mod/BDNF_TrkB2*_clx REAC B A addmsg /kinetics/TrKB_mod/BDNF_TrkB2*_clx/PLC_g_phospho /kinetics/TrKB_mod/BDNF_TrkB2*_clx REAC eA B addmsg /kinetics/TrKB_mod/LR_Internalize /kinetics/TrKB_mod/BDNF_TrkB2*_clx REAC A B addmsg /kinetics/TrKB_mod/BDNF_TrkB2*_clx/Shc_phospho /kinetics/TrKB_mod/BDNF_TrkB2*_clx REAC eA B addmsg /kinetics/TrKB_mod/BDNF_TrkB2*_clx /kinetics/TrKB_mod/BDNF_TrkB2*_clx/PLC_g_phospho ENZYME n addmsg /kinetics/PLC_g /kinetics/TrKB_mod/BDNF_TrkB2*_clx/PLC_g_phospho SUBSTRATE n addmsg /kinetics/TrKB_mod/BDNF_TrkB2*_clx /kinetics/TrKB_mod/BDNF_TrkB2*_clx/Shc_phospho ENZYME n addmsg /kinetics/PI3K_mod/Shc /kinetics/TrKB_mod/BDNF_TrkB2*_clx/Shc_phospho SUBSTRATE n addmsg /kinetics/PLC_g* /kinetics/TrKB_mod/PLC_g*_dephospho SUBSTRATE n addmsg /kinetics/PLC_g /kinetics/TrKB_mod/PLC_g*_dephospho PRODUCT n addmsg /kinetics/PI3K_mod/PI3K_act /kinetics/TrKB_mod/Shc*_Grb2-Gab1_PI3K_clx REAC B A addmsg /kinetics/TrKB_mod/Shc*_Grb2-Gab1_PI3K_clx/Phospho /kinetics/TrKB_mod/Shc*_Grb2-Gab1_PI3K_clx REAC eA B addmsg /kinetics/TrKB_mod/Shc*_Grb2-Gab1_PI3K_clx /kinetics/TrKB_mod/Shc*_Grb2-Gab1_PI3K_clx/Phospho ENZYME n addmsg /kinetics/PI3K_mod/PIP2 /kinetics/TrKB_mod/Shc*_Grb2-Gab1_PI3K_clx/Phospho SUBSTRATE n addmsg /kinetics/TrKB_mod/Int_BDNF_TrKB2*_clx /kinetics/TrKB_mod/LR_Internalize PRODUCT n addmsg /kinetics/TrKB_mod/BDNF_TrkB2*_clx /kinetics/TrKB_mod/LR_Internalize SUBSTRATE n addmsg /kinetics/TrKB_mod/Int_BDNF_TrKB2*_clx /kinetics/TrKB_mod/LR_Internalize PRODUCT n addmsg /kinetics/TrKB_mod/Int_BDNF_TrKB2*_clx /kinetics/TrKB_mod/LR_cycling SUBSTRATE n addmsg /kinetics/TrKB_mod/TrKB /kinetics/TrKB_mod/LR_cycling PRODUCT n addmsg /kinetics/PI3K_mod/PI3K_act /kinetics/PI3K_mod/PI3K REAC A B addmsg /kinetics/PI3K_mod/basal_PI3K_act /kinetics/PI3K_mod/PI3K REAC A B addmsg /kinetics/PI3K_bind_Ras-GTP /kinetics/PI3K_mod/PI3K REAC A B addmsg /kinetics/PI3K_mod/PI3K_basal/basal_phosp /kinetics/PI3K_mod/PI3K_basal REAC eA B addmsg /kinetics/PI3K_mod/basal_PI3K_act /kinetics/PI3K_mod/PI3K_basal REAC B A addmsg /kinetics/PI3K_mod/PI3K_basal /kinetics/PI3K_mod/PI3K_basal/basal_phosp ENZYME n addmsg /kinetics/PI3K_mod/PIP2 /kinetics/PI3K_mod/PI3K_basal/basal_phosp SUBSTRATE n addmsg /kinetics/TrKB_mod/Shc*_Grb2-Gab1_PI3K_clx/Phospho /kinetics/PI3K_mod/PIP2 REAC sA B addmsg /kinetics/PI3K_mod/PI3K_basal/basal_phosp /kinetics/PI3K_mod/PIP2 REAC sA B addmsg /kinetics/PTEN/PIP3_dephosp /kinetics/PI3K_mod/PIP2 MM_PRD pA addmsg /kinetics/Ras-GTP_PI3K/PIP2_phospho_Ras-GTP /kinetics/PI3K_mod/PIP2 REAC sA B addmsg /kinetics/TrKB_mod/BDNF_TrkB2*_clx/Shc_phospho /kinetics/PI3K_mod/Shc REAC sA B addmsg /kinetics/PI3K_mod/Shc*_dephospho /kinetics/PI3K_mod/Shc REAC B A addmsg /kinetics/Shc* /kinetics/PI3K_mod/Shc*_dephospho SUBSTRATE n addmsg /kinetics/PI3K_mod/Shc /kinetics/PI3K_mod/Shc*_dephospho PRODUCT n addmsg /kinetics/Grb2 /kinetics/PI3K_mod/Grb2_bind_Shc SUBSTRATE n addmsg /kinetics/Shc* /kinetics/PI3K_mod/Grb2_bind_Shc SUBSTRATE n addmsg /kinetics/PI3K_mod/Shc*_Grb2_clx /kinetics/PI3K_mod/Grb2_bind_Shc PRODUCT n addmsg /kinetics/PI3K_mod/Grb2_bind_Shc /kinetics/PI3K_mod/Shc*_Grb2_clx REAC B A addmsg /kinetics/PI3K_mod/bind_Gab1 /kinetics/PI3K_mod/Shc*_Grb2_clx REAC A B addmsg /kinetics/PI3K_mod/bind_Gab1 /kinetics/PI3K_mod/Gab1 REAC A B addmsg /kinetics/PI3K_mod/Shc*_Grb2-Gab1_clx /kinetics/PI3K_mod/bind_Gab1 PRODUCT n addmsg /kinetics/PI3K_mod/Gab1 /kinetics/PI3K_mod/bind_Gab1 SUBSTRATE n addmsg /kinetics/PI3K_mod/Shc*_Grb2_clx /kinetics/PI3K_mod/bind_Gab1 SUBSTRATE n addmsg /kinetics/PI3K_mod/bind_Gab1 /kinetics/PI3K_mod/Shc*_Grb2-Gab1_clx REAC B A addmsg /kinetics/PI3K_mod/PI3K_act /kinetics/PI3K_mod/Shc*_Grb2-Gab1_clx REAC A B addmsg /kinetics/PI3K_mod/PI3K /kinetics/PI3K_mod/PI3K_act SUBSTRATE n addmsg /kinetics/TrKB_mod/Shc*_Grb2-Gab1_PI3K_clx /kinetics/PI3K_mod/PI3K_act PRODUCT n addmsg /kinetics/PI3K_mod/Shc*_Grb2-Gab1_clx /kinetics/PI3K_mod/PI3K_act SUBSTRATE n addmsg /kinetics/PI3K_mod/PI3K /kinetics/PI3K_mod/basal_PI3K_act SUBSTRATE n addmsg /kinetics/PI3K_mod/PI3K_basal /kinetics/PI3K_mod/basal_PI3K_act PRODUCT n addmsg /kinetics/PLCg_basal/PLC_g_phospho /kinetics/PLCg_basal REAC eA B addmsg /kinetics/PLCg_basal /kinetics/PLCg_basal/PLC_g_phospho ENZYME n addmsg /kinetics/PLC_g /kinetics/PLCg_basal/PLC_g_phospho SUBSTRATE n addmsg /kinetics/PI3K_mod/Grb2_bind_Shc /kinetics/Grb2 REAC A B addmsg /kinetics/TrKB_mod/BDNF_TrkB2*_clx/Shc_phospho /kinetics/Shc* MM_PRD pA addmsg /kinetics/PI3K_mod/Shc*_dephospho /kinetics/Shc* REAC A B addmsg /kinetics/PI3K_mod/Grb2_bind_Shc /kinetics/Shc* REAC A B addmsg /kinetics/PTEN/PIP3_dephosp /kinetics/PTEN REAC eA B addmsg /kinetics/PTEN /kinetics/PTEN/PIP3_dephosp ENZYME n addmsg /kinetics/PIP3 /kinetics/PTEN/PIP3_dephosp SUBSTRATE n addmsg /kinetics/PI3K_bind_Ras-GTP /kinetics/Ras-GTP_PI3K REAC B A addmsg /kinetics/Ras-GTP_PI3K/PIP2_phospho_Ras-GTP /kinetics/Ras-GTP_PI3K REAC eA B addmsg /kinetics/Ras-GTP_PI3K /kinetics/Ras-GTP_PI3K/PIP2_phospho_Ras-GTP ENZYME n addmsg /kinetics/PI3K_mod/PIP2 /kinetics/Ras-GTP_PI3K/PIP2_phospho_Ras-GTP SUBSTRATE n addmsg /kinetics/PI3K_mod/PI3K /kinetics/PI3K_bind_Ras-GTP SUBSTRATE n addmsg /kinetics/Ras-GTP_PI3K /kinetics/PI3K_bind_Ras-GTP PRODUCT n addmsg /kinetics/TrKB_mod/BDNF_TrkB2*_clx /graphs/conc2/BDNF_TrkB2*_clx.Co PLOT Co *BDNF_TrkB2*_clx.Co *red addmsg /kinetics/TrKB_mod/BDNF_TrkB_clx /graphs/conc2/BDNF_TrkB_clx.Co PLOT Co *BDNF_TrkB_clx.Co *45 addmsg /kinetics/Shc* /moregraphs/conc3/Shc*.Co PLOT Co *Shc*.Co *orange addmsg /kinetics/PIP3 /moregraphs/conc3/PIP3.Co PLOT Co *PIP3.Co *43 addmsg /kinetics/TrKB_mod/Shc*_Grb2-Gab1_PI3K_clx /moregraphs/conc3/Shc*_Grb2-Gab1_PI3K_clx.Co PLOT Co *Shc*_Grb2-Gab1_PI3K_clx.Co *brown addmsg /kinetics/PI3K_mod/PI3K_basal /moregraphs/conc3/PI3K_basal.Co PLOT Co *PI3K_basal.Co *10 addmsg /kinetics/PI3K_mod/Shc*_Grb2_clx /moregraphs/conc3/Shc*_Grb2_clx.Co PLOT Co *Shc*_Grb2_clx.Co *42 addmsg /kinetics/TrKB_mod/TrKB /moregraphs/conc3/TrKB.Co PLOT Co *TrKB.Co *3 addmsg /kinetics/PI3K_mod/Shc*_Grb2-Gab1_clx /moregraphs/conc3/Shc*_Grb2-Gab1_clx.Co PLOT Co *Shc*_Grb2-Gab1_clx.Co *50 addmsg /kinetics/Ras-GTP_PI3K /moregraphs/conc3/Ras-GTP_PI3K.Co PLOT Co *Ras-GTP_PI3K.Co *31 enddump // End of dump call /kinetics/Grb2/notes LOAD \ "There is probably a lot of it in the cell: it is also known" \ "as Ash (abundant src homology protein I think). Also " \ "Waters et al JBC 271:30 18224 1996 say that only a small" \ "fraction of cellular Grb is precipitated out when SoS is" \ "precipitated. As most of the Sos seems to be associated" \ "with Grb2, it would seem like there is a lot of the latter." \ "Say 1 uM. I haven't been able to find a decent...." call /kinetics/doqcsinfo/notes LOAD \ "BDNF recetor signaling is one of the sub-model in BDNF signaling cascade. " \ "BDNF activates TrKB, leading to the stimulation of PI3K and formation of PIP3. " complete_loading