//genesis
// kkit Version 9 flat dumpfile
 
// Saved on Fri Mar 14 12:46:38 2003
 
include kkit {argv 1}
 
FASTDT = 0.005
SIMDT = 0.005
CONTROLDT = 1
PLOTDT = 1
MAXTIME = 2000
TRANSIENT_TIME = 2
VARIABLE_DT_FLAG = 0
DEFAULT_VOL = 1.6667e-21
VERSION = 9.0
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 kpool CoTotal CoInit Co n nInit nTotal nMin vol slave_enable notes \
  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 linkinfo xtree_fg_req xtree_textfg_req uplink downlink x y z
simobjdump uplink xtree_fg_req xtree_textfg_req x y z
simobjdump downlink xtree_fg_req xtree_textfg_req x y z
simobjdump mirror notes xtree_fg_req x y z
simundump group /kinetics/PKC 0 blue black x 0 0 "" defaultfile defaultfile.g \
  0 0 0 -3.0493 8.2163 0
simundump kpool /kinetics/PKC/PKC-Ca 0 0.28282 3.7208e-17 3.7208e-17 \
  2.2325e-11 2.2325e-11 1.6969e+05 0 6e+05 0 "" red black -4.0752 1.5108 0
simundump kreac /kinetics/PKC/PKC-act-by-Ca 0 1e-06 0.5 "" white blue -4.0752 \
  -0.12295 0
simundump kreac /kinetics/PKC/PKC-act-by-DAG 0 1.3333e-08 8.6348 "" white \
  blue -2.0612 0.69395 0
simundump kreac /kinetics/PKC/PKC-Ca-to-memb 0 1.2705 3.5026 "" white blue \
  -3.7974 4.2533 0
simundump kreac /kinetics/PKC/PKC-DAG-to-memb 0 1 0.1 "" white blue -2.6168 \
  2.7362 0
simundump kreac /kinetics/PKC/PKC-act-by-Ca-AA 0 2e-09 0.1 "" white blue \
  -0.78797 3.8157 0
simundump kreac /kinetics/PKC/PKC-act-by-DAG-AA 0 2 0.2 "" white blue 1.2492 \
  3.2322 0
simundump kpool /kinetics/PKC/PKC-DAG-AA* 0 0.12061 4.9137e-18 4.9137e-18 \
  2.9482e-12 2.9482e-12 72366 0 6e+05 0 "" cyan blue 0.60098 5.537 0
simundump kpool /kinetics/PKC/PKC-Ca-AA* 0 0.16962 1.75e-16 1.75e-16 1.05e-10 \
  1.05e-10 1.0177e+05 0 6e+05 0 "" orange blue -0.60278 6.2956 0
simundump kpool /kinetics/PKC/PKC-Ca-memb* 0 0.10258 1.3896e-17 1.3896e-17 \
  8.3376e-12 8.3376e-12 61549 0 6e+05 0 "" pink blue -2.7788 6.529 0
simundump kpool /kinetics/PKC/PKC-DAG-memb* 0 0.023753 9.4352e-21 9.4352e-21 \
  5.6611e-15 5.6611e-15 14252 0 6e+05 0 "" yellow blue -1.8297 5.5078 0
simundump kpool /kinetics/PKC/PKC-basal* 0 0.0432 0.02 0.02 12000 12000 25920 \
  0 6e+05 0 "" pink blue -4.7465 5.5662 0
simundump kreac /kinetics/PKC/PKC-basal-act 0 1 50 "" white blue -4.978 \
  3.0571 0
simundump kpool /kinetics/PKC/PKC-AA* 0 1 1.8133e-17 1.8133e-17 1.088e-11 \
  1.088e-11 6e+05 0 6e+05 0 "" cyan blue 1.7816 6.8207 0
simundump kreac /kinetics/PKC/PKC-act-by-AA 0 2e-10 0.1 "" white blue -4.9925 \
  -1.8654 0
simundump kpool /kinetics/PKC/PKC-Ca-DAG 0 0.0017993 8.4632e-23 8.4632e-23 \
  5.0779e-17 5.0779e-17 1079.6 0 6e+05 0 "" white blue 0.2306 1.8026 0
simundump kreac /kinetics/PKC/PKC-n-DAG 0 1e-09 0.1 "" white blue -3.0103 \
  -1.9902 0
simundump kpool /kinetics/PKC/PKC-DAG 0 0.08533 1.161e-16 1.161e-16 \
  6.9661e-11 6.9661e-11 51198 0 6e+05 0 "" white blue -0.99631 -1.0857 0
simundump kreac /kinetics/PKC/PKC-n-DAG-AA 0 3e-08 2 "" white blue -1.2278 \
  -2.9529 0
simundump kpool /kinetics/PKC/PKC-DAG-AA 0 0.012093 2.5188e-19 2.5188e-19 \
  1.5113e-13 1.5113e-13 7255.5 0 6e+05 0 "" white blue 0.62413 0.22715 0
simundump kpool /kinetics/PKC/PKC-cytosolic 0 1.5489 1 1 6e+05 6e+05 \
  9.2935e+05 0 6e+05 0 "" white blue -6.1315 0.59711 0
simundump kpool /kinetics/DAG 1 150 11 11 6.6e+06 6.6e+06 9e+07 0 6e+05 4 "" \
  green black -3.2051 -4.7168 0
simundump kpool /kinetics/Ca 1 1 0.08 0.08 48000 48000 6e+05 0 6e+05 4 "" red \
  black -8.3874 -2.7634 0
simundump kpool /kinetics/AA 0 50 5 5 3e+06 3e+06 3e+07 0 6e+05 4 "" \
  darkgreen black -3.2898 -9.3376 0
simundump kpool /kinetics/PKC-active 0 0.02 2.1222e-16 2.1222e-16 1.2733e-10 \
  1.2733e-10 12000 0 6e+05 2 "" yellow black 2.1325 8.477 0
simundump xgraph /graphs/conc1 0 0 500 0 1 0
simundump xgraph /graphs/conc2 0 0 500 0 50 0
simundump xplot /graphs/conc1/PKC-active.Co 3 524288 \
  "delete_plot.w <s> <d>; edit_plot.D <w>" yellow 0 0 1
simundump xgraph /moregraphs/conc3 0 0 500 0 1 0
simundump xgraph /moregraphs/conc4 0 0 500 0 1 0
simundump xcoredraw /edit/draw 0 -12.002 6.3591 -14.342 4.0202
simundump xtree /edit/draw/tree 0 /kinetics/##[] \
  "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 \
"Demo for figures. Set up some plots." \
"Same as pkc46.g, fixed up plots, changed basal levels of DAG and" \
"AA"
addmsg /kinetics/PKC/PKC-act-by-Ca /kinetics/PKC/PKC-Ca REAC B A 
addmsg /kinetics/PKC/PKC-act-by-DAG /kinetics/PKC/PKC-Ca REAC A B 
addmsg /kinetics/PKC/PKC-Ca-to-memb /kinetics/PKC/PKC-Ca REAC A B 
addmsg /kinetics/PKC/PKC-act-by-Ca-AA /kinetics/PKC/PKC-Ca REAC A B 
addmsg /kinetics/PKC/PKC-cytosolic /kinetics/PKC/PKC-act-by-Ca SUBSTRATE n 
addmsg /kinetics/Ca /kinetics/PKC/PKC-act-by-Ca SUBSTRATE n 
addmsg /kinetics/PKC/PKC-Ca /kinetics/PKC/PKC-act-by-Ca PRODUCT n 
addmsg /kinetics/DAG /kinetics/PKC/PKC-act-by-DAG SUBSTRATE n 
addmsg /kinetics/PKC/PKC-Ca /kinetics/PKC/PKC-act-by-DAG SUBSTRATE n 
addmsg /kinetics/PKC/PKC-Ca-DAG /kinetics/PKC/PKC-act-by-DAG PRODUCT n 
addmsg /kinetics/PKC/PKC-Ca /kinetics/PKC/PKC-Ca-to-memb SUBSTRATE n 
addmsg /kinetics/PKC/PKC-Ca-memb* /kinetics/PKC/PKC-Ca-to-memb PRODUCT n 
addmsg /kinetics/PKC/PKC-Ca-DAG /kinetics/PKC/PKC-DAG-to-memb SUBSTRATE n 
addmsg /kinetics/PKC/PKC-DAG-memb* /kinetics/PKC/PKC-DAG-to-memb PRODUCT n 
addmsg /kinetics/PKC/PKC-Ca /kinetics/PKC/PKC-act-by-Ca-AA SUBSTRATE n 
addmsg /kinetics/AA /kinetics/PKC/PKC-act-by-Ca-AA SUBSTRATE n 
addmsg /kinetics/PKC/PKC-Ca-AA* /kinetics/PKC/PKC-act-by-Ca-AA PRODUCT n 
addmsg /kinetics/PKC/PKC-DAG-AA* /kinetics/PKC/PKC-act-by-DAG-AA PRODUCT n 
addmsg /kinetics/PKC/PKC-DAG-AA /kinetics/PKC/PKC-act-by-DAG-AA SUBSTRATE n 
addmsg /kinetics/PKC/PKC-act-by-DAG-AA /kinetics/PKC/PKC-DAG-AA* REAC B A 
addmsg /kinetics/PKC/PKC-act-by-Ca-AA /kinetics/PKC/PKC-Ca-AA* REAC B A 
addmsg /kinetics/PKC/PKC-Ca-to-memb /kinetics/PKC/PKC-Ca-memb* REAC B A 
addmsg /kinetics/PKC/PKC-DAG-to-memb /kinetics/PKC/PKC-DAG-memb* REAC B A 
addmsg /kinetics/PKC/PKC-basal-act /kinetics/PKC/PKC-basal* REAC B A 
addmsg /kinetics/PKC/PKC-cytosolic /kinetics/PKC/PKC-basal-act SUBSTRATE n 
addmsg /kinetics/PKC/PKC-basal* /kinetics/PKC/PKC-basal-act PRODUCT n 
addmsg /kinetics/PKC/PKC-act-by-AA /kinetics/PKC/PKC-AA* REAC B A 
addmsg /kinetics/AA /kinetics/PKC/PKC-act-by-AA SUBSTRATE n 
addmsg /kinetics/PKC/PKC-AA* /kinetics/PKC/PKC-act-by-AA PRODUCT n 
addmsg /kinetics/PKC/PKC-cytosolic /kinetics/PKC/PKC-act-by-AA SUBSTRATE n 
addmsg /kinetics/PKC/PKC-act-by-DAG /kinetics/PKC/PKC-Ca-DAG REAC B A 
addmsg /kinetics/PKC/PKC-DAG-to-memb /kinetics/PKC/PKC-Ca-DAG REAC A B 
addmsg /kinetics/PKC/PKC-cytosolic /kinetics/PKC/PKC-n-DAG SUBSTRATE n 
addmsg /kinetics/DAG /kinetics/PKC/PKC-n-DAG SUBSTRATE n 
addmsg /kinetics/PKC/PKC-DAG /kinetics/PKC/PKC-n-DAG PRODUCT n 
addmsg /kinetics/PKC/PKC-n-DAG /kinetics/PKC/PKC-DAG REAC B A 
addmsg /kinetics/PKC/PKC-n-DAG-AA /kinetics/PKC/PKC-DAG REAC A B 
addmsg /kinetics/PKC/PKC-DAG /kinetics/PKC/PKC-n-DAG-AA SUBSTRATE n 
addmsg /kinetics/AA /kinetics/PKC/PKC-n-DAG-AA SUBSTRATE n 
addmsg /kinetics/PKC/PKC-DAG-AA /kinetics/PKC/PKC-n-DAG-AA PRODUCT n 
addmsg /kinetics/PKC/PKC-n-DAG-AA /kinetics/PKC/PKC-DAG-AA REAC B A 
addmsg /kinetics/PKC/PKC-act-by-DAG-AA /kinetics/PKC/PKC-DAG-AA REAC A B 
addmsg /kinetics/PKC/PKC-act-by-Ca /kinetics/PKC/PKC-cytosolic REAC A B 
addmsg /kinetics/PKC/PKC-basal-act /kinetics/PKC/PKC-cytosolic REAC A B 
addmsg /kinetics/PKC/PKC-act-by-AA /kinetics/PKC/PKC-cytosolic REAC A B 
addmsg /kinetics/PKC/PKC-n-DAG /kinetics/PKC/PKC-cytosolic REAC A B 
addmsg /kinetics/PKC/PKC-act-by-DAG /kinetics/DAG REAC A B 
addmsg /kinetics/PKC/PKC-n-DAG /kinetics/DAG REAC A B 
addmsg /kinetics/PKC/PKC-act-by-Ca /kinetics/Ca REAC A B 
addmsg /kinetics/PKC/PKC-act-by-Ca-AA /kinetics/AA REAC A B 
addmsg /kinetics/PKC/PKC-act-by-AA /kinetics/AA REAC A B 
addmsg /kinetics/PKC/PKC-n-DAG-AA /kinetics/AA REAC A B 
addmsg /kinetics/PKC/PKC-DAG-AA* /kinetics/PKC-active SUMTOTAL n nInit 
addmsg /kinetics/PKC/PKC-Ca-memb* /kinetics/PKC-active SUMTOTAL n nInit 
addmsg /kinetics/PKC/PKC-Ca-AA* /kinetics/PKC-active SUMTOTAL n nInit 
addmsg /kinetics/PKC/PKC-DAG-memb* /kinetics/PKC-active SUMTOTAL n nInit 
addmsg /kinetics/PKC/PKC-basal* /kinetics/PKC-active SUMTOTAL n nInit 
addmsg /kinetics/PKC/PKC-AA* /kinetics/PKC-active SUMTOTAL n nInit 
addmsg /kinetics/PKC-active /graphs/conc1/PKC-active.Co PLOT Co *PKC-active.Co *yellow 
enddump
// End of dump

call /kinetics/PKC/PKC-act-by-Ca/notes LOAD \
"Need est of rate of assoc of Ca and PKC. Assume it is fast" \
"The original parameter-searched kf of 439.4 has been" \
"scaled by 1/6e8 to account for change of units to n. Kf now 8.16e-7, kb=.6085" \
"Raised kf to 1e-6 to match Ca curve, kb to .5" \
""
call /kinetics/PKC/PKC-act-by-DAG/notes LOAD \
"Need est of rate. Assume it is fast" \
"Obtained from param search" \
"kf raised 10 X : see Shinomura et al PNAS 88 5149-5153 1991." \
"kf changed from 3.865e-7 to 2.0e-7 in line with closer analysis of" \
"Shinomura data." \
"26 June 1996: Corrected DAG data: reduce kf 15x from " \
"2e-7 to 1.333e-8"
call /kinetics/PKC/PKC-DAG-to-memb/notes LOAD \
"Raise kb from .087 to 0.1 to match data from Shinomura et al." \
"Lower kf from 1.155 to 1.0 to match data from Shinomura et al."
call /kinetics/PKC/PKC-act-by-Ca-AA/notes LOAD \
"Schaechter and Benowitz We have to increase Kf for conc scaling" \
"Changed kf to 2e-9 on Sept 19, 94. This gives better match." \
""
call /kinetics/PKC/PKC-act-by-DAG-AA/notes LOAD \
"Assume slowish too. Schaechter and Benowitz"
call /kinetics/PKC/PKC-basal-act/notes LOAD \
"Initial basal levels were set by kf = 1, kb = 20. In model, though, the" \
"basal levels of PKC activity are higher."
call /kinetics/PKC/PKC-act-by-AA/notes LOAD \
"Raise kf from 1.667e-10 to 2e-10 to get better match to data."
call /kinetics/PKC/PKC-n-DAG/notes LOAD \
"kf raised 10 X based on Shinomura et al PNAS 88 5149-5153 1991" \
"closer analysis of Shinomura et al: kf now 1e-8 (was 1.66e-8)." \
"Further tweak. To get sufficient AA synergy, increase kf to 1.5e-8" \
"26 June 1996: Corrected DAG levels: reduce kf by 15x from" \
"1.5e-8 to 1e-9"
call /kinetics/PKC/PKC-DAG/notes LOAD \
"CoInit was .0624" \
""
call /kinetics/PKC/PKC-n-DAG-AA/notes LOAD \
"Reduced kf to 0.66X to match Shinomura et al data." \
"Initial: kf = 3.3333e-9" \
"New: 2e-9" \
"Newer: 2e-8" \
"kb was 0.2" \
"now 2."
call /kinetics/PKC/PKC-cytosolic/notes LOAD \
"Marquez et al J. Immun 149,2560(92) est 1e6/cell for chromaffin cells" \
"We will use 1 uM as our initial concen" \
""
call /kinetics/DAG/notes LOAD \
"The conc of this has been a problem. Schaecter and Benowitz use 50 uM," \
"but Shinomura et al have < 5. So I have altered the DAG-dependent " \
"rates in the PKC model to reflect this."
call /kinetics/PKC-active/notes LOAD \
"Conc of PKC in brain is about 1 uM (?)"
complete_loading