//  DOQCS :http://doqcs.ncbs.res.in/ 
//  Accession Name = CaMKII 
//  Accession Number = 33 
//  Pathway Name = CaM 
//  Pathway Number = 173 
//  Transcriber = Upinder S. Bhalla, NCBS 
//  Developer = William R. Holmes 
//  Species = Generic mammalian 
//  Tissue =  Brain - Neuronal 
//  Cell Compartment = Synapse 
//  Notes =  This is a deterministic, point kinetics approximation to the dendritic spine CaMKII model described in <a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10798500>William R. Holmes J Comput Neurosci. (2000) 8(1):65-85</a>. Rates are the same but the responses differ somewhat because this model does not include the stochastic and diffusive calculations of the original.
 
//genesis
// kkit Version 11 flat dumpfile
 
// Saved on Fri Dec  9 17:19:48 2005
 
include kkit {argv 1}
 
FASTDT = 0.0001
SIMDT = 2e-05
CONTROLDT = 5
PLOTDT = 0.005
MAXTIME = 30
TRANSIENT_TIME = 2
VARIABLE_DT_FLAG = 0
DEFAULT_VOL = 1.309e-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
simundump geometry /kinetics/geometry 0 1.309e-19 3 sphere "" white black 22 \
  -5 0
simundump kpool /kinetics/Ca 0 0 0.07 0.07 5.4977 5.4977 0 0 78.539 2 \
  /kinetics/geometry 62 black 19 -6 0
simundump xtab /kinetics/Ca_tab 0 -10 0 1 2 0 "" edit_xtab white red 0 0 0 1 \
  18 6 0
loadtab /kinetics/Ca_tab table 0 799 0 4 \
 0.07 3.5 7.5 8.5 6 4.5 3.5 2.5 2 1.6 1.3 1.2 1.1 1 0.95 0.9 0.85 0.8 0.75 \
 0.7 0.65 0.63568 0.621713 0.608091 0.594806 0.581848 0.569211 0.556885 \
 0.544864 0.533139 0.521704 0.510552 0.499675 0.489066 0.478719 0.468628 \
 0.458786 0.449186 0.439824 0.430693 0.421788 0.413102 0.404631 0.396369 \
 0.388311 0.380452 0.372787 0.365311 0.358019 0.350908 0.343973 0.337208 \
 0.330611 0.324176 0.317901 0.31178 0.30581 0.299988 0.29431 0.288772 0.28337 \
 0.278102 0.272964 0.267953 0.263065 0.258298 0.253649 0.249115 0.244693 \
 0.240379 0.236173 0.23207 0.228068 0.224166 0.220359 0.216647 0.213026 \
 0.209495 0.206051 0.202692 0.199415 0.19622 0.193104 0.190064 0.1871 \
 0.184209 0.181389 0.178639 0.175956 0.17334 0.170789 0.1683 0.165873 \
 0.163506 0.161198 0.158946 0.15675 0.154608 0.152519 0.150482 0.148494 \
 0.146556 0.144666 0.142823 0.141025 0.139271 0.137561 0.135893 0.134266 \
 0.132679 0.131132 0.129622 0.12815 0.126714 0.125314 0.123948 0.122616 \
 0.121317 0.12005 0.118815 0.117609 0.116434 0.115287 0.114169 0.113079 \
 0.112015 0.110978 0.109966 0.108979 0.108017 0.107078 0.106163 0.10527 \
 0.104399 0.10355 0.102721 0.101913 0.101126 0.100357 0.0996075 0.0988765 \
 0.0981635 0.0974682 0.09679 0.0961285 0.0954834 0.0948542 0.0942406 \
 0.0936421 0.0930584 0.092489 0.0919338 0.0913922 0.0908641 0.0903489 \
 0.0898465 0.0893565 0.0888786 0.0884125 0.0879579 0.0875145 0.0870821 \
 0.0866603 0.0862489 0.0858478 0.0854565 0.0850749 0.0847027 0.0843396 \
 0.0839856 0.0836403 0.0833035 0.082975 0.0826547 0.0823422 0.0820375 \
 0.0817403 0.0814504 0.0811677 0.080892 0.0806231 0.0803608 0.080105 \
 0.0798555 0.0796122 0.0793748 0.0791434 0.0789176 0.0786974 0.0784827 \
 0.0782733 0.078069 0.0778698 0.0776755 0.0774859 0.0773011 0.0771209 \
 0.076945 0.0767736 0.0766063 
loadtab -continue \
 0.0764432 0.0762841 0.076129 0.0759777 0.0758301 0.0756861 0.0755457 \
 0.0754088 0.0752753 0.075145 0.075018 0.0748941 0.0747733 0.0746554 \
 0.0745405 0.0744284 0.074319 0.0742124 0.0741084 0.0740069 0.073908 \
 0.0738115 0.0737174 0.0736256 0.0735361 0.0734488 0.0733637 0.0732806 \
 0.0731996 0.0731206 0.0730436 0.0729684 0.0728951 0.0728236 0.0727539 \
 0.0726859 0.0726196 0.0725549 0.0724919 0.0724303 0.0723703 0.0723118 \
 0.0722547 0.0721991 0.0721448 0.0720918 0.0720402 0.0719898 0.0719407 \
 0.0718927 0.071846 0.0718004 0.071756 0.0717126 0.0716703 0.0716291 \
 0.0715889 0.0715496 0.0715114 0.0714741 0.0714377 0.0714022 0.0713676 \
 0.0713338 0.0713009 0.0712687 0.0712374 0.0712069 0.0711771 0.071148 \
 0.0711197 0.071092 0.0710651 0.0710388 0.0710131 0.0709881 0.0709637 \
 0.0709399 0.0709167 0.0708941 0.070872 0.0708505 0.0708295 0.070809 0.070789 \
 0.0707695 0.0707505 0.070732 0.0707139 0.0706963 0.0706791 0.0706623 \
 0.070646 0.07063 0.0706145 0.0705993 0.0705845 0.0705701 0.070556 0.0705423 \
 0.0705289 0.0705158 0.0705031 0.0704907 0.0704786 0.0704667 0.0704552 \
 0.070444 0.070433 0.0704223 0.0704119 0.0704017 0.0703918 0.0703821 \
 0.0703727 0.0703635 0.0703545 0.0703458 0.0703372 0.0703289 0.0703208 \
 0.0703129 0.0703051 0.0702976 0.0702903 0.0702831 0.0702761 0.0702693 \
 0.0702626 0.0702562 0.0702498 0.0702437 0.0702376 0.0702318 0.0702261 \
 0.0702205 0.070215 0.0702097 0.0702045 0.0701995 0.0701946 0.0701898 \
 0.0701851 0.0701805 0.0701761 0.0701717 0.0701675 0.0701633 0.0701593 \
 0.0701554 0.0701515 0.0701478 0.0701441 0.0701406 0.0701371 0.0701337 \
 0.0701304 0.0701272 0.0701241 0.070121 0.070118 0.0701151 0.0701123 \
 0.0701095 0.0701068 0.0701041 0.0701016 0.0700991 0.0700966 0.0700942 \
 0.0700919 0.0700896 0.0700874 0.0700853 0.0700832 0.0700811 0.0700791 \
 0.0700772 0.0700753 0.0700734 0.0700716 0.0700698 0.0700681 0.0700664 \
 0.0700648 0.0700632 0.0700616 0.0700601 0.0700586 0.0700572 0.0700557 \
 0.0700544 0.070053 0.0700517 0.0700504 0.0700492 0.070048 0.0700468 \
 0.0700456 0.0700445 
loadtab -continue \
 0.0700434 0.0700423 0.0700413 0.0700403 0.0700393 0.0700383 0.0700374 \
 0.0700364 0.0700355 0.0700347 0.0700338 0.070033 0.0700322 0.0700314 \
 0.0700306 0.0700298 0.0700291 0.0700284 0.0700277 0.070027 0.0700263 \
 0.0700257 0.070025 0.0700244 0.0700238 0.0700232 0.0700227 0.0700221 \
 0.0700216 0.070021 0.0700205 0.07002 0.0700195 0.070019 0.0700186 0.0700181 \
 0.0700177 0.0700172 0.0700168 0.0700164 0.070016 0.0700156 0.0700152 \
 0.0700148 0.0700145 0.0700141 0.0700137 0.0700134 0.0700131 0.0700128 \
 0.0700124 0.0700121 0.0700118 0.0700115 0.0700113 0.070011 0.0700107 \
 0.0700104 0.0700102 0.0700099 0.0700097 0.0700094 0.0700092 0.070009 \
 0.0700088 0.0700085 0.0700083 0.0700081 0.0700079 0.0700077 0.0700075 \
 0.0700074 0.0700072 0.070007 0.0700068 0.0700067 0.0700065 0.0700063 \
 0.0700062 0.070006 0.0700059 0.0700057 0.0700056 0.0700055 0.0700053 \
 0.0700052 0.0700051 0.0700049 0.0700048 0.0700047 0.0700046 0.0700045 \
 0.0700044 0.0700042 0.0700041 0.070004 0.0700039 0.0700038 0.0700037 \
 0.0700037 0.0700036 0.0700035 0.0700034 0.0700033 0.0700032 0.0700031 \
 0.0700031 0.070003 0.0700029 0.0700028 0.0700028 0.0700027 0.0700026 \
 0.0700026 0.0700025 0.0700025 0.0700024 0.0700023 0.0700023 0.0700022 \
 0.0700022 0.0700021 0.0700021 0.070002 0.070002 0.0700019 0.0700019 \
 0.0700018 0.0700018 0.0700017 0.0700017 0.0700016 0.0700016 0.0700016 \
 0.0700015 0.0700015 0.0700014 0.0700014 0.0700014 0.0700013 0.0700013 \
 0.0700013 0.0700012 0.0700012 0.0700012 0.0700012 0.0700011 0.0700011 \
 0.0700011 0.070001 0.070001 0.070001 0.070001 0.0700009 0.0700009 0.0700009 \
 0.0700009 0.0700009 0.0700008 0.0700008 0.0700008 0.0700008 0.0700008 \
 0.0700007 0.0700007 0.0700007 0.0700007 0.0700007 0.0700006 0.0700006 \
 0.0700006 0.0700006 0.0700006 0.0700006 0.0700006 0.0700005 0.0700005 \
 0.0700005 0.0700005 0.0700005 0.0700005 0.0700005 0.0700005 0.0700004 \
 0.0700004 0.0700004 0.0700004 0.0700004 0.0700004 0.0700004 0.0700004 \
 0.0700004 0.0700004 0.0700004 0.0700003 0.0700003 0.0700003 0.0700003 \
 0.0700003 0.0700003 
loadtab -continue \
 0.0700003 0.0700003 0.0700003 0.0700003 0.0700003 0.0700003 0.0700003 \
 0.0700002 0.0700002 0.0700002 0.0700002 0.0700002 0.0700002 0.0700002 \
 0.0700002 0.0700002 0.0700002 0.0700002 0.0700002 0.0700002 0.0700002 \
 0.0700002 0.0700002 0.0700002 0.0700002 0.0700002 0.0700001 0.0700001 \
 0.0700001 0.0700001 0.0700001 0.0700001 0.0700001 0.0700001 0.0700001 \
 0.0700001 0.0700001 0.0700001 0.0700001 0.0700001 0.0700001 0.0700001 \
 0.0700001 0.0700001 0.0700001 0.0700001 0.0700001 0.0700001 0.0700001 \
 0.0700001 0.0700001 0.0700001 0.0700001 0.0700001 0.0700001 0.0700001 \
 0.0700001 0.0700001 0.0700001 0.0700001 0.0700001 0.0700001 0.0700001 \
 0.0700001 0.0700001 0.0700001 0.0700001 0.0700001 0.0700001 0.0700001 \
 0.0700001 0.0700001 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 \
 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 \
 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 \
 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 \
 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 \
 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 \
 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 \
 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 \
 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07
simundump group /kinetics/CaM 0 45 black x 0 0 "" CaM \
  /home2/bhalla/scripts/modules/CaM_0.g 0 0 0 14 6 0
simundump kpool /kinetics/CaM/CaM 0 0 80 80 6283.1 6283.1 0 0 78.539 0 \
  /kinetics/geometry 2 45 14 2 0
simundump kreac /kinetics/CaM/CaM-bind-Ca 0 0.012733 20 "" white 45 14 0 0
simundump kpool /kinetics/CaM/CaMCa 0 0 0 0 0 0 0 0 78.539 0 \
  /kinetics/geometry 4 45 14 -2 0
simundump kreac /kinetics/CaM/CaMCa-bind-Ca 0 0.42399 20 "" white 45 14 -4 0
simundump kpool /kinetics/CaM/CaMCa2 0 0 0 0 0 0 0 0 78.539 0 \
  /kinetics/geometry 8 45 14 -6 0
simundump kreac /kinetics/CaM/CaMCa2-bind-Ca 0 0.063663 500 "" white 45 14 -8 \
  0
simundump kpool /kinetics/CaM/CaMCa3 0 0 0 0 0 0 0 0 78.539 0 \
  /kinetics/geometry blue 45 14 -10 0
simundump kreac /kinetics/CaM/CaMCa3-bind-Ca 0 1.2733 500 "" white 45 14 -12 \
  0
simundump kpool /kinetics/CaM/CaMCa4 0 0 0 0 0 0 0 0 78.539 0 \
  /kinetics/geometry 18 45 14 -14 0
simundump doqcsinfo /kinetics/doqcsinfo 0 pdb173.g CaM pathway \
  "Upinder S. Bhalla, NCBS" " William R. Holmes" "citation here" \
  "General Mammalian" "Brain - Neuronal" Synapse Qualitative \
  "<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10798500>William R. Holmes J Comput Neurosci. (2000) 8(1):65-85</a> ( peer-reviewed publication )" \
  "Approximate implementation" "Approximates original data " 22 -1 0
simundump xgraph /graphs/conc1 0 0 30 0 5.3812 0
simundump xgraph /graphs/conc2 0 0 30 0 0.1415 0
simundump xgraph /moregraphs/conc3 0 0 30 0 1 0
simundump xgraph /moregraphs/conc4 0 0 30 0 1 0
simundump xcoredraw /edit/draw 0 12 24 -16 8
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 \
"Just the CaM model from Holmes 2000 JCNS"
addmsg /kinetics/CaM/CaM-bind-Ca /kinetics/Ca REAC A B 
addmsg /kinetics/CaM/CaMCa-bind-Ca /kinetics/Ca REAC A B 
addmsg /kinetics/CaM/CaMCa2-bind-Ca /kinetics/Ca REAC A B 
addmsg /kinetics/CaM/CaMCa3-bind-Ca /kinetics/Ca REAC A B 
addmsg /kinetics/Ca_tab /kinetics/Ca SLAVE output 
addmsg /kinetics/CaM/CaM-bind-Ca /kinetics/CaM/CaM REAC A B 
addmsg /kinetics/CaM/CaM /kinetics/CaM/CaM-bind-Ca SUBSTRATE n 
addmsg /kinetics/CaM/CaMCa /kinetics/CaM/CaM-bind-Ca PRODUCT n 
addmsg /kinetics/Ca /kinetics/CaM/CaM-bind-Ca SUBSTRATE n 
addmsg /kinetics/CaM/CaM-bind-Ca /kinetics/CaM/CaMCa REAC B A 
addmsg /kinetics/CaM/CaMCa-bind-Ca /kinetics/CaM/CaMCa REAC A B 
addmsg /kinetics/CaM/CaMCa /kinetics/CaM/CaMCa-bind-Ca SUBSTRATE n 
addmsg /kinetics/CaM/CaMCa2 /kinetics/CaM/CaMCa-bind-Ca PRODUCT n 
addmsg /kinetics/Ca /kinetics/CaM/CaMCa-bind-Ca SUBSTRATE n 
addmsg /kinetics/CaM/CaMCa-bind-Ca /kinetics/CaM/CaMCa2 REAC B A 
addmsg /kinetics/CaM/CaMCa2-bind-Ca /kinetics/CaM/CaMCa2 REAC A B 
addmsg /kinetics/CaM/CaMCa2 /kinetics/CaM/CaMCa2-bind-Ca SUBSTRATE n 
addmsg /kinetics/CaM/CaMCa3 /kinetics/CaM/CaMCa2-bind-Ca PRODUCT n 
addmsg /kinetics/Ca /kinetics/CaM/CaMCa2-bind-Ca SUBSTRATE n 
addmsg /kinetics/CaM/CaMCa2-bind-Ca /kinetics/CaM/CaMCa3 REAC B A 
addmsg /kinetics/CaM/CaMCa3-bind-Ca /kinetics/CaM/CaMCa3 REAC A B 
addmsg /kinetics/CaM/CaMCa3 /kinetics/CaM/CaMCa3-bind-Ca SUBSTRATE n 
addmsg /kinetics/CaM/CaMCa4 /kinetics/CaM/CaMCa3-bind-Ca PRODUCT n 
addmsg /kinetics/Ca /kinetics/CaM/CaMCa3-bind-Ca SUBSTRATE n 
addmsg /kinetics/CaM/CaMCa3-bind-Ca /kinetics/CaM/CaMCa4 REAC B A 
enddump
// End of dump

setfield /kinetics/Ca_tab table->dx 0.0050063
setfield /kinetics/Ca_tab table->invdx 199.75
call /kinetics/Ca/notes LOAD \
"70 nM initial conc from Holmes." \
""
call /kinetics/CaM/CaM/notes LOAD \
"Init conc form model is 80 uM."
call /kinetics/doqcsinfo/notes LOAD \
"This is a deterministic, point kinetics approximation to the dendritic spine CaMKII model described in <a href = http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10798500>William R. Holmes J Comput Neurosci. (2000) 8(1):65-85.</a> Rates are the same but the responses differ somewhat because this model does not include the stochastic and diffusive calculations of the original."
complete_loading