//genesis
// kkit Version 11 flat dumpfile
 
// Saved on Thu Feb 12 16:28:29 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 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
simobjdump doqcsinfo filename accessname accesstype transcriber developer \
  citation species tissue cellcompartment methodology sources \
  model_implementation model_validation editfunc
simundump geometry /kinetics/geometry 0 9.9997e-16 3 sphere "" white black 0 \
  0 0
simundump text /kinetics/notes 0 ""
call /kinetics/notes LOAD \
""
simundump text /kinetics/geometry/notes 0 ""
call /kinetics/geometry/notes LOAD \
""
simundump group /kinetics/AKT_mod 0 yellow black x 0 0 "" AKT_mod \
  defaultfile.g 0 a44d80224b3711204bfc2283c8c64702 0 5 8 0
simundump text /kinetics/AKT_mod/notes 0 ""
call /kinetics/AKT_mod/notes LOAD \
""
simundump kpool /kinetics/AKT_mod/PIP3_AKT 0 0 0 0 0 0 0 0 5.9998e+05 0 \
  /kinetics/geometry 53 yellow -8 4 0
simundump text /kinetics/AKT_mod/PIP3_AKT/notes 0 ""
call /kinetics/AKT_mod/PIP3_AKT/notes LOAD \
""
simundump kpool /kinetics/AKT_mod/PIP3_PDK1 0 0 0 0 0 0 0 0 6e+05 0 \
  /kinetics/geometry 9 yellow -4 10 0
simundump text /kinetics/AKT_mod/PIP3_PDK1/notes 0 ""
call /kinetics/AKT_mod/PIP3_PDK1/notes LOAD \
""
simundump kenz /kinetics/AKT_mod/PIP3_PDK1/phospho_thr308 0 0 0 0 0 2999.9 \
  0.00020834 40 10 0 0 "" red 9 "" -4 8 0
simundump text /kinetics/AKT_mod/PIP3_PDK1/phospho_thr308/notes 0 ""
call /kinetics/AKT_mod/PIP3_PDK1/phospho_thr308/notes LOAD \
""
simundump kpool /kinetics/AKT_mod/PIP3_PDK2 0 0 0.003 0.003 1800 1800 0 0 \
  6e+05 0 /kinetics/geometry 39 yellow 2 11 0
simundump text /kinetics/AKT_mod/PIP3_PDK2/notes 0 ""
call /kinetics/AKT_mod/PIP3_PDK2/notes LOAD \
""
simundump kenz /kinetics/AKT_mod/PIP3_PDK2/phosp_AKTser473 0 0 0 0 0 6e+05 \
  0.00020833 80 20 0 0 "" red 39 "" 2 9 0
simundump text /kinetics/AKT_mod/PIP3_PDK2/phosp_AKTser473/notes 0 ""
call /kinetics/AKT_mod/PIP3_PDK2/phosp_AKTser473/notes LOAD \
""
simundump kpool /kinetics/AKT_mod/PIP3_AKT_thr308 0 0 0 0 0 0 0 0 5.9998e+05 \
  0 /kinetics/geometry 60 yellow -1 4 0
simundump text /kinetics/AKT_mod/PIP3_AKT_thr308/notes 0 ""
call /kinetics/AKT_mod/PIP3_AKT_thr308/notes LOAD \
""
simundump kpool /kinetics/AKT_mod/PIP3_AKT-t308_s473 0 0 0 0 0 0 0 0 6e+05 0 \
  /kinetics/geometry 25 yellow 9 11 0
simundump text /kinetics/AKT_mod/PIP3_AKT-t308_s473/notes 0 aaa
call /kinetics/AKT_mod/PIP3_AKT-t308_s473/notes LOAD \
"aaa"
simundump kenz /kinetics/AKT_mod/PIP3_AKT-t308_s473/TSC2_phospho 0 0 0 0 0 \
  6e+05 4.8544e-06 24 6 0 0 "" red 25 "" 9 9 0
simundump text /kinetics/AKT_mod/PIP3_AKT-t308_s473/TSC2_phospho/notes 0 ""
call /kinetics/AKT_mod/PIP3_AKT-t308_s473/TSC2_phospho/notes LOAD \
""
simundump kpool /kinetics/AKT_mod/AKT 0 0 0.20001 0.20001 1.2e+05 1.2e+05 0 0 \
  5.9998e+05 0 /kinetics/geometry 4 yellow -11 1 0
simundump text /kinetics/AKT_mod/AKT/notes 0 ""
call /kinetics/AKT_mod/AKT/notes LOAD \
""
simundump kpool /kinetics/AKT_mod/TSC1-TSC2* 0 0 0 0 0 0 0 0 6e+05 0 \
  /kinetics/geometry 40 yellow 3 3 0
simundump text /kinetics/AKT_mod/TSC1-TSC2*/notes 0 ""
call /kinetics/AKT_mod/TSC1-TSC2*/notes LOAD \
""
simundump kreac /kinetics/AKT_mod/PIP3_bind_AKT 0 7.5003e-05 0.089 "" white \
  yellow -11 4 0
simundump text /kinetics/AKT_mod/PIP3_bind_AKT/notes 0 ""
call /kinetics/AKT_mod/PIP3_bind_AKT/notes LOAD \
""
simundump kreac /kinetics/AKT_mod/PIP3_bind_PDK1 0 1.1667e-06 0.98 "" white \
  yellow -8 6 0
simundump text /kinetics/AKT_mod/PIP3_bind_PDK1/notes 0 ""
call /kinetics/AKT_mod/PIP3_bind_PDK1/notes LOAD \
""
simundump kreac /kinetics/AKT_mod/TSC1-2_dephospho 0 0.01 0 "" white yellow 5 \
  0 0
simundump text /kinetics/AKT_mod/TSC1-2_dephospho/notes 0 ""
call /kinetics/AKT_mod/TSC1-2_dephospho/notes LOAD \
""
simundump kpool /kinetics/PIP3 0 0 0 0 0 0 0 0 5.9998e+05 0 \
  /kinetics/geometry 43 black -11 11 0
simundump text /kinetics/PIP3/notes 0 ""
call /kinetics/PIP3/notes LOAD \
""
simundump kpool /kinetics/PDK1 0 0 1 1 6e+05 6e+05 0 0 6e+05 0 \
  /kinetics/geometry 37 black -7 11 0
simundump text /kinetics/PDK1/notes 0 ""
call /kinetics/PDK1/notes LOAD \
""
simundump kpool /kinetics/PP2A 0 0 0.15 0.15 90000 90000 0 0 6e+05 0 \
  /kinetics/geometry 4 black 11 1 0
simundump text /kinetics/PP2A/notes 0 "Protein Phosphatase"
call /kinetics/PP2A/notes LOAD \
"Protein Phosphatase"
simundump kenz /kinetics/PP2A/Dephos_AKTser473 0 0 0 0 0 6e+05 3.125e-06 7.2 \
  1.8 0 0 "" red 46 "" 3 -8 0
simundump text /kinetics/PP2A/Dephos_AKTser473/notes 0 ""
call /kinetics/PP2A/Dephos_AKTser473/notes LOAD \
""
simundump kenz /kinetics/PP2A/Dephosph_AKTthr308 0 0 0 0 0 6e+05 3.1249e-06 \
  7.2 1.8 0 0 "" red 46 "" 0 -8 0
simundump text /kinetics/PP2A/Dephosph_AKTthr308/notes 0 ""
call /kinetics/PP2A/Dephosph_AKTthr308/notes LOAD \
""
simundump kpool /kinetics/TSC1-TSC2 0 0 1 1 6e+05 6e+05 0 0 6e+05 0 \
  /kinetics/geometry 51 black 9 4 0
simundump text /kinetics/TSC1-TSC2/notes 0 ""
call /kinetics/TSC1-TSC2/notes LOAD \
""
simundump kenz /kinetics/TSC1-TSC2/TSC2phospho 0 0 0 0 0 6e+05 0.00055556 80 \
  20 0 0 "" red 51 "" 9 3 0
simundump text /kinetics/TSC1-TSC2/TSC2phospho/notes 0 ""
call /kinetics/TSC1-TSC2/TSC2phospho/notes LOAD \
""
simundump kpool /kinetics/Rheb-GTP 0 0 1 1 6e+05 6e+05 0 0 6e+05 0 \
  /kinetics/geometry 28 black 12 -2 0
simundump text /kinetics/Rheb-GTP/notes 0 ""
call /kinetics/Rheb-GTP/notes LOAD \
""
simundump kpool /kinetics/Rheb-GDP 0 0 0 0 0 0 0 0 6e+05 0 /kinetics/geometry \
  39 black 7 -1 0
simundump text /kinetics/Rheb-GDP/notes 0 ""
call /kinetics/Rheb-GDP/notes LOAD \
""
simundump kreac /kinetics/GDP_to_GTP 0 0.2 0 "" white black 9 -6 0
simundump text /kinetics/GDP_to_GTP/notes 0 ""
call /kinetics/GDP_to_GTP/notes LOAD \
""
simundump doqcsinfo /kinetics/doqcsinfo 0 AKT.g AKT Network \
  "Pragati Jain, NCBS" "Pragati Jain, NCBS" "citation here" \
  "General Mammalian" Brain "Surface, Cytosol" Qualitative "<a href=http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000287>Jain P, and Bhalla, U.S. PLoS Comput Biol. 2009 Feb;5(2).</a> ( Peer-reviewed publication )" \
  "Exact GENESIS implementation" "Approximates original data " show_dumpdb
simundump text /kinetics/doqcsinfo/notes 0 \
  "This is one of the sub-model of BDNF signaling cascade.\nPIP3 activies AKT, leading to accumulation of Rheb-GTP, a regulator of mTOR."
call /kinetics/doqcsinfo/notes LOAD \
"This is one of the sub-model of BDNF signaling cascade." \
"PIP3 activies AKT, leading to accumulation of Rheb-GTP, a regulator of mTOR."
simundump xgraph /graphs/conc1 0 0 1000 0 1 0
simundump xgraph /graphs/conc2 0 0 1000 0 1 0
simundump xplot /graphs/conc1/PIP3_AKT-t308_s473.Co 3 524288 \
  "delete_plot.w <s> <d>; edit_plot.D <w>" 25 0 0 1
simundump xplot /graphs/conc1/PIP3_AKT_thr308.Co 3 524288 \
  "delete_plot.w <s> <d>; edit_plot.D <w>" 60 0 0 1
simundump xgraph /moregraphs/conc3 0 0 100 0 1 0
simundump xgraph /moregraphs/conc4 0 0 100 0 1 0
simundump xcoredraw /edit/draw 0 -13 14 -10 13
simundump xtree /edit/draw/tree 0 \
  /kinetics/#[],/kinetics/#[]/#[],/kinetics/#[]/#[]/#[][TYPE!=proto],/kinetics/#[]/#[]/#[][TYPE!=linkinfo]/##[] \
  "edit_elm.D <v>; drag_from_edit.w <d> <S> <x> <y> <z>" auto 0.6
simundump xtext /file/notes 0 1
xtextload /file/notes \
"" \
" "
addmsg /kinetics/AKT_mod/PIP3_bind_AKT /kinetics/AKT_mod/PIP3_AKT REAC B A 
addmsg /kinetics/AKT_mod/PIP3_PDK1/phospho_thr308 /kinetics/AKT_mod/PIP3_AKT REAC sA B 
addmsg /kinetics/PP2A/Dephosph_AKTthr308 /kinetics/AKT_mod/PIP3_AKT MM_PRD pA 
addmsg /kinetics/AKT_mod/PIP3_bind_PDK1 /kinetics/AKT_mod/PIP3_PDK1 REAC B A 
addmsg /kinetics/AKT_mod/PIP3_PDK1/phospho_thr308 /kinetics/AKT_mod/PIP3_PDK1 REAC eA B 
addmsg /kinetics/AKT_mod/PIP3_PDK1 /kinetics/AKT_mod/PIP3_PDK1/phospho_thr308 ENZYME n 
addmsg /kinetics/AKT_mod/PIP3_AKT /kinetics/AKT_mod/PIP3_PDK1/phospho_thr308 SUBSTRATE n 
addmsg /kinetics/AKT_mod/PIP3_PDK2/phosp_AKTser473 /kinetics/AKT_mod/PIP3_PDK2 REAC eA B 
addmsg /kinetics/AKT_mod/PIP3_PDK2 /kinetics/AKT_mod/PIP3_PDK2/phosp_AKTser473 ENZYME n 
addmsg /kinetics/AKT_mod/PIP3_AKT_thr308 /kinetics/AKT_mod/PIP3_PDK2/phosp_AKTser473 SUBSTRATE n 
addmsg /kinetics/AKT_mod/PIP3_PDK1/phospho_thr308 /kinetics/AKT_mod/PIP3_AKT_thr308 MM_PRD pA 
addmsg /kinetics/AKT_mod/PIP3_PDK2/phosp_AKTser473 /kinetics/AKT_mod/PIP3_AKT_thr308 REAC sA B 
addmsg /kinetics/PP2A/Dephos_AKTser473 /kinetics/AKT_mod/PIP3_AKT_thr308 MM_PRD pA 
addmsg /kinetics/PP2A/Dephosph_AKTthr308 /kinetics/AKT_mod/PIP3_AKT_thr308 REAC sA B 
addmsg /kinetics/AKT_mod/PIP3_PDK2/phosp_AKTser473 /kinetics/AKT_mod/PIP3_AKT-t308_s473 MM_PRD pA 
addmsg /kinetics/PP2A/Dephos_AKTser473 /kinetics/AKT_mod/PIP3_AKT-t308_s473 REAC sA B 
addmsg /kinetics/AKT_mod/PIP3_AKT-t308_s473/TSC2_phospho /kinetics/AKT_mod/PIP3_AKT-t308_s473 REAC eA B 
addmsg /kinetics/AKT_mod/PIP3_AKT-t308_s473 /kinetics/AKT_mod/PIP3_AKT-t308_s473/TSC2_phospho ENZYME n 
addmsg /kinetics/TSC1-TSC2 /kinetics/AKT_mod/PIP3_AKT-t308_s473/TSC2_phospho SUBSTRATE n 
addmsg /kinetics/AKT_mod/PIP3_bind_AKT /kinetics/AKT_mod/AKT REAC A B 
addmsg /kinetics/AKT_mod/PIP3_AKT-t308_s473/TSC2_phospho /kinetics/AKT_mod/TSC1-TSC2* MM_PRD pA 
addmsg /kinetics/AKT_mod/TSC1-2_dephospho /kinetics/AKT_mod/TSC1-TSC2* REAC A B 
addmsg /kinetics/AKT_mod/AKT /kinetics/AKT_mod/PIP3_bind_AKT SUBSTRATE n 
addmsg /kinetics/PIP3 /kinetics/AKT_mod/PIP3_bind_AKT SUBSTRATE n 
addmsg /kinetics/AKT_mod/PIP3_AKT /kinetics/AKT_mod/PIP3_bind_AKT PRODUCT n 
addmsg /kinetics/PDK1 /kinetics/AKT_mod/PIP3_bind_PDK1 SUBSTRATE n 
addmsg /kinetics/PIP3 /kinetics/AKT_mod/PIP3_bind_PDK1 SUBSTRATE n 
addmsg /kinetics/AKT_mod/PIP3_PDK1 /kinetics/AKT_mod/PIP3_bind_PDK1 PRODUCT n 
addmsg /kinetics/AKT_mod/TSC1-TSC2* /kinetics/AKT_mod/TSC1-2_dephospho SUBSTRATE n 
addmsg /kinetics/TSC1-TSC2 /kinetics/AKT_mod/TSC1-2_dephospho PRODUCT n 
addmsg /kinetics/AKT_mod/PIP3_bind_PDK1 /kinetics/PIP3 REAC A B 
addmsg /kinetics/AKT_mod/PIP3_bind_AKT /kinetics/PIP3 REAC A B 
addmsg /kinetics/AKT_mod/PIP3_bind_PDK1 /kinetics/PDK1 REAC A B 
addmsg /kinetics/PP2A/Dephos_AKTser473 /kinetics/PP2A REAC eA B 
addmsg /kinetics/PP2A/Dephosph_AKTthr308 /kinetics/PP2A REAC eA B 
addmsg /kinetics/PP2A /kinetics/PP2A/Dephos_AKTser473 ENZYME n 
addmsg /kinetics/AKT_mod/PIP3_AKT-t308_s473 /kinetics/PP2A/Dephos_AKTser473 SUBSTRATE n 
addmsg /kinetics/PP2A /kinetics/PP2A/Dephosph_AKTthr308 ENZYME n 
addmsg /kinetics/AKT_mod/PIP3_AKT_thr308 /kinetics/PP2A/Dephosph_AKTthr308 SUBSTRATE n 
addmsg /kinetics/AKT_mod/PIP3_AKT-t308_s473/TSC2_phospho /kinetics/TSC1-TSC2 REAC sA B 
addmsg /kinetics/AKT_mod/TSC1-2_dephospho /kinetics/TSC1-TSC2 REAC B A 
addmsg /kinetics/TSC1-TSC2/TSC2phospho /kinetics/TSC1-TSC2 REAC eA B 
addmsg /kinetics/TSC1-TSC2 /kinetics/TSC1-TSC2/TSC2phospho ENZYME n 
addmsg /kinetics/Rheb-GTP /kinetics/TSC1-TSC2/TSC2phospho SUBSTRATE n 
addmsg /kinetics/TSC1-TSC2/TSC2phospho /kinetics/Rheb-GTP REAC sA B 
addmsg /kinetics/GDP_to_GTP /kinetics/Rheb-GTP REAC B A 
addmsg /kinetics/TSC1-TSC2/TSC2phospho /kinetics/Rheb-GDP MM_PRD pA 
addmsg /kinetics/GDP_to_GTP /kinetics/Rheb-GDP REAC A B 
addmsg /kinetics/Rheb-GDP /kinetics/GDP_to_GTP SUBSTRATE n 
addmsg /kinetics/Rheb-GTP /kinetics/GDP_to_GTP PRODUCT n 
addmsg /kinetics/AKT_mod/PIP3_AKT-t308_s473 /graphs/conc1/PIP3_AKT-t308_s473.Co PLOT Co *PIP3_AKT-t308_s473.Co *25 
addmsg /kinetics/AKT_mod/PIP3_AKT_thr308 /graphs/conc1/PIP3_AKT_thr308.Co PLOT Co *PIP3_AKT_thr308.Co *60 
enddump
// End of dump

call /kinetics/AKT_mod/PIP3_AKT-t308_s473/notes LOAD \
"aaa"
call /kinetics/PP2A/notes LOAD \
"Protein Phosphatase"
call /kinetics/doqcsinfo/notes LOAD \
"This is one of the sub-model of BDNF signaling cascade." \
"PIP3 activies AKT, leading to accumulation of Rheb-GTP, a regulator of mTOR."
complete_loading