//genesis
// kkit Version 11 flat dumpfile
// Saved on Fri Jan 7 17:31:17 2011
include kkit {argv 1}
FASTDT = 1e-05
SIMDT = 0.0001
CONTROLDT = 1
PLOTDT = 0.2
MAXTIME = 200
TRANSIENT_TIME = 2
VARIABLE_DT_FLAG = 1
DEFAULT_VOL = 1e-19
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 1.6667e-21 3 sphere "" white black 5 \
-4 0
simundump geometry /kinetics/geometry[1] 0 1e-19 3 sphere "" white black 5 -2 \
0
simundump geometry /kinetics/geometry[2] 0 1e-20 3 sphere "" white black 0 0 \
0
simundump geometry /kinetics/geometry[3] 0 1e-20 3 sphere "" white black 0 0 \
0
simundump geometry /kinetics/geometry[4] 0 1e-20 3 sphere "" white black 0 0 \
0
simundump geometry /kinetics/geometry[5] 0 1e-20 3 sphere "" white black 0 0 \
0
simundump geometry /kinetics/geometry[6] 0 1e-19 3 sphere "" white black 0 0 \
0
simundump geometry /kinetics/geometry[7] 0 1e-20 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 text /kinetics/geometry[1]/notes 0 ""
call /kinetics/geometry[1]/notes LOAD \
""
simundump text /kinetics/geometry[2]/notes 0 ""
call /kinetics/geometry[2]/notes LOAD \
""
simundump text /kinetics/geometry[3]/notes 0 ""
call /kinetics/geometry[3]/notes LOAD \
""
simundump text /kinetics/geometry[4]/notes 0 ""
call /kinetics/geometry[4]/notes LOAD \
""
simundump text /kinetics/geometry[5]/notes 0 ""
call /kinetics/geometry[5]/notes LOAD \
""
simundump text /kinetics/geometry[6]/notes 0 ""
call /kinetics/geometry[6]/notes LOAD \
""
simundump text /kinetics/geometry[7]/notes 0 ""
call /kinetics/geometry[7]/notes LOAD \
""
simundump kreac /kinetics/exocytosis 0 0.01 0 "" white black 4 -5 0
simundump text /kinetics/exocytosis/notes 0 ""
call /kinetics/exocytosis/notes LOAD \
""
simundump kreac /kinetics/endocytosis 0 4 0 "" white black -7 -5 0
simundump text /kinetics/endocytosis/notes 0 ""
call /kinetics/endocytosis/notes LOAD \
""
simundump group /kinetics/PSD 0 0 black x 0 1 "" PSD defaultfile.g 0 0 0 -10 \
-3 0
simundump text /kinetics/PSD/notes 0 ""
call /kinetics/PSD/notes LOAD \
""
simundump kpool /kinetics/PSD/Rp 0 0 0 0 0 0 0 0 6 0 /kinetics/geometry[1] \
blue 0 -4 1 0
simundump text /kinetics/PSD/Rp/notes 0 ""
call /kinetics/PSD/Rp/notes LOAD \
""
simundump kpool /kinetics/PSD/P 0 0 0.5 0.5 3 3 0 0 6 0 /kinetics/geometry[1] \
61 0 -4 -2 0
simundump text /kinetics/PSD/P/notes 0 ""
call /kinetics/PSD/P/notes LOAD \
""
simundump kenz /kinetics/PSD/P/P1 0 0 0 0 0 60 41.667 40 10 0 0 "" red 61 "" \
-6 -1 0
simundump text /kinetics/PSD/P/P1/notes 0 ""
call /kinetics/PSD/P/P1/notes LOAD \
""
simundump kenz /kinetics/PSD/P/P2 0 0 0 0 0 60 41.667 40 10 0 0 "" red 61 "" \
-2 -1 0
simundump text /kinetics/PSD/P/P2/notes 0 ""
call /kinetics/PSD/P/P2/notes LOAD \
""
simundump kpool /kinetics/PSD/KK 0 0 1 1 6 6 0 0 6 0 /kinetics/geometry[1] 49 \
0 -4 4 0
simundump text /kinetics/PSD/KK/notes 0 ""
call /kinetics/PSD/KK/notes LOAD \
""
simundump kenz /kinetics/PSD/KK/KK1 0 0 0 0 0 60 8.3333 40 10 0 0 "" red 49 \
"" -6 3 0
simundump text /kinetics/PSD/KK/KK1/notes 0 ""
call /kinetics/PSD/KK/KK1/notes LOAD \
""
simundump kenz /kinetics/PSD/KK/KK2 0 0 0 0 0 60 8.3333 40 10 0 0 "" red 49 \
"" -2 3 0
simundump text /kinetics/PSD/KK/KK2/notes 0 ""
call /kinetics/PSD/KK/KK2/notes LOAD \
""
simundump kpool /kinetics/PSD/Rpp 0 0 0 0 0 0 0 0 6 0 /kinetics/geometry[1] \
28 0 0 1 0
simundump text /kinetics/PSD/Rpp/notes 0 ""
call /kinetics/PSD/Rpp/notes LOAD \
""
simundump kpool /kinetics/PSD/R 0 0 0 0 0 0 0 0 6 0 /kinetics/geometry[1] 4 0 \
-8 1 0
simundump text /kinetics/PSD/R/notes 0 ""
call /kinetics/PSD/R/notes LOAD \
""
simundump kpool /kinetics/PSD/tot_PSD_R 0 0 0 0 0 0 0 0 6 0 \
/kinetics/geometry[4] blue 0 -4 7 0
simundump text /kinetics/PSD/tot_PSD_R/notes 0 ""
call /kinetics/PSD/tot_PSD_R/notes LOAD \
""
simundump kpool /kinetics/PSD/Ca_PSD 0 0 0.1 0.1 0.6 0.6 0 0 6 4 \
/kinetics/geometry[5] 53 0 -15 2 0
simundump text /kinetics/PSD/Ca_PSD/notes 0 ""
call /kinetics/PSD/Ca_PSD/notes LOAD \
""
simundump kpool /kinetics/PSD/psd_inact_CaN 0 0 0.5 0.5 3 3 0 0 6 0 \
/kinetics/geometry[7] blue 0 -12 5 0
simundump text /kinetics/PSD/psd_inact_CaN/notes 0 ""
call /kinetics/PSD/psd_inact_CaN/notes LOAD \
""
simundump kreac /kinetics/PSD/psd_activate_CaN 0 0.27778 1 "" white 0 -11 1 0
simundump text /kinetics/PSD/psd_activate_CaN/notes 0 ""
call /kinetics/PSD/psd_activate_CaN/notes LOAD \
""
simundump kpool /kinetics/PSD/Ca.P 0 0 0 0 0 0 0 0 6 0 /kinetics/geometry[7] \
blue 0 -4 -4 0
simundump text /kinetics/PSD/Ca.P/notes 0 ""
call /kinetics/PSD/Ca.P/notes LOAD \
""
simundump kenz /kinetics/PSD/Ca.P/Ca.P2 0 0 0 0 0 6 1.6667 40 10 0 0 "" red \
blue "" -2 -3 0
simundump text /kinetics/PSD/Ca.P/Ca.P2/notes 0 ""
call /kinetics/PSD/Ca.P/Ca.P2/notes LOAD \
""
simundump kenz /kinetics/PSD/Ca.P/Ca.P1 0 0 0 0 0 6 1.6667 40 10 0 0 "" red \
blue "" -6 -3 0
simundump text /kinetics/PSD/Ca.P/Ca.P1/notes 0 ""
call /kinetics/PSD/Ca.P/Ca.P1/notes LOAD \
""
simundump group /kinetics/Bulk 0 yellow black x 0 0 "" Bulk defaultfile.g 0 0 \
0 -6 -16 0
simundump text /kinetics/Bulk/notes 0 ""
call /kinetics/Bulk/notes LOAD \
""
simundump kpool /kinetics/Bulk/iRpp 0 0 0 0 0 0 0 0 59.999 0 \
/kinetics/geometry 29 yellow 2 -11 0
simundump text /kinetics/Bulk/iRpp/notes 0 ""
call /kinetics/Bulk/iRpp/notes LOAD \
""
simundump kpool /kinetics/Bulk/iRp 0 0 0 0 0 0 0 0 59.999 0 \
/kinetics/geometry blue yellow -2 -11 0
simundump text /kinetics/Bulk/iRp/notes 0 ""
call /kinetics/Bulk/iRp/notes LOAD \
""
simundump kpool /kinetics/Bulk/iR 0 0 8.0001 8.0001 480 480 0 0 59.999 0 \
/kinetics/geometry 0 yellow -6 -11 0
simundump text /kinetics/Bulk/iR/notes 0 "Same as Fus3\n"
call /kinetics/Bulk/iR/notes LOAD \
"Same as Fus3" \
""
simundump kpool /kinetics/Bulk/iKK 0 0 1 1 59.999 59.999 0 0 59.999 0 \
/kinetics/geometry 50 yellow -2 -8 0
simundump text /kinetics/Bulk/iKK/notes 0 "Same as Ste7\n"
call /kinetics/Bulk/iKK/notes LOAD \
"Same as Ste7" \
""
simundump kenz /kinetics/Bulk/iKK/iKK1 0 0 0 0 0 59.999 0.83335 40 10 0 0 "" \
red 50 "" -4 -9 0
simundump text /kinetics/Bulk/iKK/iKK1/notes 0 ""
call /kinetics/Bulk/iKK/iKK1/notes LOAD \
""
simundump kenz /kinetics/Bulk/iKK/iKK2 0 0 0 0 0 59.999 0.83335 40 10 0 0 "" \
red 50 "" 0 -9 0
simundump text /kinetics/Bulk/iKK/iKK2/notes 0 ""
call /kinetics/Bulk/iKK/iKK2/notes LOAD \
""
simundump kpool /kinetics/Bulk/iP 0 0 0.50001 0.50001 30 30 0 0 59.999 0 \
/kinetics/geometry 62 yellow -2 -14 0
simundump text /kinetics/Bulk/iP/notes 0 "Same as Msg5\n"
call /kinetics/Bulk/iP/notes LOAD \
"Same as Msg5" \
""
simundump kenz /kinetics/Bulk/iP/iP1 0 0 0 0 0 59.999 6.2501 60 15 0 0 "" red \
62 "" -4 -13 0
simundump text /kinetics/Bulk/iP/iP1/notes 0 ""
call /kinetics/Bulk/iP/iP1/notes LOAD \
""
simundump kenz /kinetics/Bulk/iP/iP2 0 0 0 0 0 59.999 6.2501 60 15 0 0 "" red \
62 "" 0 -13 0
simundump text /kinetics/Bulk/iP/iP2/notes 0 ""
call /kinetics/Bulk/iP/iP2/notes LOAD \
""
simundump kpool /kinetics/Bulk/PKA 0 0 0 0 0 0 0 0 60 0 /kinetics/geometry[3] \
43 yellow -3 -5 0
simundump text /kinetics/Bulk/PKA/notes 0 ""
call /kinetics/Bulk/PKA/notes LOAD \
""
simundump kenz /kinetics/Bulk/PKA/PKA1 0 0 0 0 0 60 0.41667 40 10 0 0 "" red \
43 "" -4 -7 0
simundump text /kinetics/Bulk/PKA/PKA1/notes 0 ""
call /kinetics/Bulk/PKA/PKA1/notes LOAD \
""
simundump kenz /kinetics/Bulk/PKA/PKA2 0 0 0 0 0 60 0.41667 40 10 0 0 "" red \
43 "" 0 -7 0
simundump text /kinetics/Bulk/PKA/PKA2/notes 0 ""
call /kinetics/Bulk/PKA/PKA2/notes LOAD \
""
simundump kenz /kinetics/Bulk/PKA/PKA_exo 0 0 0 0 0 60 0.016667 8 2 0 0 "" \
red 43 "" 1 -5 0
simundump text /kinetics/Bulk/PKA/PKA_exo/notes 0 ""
call /kinetics/Bulk/PKA/PKA_exo/notes LOAD \
""
simundump kreac /kinetics/Bulk/activate_PKA 0 0.0016667 5 "" white yellow -11 \
-10 0
simundump text /kinetics/Bulk/activate_PKA/notes 0 ""
call /kinetics/Bulk/activate_PKA/notes LOAD \
""
simundump kpool /kinetics/Bulk/inact_PKA 0 0 1.6 1.6 96 96 0 0 60 0 \
/kinetics/geometry[2] 51 yellow -12 -6 0
simundump text /kinetics/Bulk/inact_PKA/notes 0 ""
call /kinetics/Bulk/inact_PKA/notes LOAD \
""
simundump kpool /kinetics/Bulk/Ca_Bulk 0 0 0.1 0.1 6 6 0 0 60 0 \
/kinetics/geometry[2] 41 yellow -15 -13 0
simundump text /kinetics/Bulk/Ca_Bulk/notes 0 ""
call /kinetics/Bulk/Ca_Bulk/notes LOAD \
""
simundump kpool /kinetics/Bulk/inact_CaN 0 0 0.2 0.2 12 12 0 0 60 0 \
/kinetics/geometry[6] blue yellow -13 -18 0
simundump text /kinetics/Bulk/inact_CaN/notes 0 ""
call /kinetics/Bulk/inact_CaN/notes LOAD \
""
simundump kreac /kinetics/Bulk/activate_CaN 0 0.0055556 1 "" white yellow -10 \
-16 0
simundump text /kinetics/Bulk/activate_CaN/notes 0 ""
call /kinetics/Bulk/activate_CaN/notes LOAD \
""
simundump kreac /kinetics/Ca_to_bulk 0 100 10 "" white black -15 -3 0
simundump text /kinetics/Ca_to_bulk/notes 0 ""
call /kinetics/Ca_to_bulk/notes LOAD \
""
simundump xgraph /graphs/conc1 0 0 400 0 5.9394 0
simundump xgraph /graphs/conc2 0 0 400 0 50 0
simundump xplot /graphs/conc1/Ca_PSD.Co 3 524288 \
"delete_plot.w <s> <d>; edit_plot.D <w>" 53 0 0 1
simundump xplot /graphs/conc1/Ca_Bulk.Co 3 524288 \
"delete_plot.w <s> <d>; edit_plot.D <w>" 41 0 0 1
simundump xplot /graphs/conc1/PKA.Co 3 524288 \
"delete_plot.w <s> <d>; edit_plot.D <w>" 43 0 0 1
simundump xplot /graphs/conc2/tot_PSD_R.Co 3 524288 \
"delete_plot.w <s> <d>; edit_plot.D <w>" blue 0 0 1
simundump xgraph /moregraphs/conc3 0 0 400 0 33.241 0
simundump xgraph /moregraphs/conc4 0 0 400 0 2 0
simundump xcoredraw /edit/draw 0 -17 7 -20 9
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 \
"20 June 2009. dual_phosph_nonbis.g. Just plugged in round values." \
"2 July 2010. psd4.g. Trying to fine-tune PKA values so that the" \
"system is bistable at rest." \
"2 July 2010. psd5.g. Not bistable, probably because the kinase is" \
"building up lots of complex." \
"3 July 2010. psd8.g. Looks bistable, with the correct volumes. But" \
"needs checking" \
"3 July 2010. psd9.g. Bring out the big guns from MOOSE SteadyState" \
"solver. Rename things to help it." \
"4 July 2010. psd11.g. Speeded up kinase/phosphatase cycle. Bistable." \
"4 July 2010. psd12.g. Added in Ca control of turnon. " \
"5 August 2010. psd14.g. Renamed molecules." \
"25 August 2010. psd26.g. Changed total # of receptors, scaled" \
"endo and exo rates. Now it is more robust to changes in [P] and" \
"in [iP]" \
"25 August 2010. psd27.g Increased kcat for exo_enz from " \
"0.2 to 0.5. Should boost turnon." \
"25 August 2010. psd28.g. Tried to convert PKA to an enzyme doing" \
"the phosphorylation of the receptor in the bulk, rather than" \
"triggering transport. Doesn't help." \
"25 August 2010. psd29.g Added the exo_enz step onto the PKA" \
"as well. Now it turns on." \
"25 August 2050. psd30.g Added in a CaN reaction step as well." \
"Seems to turn on as well as turn off, but fine-tuning still" \
"needed." \
"psd31.g: Fine-tuning rates for psd30." \
"psd32.g: More fine-tuning" \
"26 Aug 2010. psd33.g: More fine-tuning. More PKA so that turnon" \
" happens with the usual brief tetanic input." \
"07 Jan 2011: psd41b.g: Fixed name-clash of enzyme sites. Otherwise" \
"identical to psd41.g" \
"" \
"" \
""
addmsg /kinetics/Bulk/iRpp /kinetics/exocytosis SUBSTRATE n
addmsg /kinetics/PSD/Rpp /kinetics/exocytosis PRODUCT n
addmsg /kinetics/PSD/R /kinetics/endocytosis SUBSTRATE n
addmsg /kinetics/Bulk/iR /kinetics/endocytosis PRODUCT n
addmsg /kinetics/PSD/KK/KK1 /kinetics/PSD/Rp MM_PRD pA
addmsg /kinetics/PSD/KK/KK2 /kinetics/PSD/Rp REAC sA B
addmsg /kinetics/PSD/P/P2 /kinetics/PSD/Rp MM_PRD pA
addmsg /kinetics/PSD/P/P1 /kinetics/PSD/Rp REAC sA B
addmsg /kinetics/PSD/Ca.P/Ca.P2 /kinetics/PSD/Rp MM_PRD pA
addmsg /kinetics/PSD/Ca.P/Ca.P1 /kinetics/PSD/Rp REAC sA B
addmsg /kinetics/PSD/P/P1 /kinetics/PSD/P REAC eA B
addmsg /kinetics/PSD/P/P2 /kinetics/PSD/P REAC eA B
addmsg /kinetics/PSD/P /kinetics/PSD/P/P1 ENZYME n
addmsg /kinetics/PSD/Rp /kinetics/PSD/P/P1 SUBSTRATE n
addmsg /kinetics/PSD/P /kinetics/PSD/P/P2 ENZYME n
addmsg /kinetics/PSD/Rpp /kinetics/PSD/P/P2 SUBSTRATE n
addmsg /kinetics/PSD/KK/KK1 /kinetics/PSD/KK REAC eA B
addmsg /kinetics/PSD/KK/KK2 /kinetics/PSD/KK REAC eA B
addmsg /kinetics/PSD/KK /kinetics/PSD/KK/KK1 ENZYME n
addmsg /kinetics/PSD/R /kinetics/PSD/KK/KK1 SUBSTRATE n
addmsg /kinetics/PSD/KK /kinetics/PSD/KK/KK2 ENZYME n
addmsg /kinetics/PSD/Rp /kinetics/PSD/KK/KK2 SUBSTRATE n
addmsg /kinetics/PSD/KK/KK2 /kinetics/PSD/Rpp MM_PRD pA
addmsg /kinetics/PSD/P/P2 /kinetics/PSD/Rpp REAC sA B
addmsg /kinetics/exocytosis /kinetics/PSD/Rpp REAC B A
addmsg /kinetics/Bulk/PKA/PKA_exo /kinetics/PSD/Rpp MM_PRD pA
addmsg /kinetics/PSD/Ca.P/Ca.P2 /kinetics/PSD/Rpp REAC sA B
addmsg /kinetics/PSD/KK/KK1 /kinetics/PSD/R REAC sA B
addmsg /kinetics/PSD/P/P1 /kinetics/PSD/R MM_PRD pA
addmsg /kinetics/endocytosis /kinetics/PSD/R REAC A B
addmsg /kinetics/PSD/Ca.P/Ca.P1 /kinetics/PSD/R MM_PRD pA
addmsg /kinetics/PSD/R /kinetics/PSD/tot_PSD_R SUMTOTAL n nInit
addmsg /kinetics/PSD/Rp /kinetics/PSD/tot_PSD_R SUMTOTAL n nInit
addmsg /kinetics/PSD/Rpp /kinetics/PSD/tot_PSD_R SUMTOTAL n nInit
addmsg /kinetics/Ca_to_bulk /kinetics/PSD/Ca_PSD REAC A B
addmsg /kinetics/PSD/psd_activate_CaN /kinetics/PSD/Ca_PSD REAC A B
addmsg /kinetics/PSD/psd_activate_CaN /kinetics/PSD/Ca_PSD REAC A B
addmsg /kinetics/PSD/psd_activate_CaN /kinetics/PSD/psd_inact_CaN REAC A B
addmsg /kinetics/PSD/psd_inact_CaN /kinetics/PSD/psd_activate_CaN SUBSTRATE n
addmsg /kinetics/PSD/Ca_PSD /kinetics/PSD/psd_activate_CaN SUBSTRATE n
addmsg /kinetics/PSD/Ca_PSD /kinetics/PSD/psd_activate_CaN SUBSTRATE n
addmsg /kinetics/PSD/Ca.P /kinetics/PSD/psd_activate_CaN PRODUCT n
addmsg /kinetics/PSD/psd_activate_CaN /kinetics/PSD/Ca.P REAC B A
addmsg /kinetics/PSD/Ca.P/Ca.P2 /kinetics/PSD/Ca.P REAC eA B
addmsg /kinetics/PSD/Ca.P/Ca.P1 /kinetics/PSD/Ca.P REAC eA B
addmsg /kinetics/PSD/Ca.P /kinetics/PSD/Ca.P/Ca.P2 ENZYME n
addmsg /kinetics/PSD/Rpp /kinetics/PSD/Ca.P/Ca.P2 SUBSTRATE n
addmsg /kinetics/PSD/Ca.P /kinetics/PSD/Ca.P/Ca.P1 ENZYME n
addmsg /kinetics/PSD/Rp /kinetics/PSD/Ca.P/Ca.P1 SUBSTRATE n
addmsg /kinetics/Bulk/iKK/iKK2 /kinetics/Bulk/iRpp MM_PRD pA
addmsg /kinetics/Bulk/iP/iP2 /kinetics/Bulk/iRpp REAC sA B
addmsg /kinetics/exocytosis /kinetics/Bulk/iRpp REAC A B
addmsg /kinetics/Bulk/PKA/PKA2 /kinetics/Bulk/iRpp MM_PRD pA
addmsg /kinetics/Bulk/PKA/PKA_exo /kinetics/Bulk/iRpp REAC sA B
addmsg /kinetics/Bulk/iKK/iKK1 /kinetics/Bulk/iRp MM_PRD pA
addmsg /kinetics/Bulk/iKK/iKK2 /kinetics/Bulk/iRp REAC sA B
addmsg /kinetics/Bulk/iP/iP2 /kinetics/Bulk/iRp MM_PRD pA
addmsg /kinetics/Bulk/iP/iP1 /kinetics/Bulk/iRp REAC sA B
addmsg /kinetics/Bulk/PKA/PKA1 /kinetics/Bulk/iRp MM_PRD pA
addmsg /kinetics/Bulk/PKA/PKA2 /kinetics/Bulk/iRp REAC sA B
addmsg /kinetics/Bulk/iKK/iKK1 /kinetics/Bulk/iR REAC sA B
addmsg /kinetics/Bulk/iP/iP1 /kinetics/Bulk/iR MM_PRD pA
addmsg /kinetics/endocytosis /kinetics/Bulk/iR REAC B A
addmsg /kinetics/Bulk/PKA/PKA1 /kinetics/Bulk/iR REAC sA B
addmsg /kinetics/Bulk/iKK/iKK1 /kinetics/Bulk/iKK REAC eA B
addmsg /kinetics/Bulk/iKK/iKK2 /kinetics/Bulk/iKK REAC eA B
addmsg /kinetics/Bulk/iKK /kinetics/Bulk/iKK/iKK1 ENZYME n
addmsg /kinetics/Bulk/iR /kinetics/Bulk/iKK/iKK1 SUBSTRATE n
addmsg /kinetics/Bulk/iKK /kinetics/Bulk/iKK/iKK2 ENZYME n
addmsg /kinetics/Bulk/iRp /kinetics/Bulk/iKK/iKK2 SUBSTRATE n
addmsg /kinetics/Bulk/iP/iP1 /kinetics/Bulk/iP REAC eA B
addmsg /kinetics/Bulk/iP/iP2 /kinetics/Bulk/iP REAC eA B
addmsg /kinetics/Bulk/activate_CaN /kinetics/Bulk/iP REAC B A
addmsg /kinetics/Bulk/iP /kinetics/Bulk/iP/iP1 ENZYME n
addmsg /kinetics/Bulk/iRp /kinetics/Bulk/iP/iP1 SUBSTRATE n
addmsg /kinetics/Bulk/iP /kinetics/Bulk/iP/iP2 ENZYME n
addmsg /kinetics/Bulk/iRpp /kinetics/Bulk/iP/iP2 SUBSTRATE n
addmsg /kinetics/Bulk/activate_PKA /kinetics/Bulk/PKA REAC B A
addmsg /kinetics/Bulk/PKA/PKA1 /kinetics/Bulk/PKA REAC eA B
addmsg /kinetics/Bulk/PKA/PKA2 /kinetics/Bulk/PKA REAC eA B
addmsg /kinetics/Bulk/PKA/PKA_exo /kinetics/Bulk/PKA REAC eA B
addmsg /kinetics/Bulk/PKA /kinetics/Bulk/PKA/PKA1 ENZYME n
addmsg /kinetics/Bulk/iR /kinetics/Bulk/PKA/PKA1 SUBSTRATE n
addmsg /kinetics/Bulk/PKA /kinetics/Bulk/PKA/PKA2 ENZYME n
addmsg /kinetics/Bulk/iRp /kinetics/Bulk/PKA/PKA2 SUBSTRATE n
addmsg /kinetics/Bulk/PKA /kinetics/Bulk/PKA/PKA_exo ENZYME n
addmsg /kinetics/Bulk/iRpp /kinetics/Bulk/PKA/PKA_exo SUBSTRATE n
addmsg /kinetics/Bulk/inact_PKA /kinetics/Bulk/activate_PKA SUBSTRATE n
addmsg /kinetics/Bulk/Ca_Bulk /kinetics/Bulk/activate_PKA SUBSTRATE n
addmsg /kinetics/Bulk/PKA /kinetics/Bulk/activate_PKA PRODUCT n
addmsg /kinetics/Bulk/Ca_Bulk /kinetics/Bulk/activate_PKA SUBSTRATE n
addmsg /kinetics/Bulk/activate_PKA /kinetics/Bulk/inact_PKA REAC A B
addmsg /kinetics/Bulk/activate_PKA /kinetics/Bulk/Ca_Bulk REAC A B
addmsg /kinetics/Bulk/activate_PKA /kinetics/Bulk/Ca_Bulk REAC A B
addmsg /kinetics/Ca_to_bulk /kinetics/Bulk/Ca_Bulk REAC B A
addmsg /kinetics/Bulk/activate_CaN /kinetics/Bulk/Ca_Bulk REAC A B
addmsg /kinetics/Bulk/activate_CaN /kinetics/Bulk/Ca_Bulk REAC A B
addmsg /kinetics/Bulk/activate_CaN /kinetics/Bulk/inact_CaN REAC A B
addmsg /kinetics/Bulk/inact_CaN /kinetics/Bulk/activate_CaN SUBSTRATE n
addmsg /kinetics/Bulk/iP /kinetics/Bulk/activate_CaN PRODUCT n
addmsg /kinetics/Bulk/Ca_Bulk /kinetics/Bulk/activate_CaN SUBSTRATE n
addmsg /kinetics/Bulk/Ca_Bulk /kinetics/Bulk/activate_CaN SUBSTRATE n
addmsg /kinetics/PSD/Ca_PSD /kinetics/Ca_to_bulk SUBSTRATE n
addmsg /kinetics/Bulk/Ca_Bulk /kinetics/Ca_to_bulk PRODUCT n
addmsg /kinetics/PSD/Ca_PSD /graphs/conc1/Ca_PSD.Co PLOT Co *Ca_PSD.Co *53
addmsg /kinetics/Bulk/Ca_Bulk /graphs/conc1/Ca_Bulk.Co PLOT Co *Ca_Bulk.Co *41
addmsg /kinetics/Bulk/PKA /graphs/conc1/PKA.Co PLOT Co *PKA.Co *43
addmsg /kinetics/PSD/tot_PSD_R /graphs/conc2/tot_PSD_R.Co PLOT Co *tot_PSD_R.Co *blue
enddump
// End of dump
call /kinetics/Bulk/iR/notes LOAD \
"Same as Fus3" \
""
call /kinetics/Bulk/iKK/notes LOAD \
"Same as Ste7" \
""
call /kinetics/Bulk/iP/notes LOAD \
"Same as Msg5" \
""
complete_loading