//genesis // kkit Version 7 dumpfile // Saved on Sun Sep 3 11:57:55 2000 include kkit {argv 1} FASTDT = 0.0001 SIMDT = 0.01 CONTROLDT = 5 PLOTDT = 1 MAXTIME = 100 float TRANSIENT_TIME = 2 int VARIABLE_DT_FLAG = 0 float DEFAULT_VOL = 1.6667e-21 kparms //genesis initdump -version 3 -ignoreorphans 1 simobjdump table input output alloced step_mode stepsize 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 kpool CoTotal CoInit Co CoRemaining n nInit nTotal nMin vol \ slave_enable notes xtree_fg_req xtree_textfg_req simobjdump xtab input output alloced step_mode stepsize notes editfunc \ xtree_fg_req xtree_textfg_req plotfield manageclass baselevel last_x last_y \ is_running simobjdump group notes editfunc xtree_fg_req xtree_textfg_req plotfield \ manageclass expanded movealone simobjdump kenz CoComplexInit CoComplex nComplexInit nComplex vol sA pA eA B \ k1 k2 k3 keepconc usecomplex ksum oldmsgmode notes editfunc xtree_fg_req \ xtree_textfg_req plotfield manageclass link_to_manage simobjdump kreac A B kf kb is_active oldmsgmode notes editfunc xtree_fg_req \ xtree_textfg_req plotfield manageclass simundump group /kinetics/epi 0 "" edit_group blue black x group 0 0 simundump xtab /kinetics/epi/xtab 0 0 0 1 1 0 "" edit_xtab white blue output \ group 0 100 0.92955 1 loadtab /kinetics/epi/xtab table 1 100 0 100 \ 0 0.0092955 0.018591 0.027887 0.037182 0.046477 0.055773 0.065069 0.074364 \ 0.083659 0.092955 0.10225 0.11155 0.12084 0.13014 0.13943 0.14873 0.15802 \ 0.16732 0.17661 0.18591 0.19521 0.2045 0.2138 0.22309 0.23239 0.24168 \ 0.25098 0.26027 0.26957 0.27887 0.28816 0.29746 0.30675 0.31605 0.32534 \ 0.33464 0.34393 0.35323 0.36252 0.37182 0.38112 0.39041 0.39971 0.409 0.4183 \ 0.42759 0.43689 0.44618 0.45548 0.46478 0.47407 0.48337 0.49266 0.50196 \ 0.51125 0.52055 0.52984 0.53914 0.54843 0.55773 0.56703 0.57632 0.58562 \ 0.59491 0.60421 0.6135 0.6228 0.63209 0.64139 0.65069 0.65998 0.66928 \ 0.67857 0.68787 0.69716 0.70646 0.71575 0.72505 0.73434 0.74364 0.75294 \ 0.76223 0.77153 0.78082 0.79012 0.79941 0.80871 0.818 0.8273 0.8366 0.84589 \ 0.85519 0.86448 0.87378 0.88307 0.89237 0.90166 0.91096 0.92025 1.0001 simundump kpool /kinetics/epi/sub 0 1 1 1 0.0006985 1 1 1 0 1 1 "" 27 blue simundump kpool /kinetics/epi/prd 0 0 0 0 0 0 0 0 0 1 0 "" 0 blue simundump kpool /kinetics/epi/enz 0 1 1 1 0.55932 1 1 1 0 1 0 "" 61 blue simundump kenz /kinetics/epi/enz/kenz 0 0 0 0 0 1 0.03348 0.00837 0.04185 \ 0.044009 0.1 0.4 0.1 0 0 0.5 0 "" edit_enz red 61 CoComplex kpool \ enzproto_to_pool_link simundump kreac /kinetics/epi/inhib 0 0.47414 0.47947 10 1 0 0 "" edit_reac \ white blue A group simundump kpool /kinetics/epi/inhib-enz 0 0 0 0 0 0 0 0 0 1 0 "" 47 blue simundump xcoredraw /edit/draw 0 -5 5 -2.5 7.5 simundump xtree /edit/draw/tree 0 /kinetics/##[] \ "edit_elm.D ; drag_from_edit.w " auto 0.6 call /edit/draw/tree ADDMSGARROW \ select all all all none -1000 0 \ "" "" "" call /edit/draw/tree ADDMSGARROW \ /kinetics/##[] /kinetics/##[TYPE=group] all all none -1001 0 \ "echo.p dragging onto group ; thing_to_group_add.p " "" "" call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=kpool] /kinetics/##[TYPE=kpool] SUMTOTAL kpool darkgreen -1002 0 \ "echo.p dragging to for sumtotal" "pool_to_pool_add_sumtot.p " "pool_to_pool_drop_sumtot.p " call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=kpool] /kinetics/##[TYPE=kpool] CONSERVE kpool blue -1003 0 \ "echo.p dragging to for conserve" "pool_to_pool_add_consv.p " "pool_to_pool_drop_consv.p " call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=kreac] /kinetics/##[TYPE=kpool] REAC kpool none -1004 0 \ "" "reac_to_pool_add.p " "reac_to_pool_drop.p " call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=kpool] /kinetics/##[TYPE=kreac] SUBSTRATE kreac green -1005 0 \ "" "pool_to_reac_add.p " "pool_to_reac_drop.p " call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=kpool] /kinetics/##[TYPE=kreac] KF kreac purple -1006 0 \ "" "" "" call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=kpool] /kinetics/##[TYPE=kreac] KB kreac hotpink -1007 0 \ "" "" "" call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=kpool] /kinetics/##[TYPE=kreac] PRODUCT kreac green -1008 1 \ "" "" "" call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=kenz] /kinetics/##[TYPE=kpool] MM_PRD kpool red -1009 0 \ "echo.p dragging to for enz product" "enz_to_pool_add.p " "enz_to_pool_drop.p " call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=kpool] /kinetics/##[TYPE=kenz] SUBSTRATE kenz red -1010 0 \ "echo.p dragging to for enz substrate" "pool_to_enz_add.p " "pool_to_enz_drop.p " call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=kenz] /kinetics/##[TYPE=kpool] SUMTOTAL kpool darkgreen -1011 0 \ "" "" "" call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=kenz] /kinetics/##[TYPE=kpool] CONSERVE kpool blue -1012 0 \ "" "" "" call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=kpool] /kinetics/##[TYPE=kenz] INTRAMOL kenz white -1013 0 \ "" "" "" call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=stim] /kinetics/##[TYPE=kpool] SLAVE kpool orange -1014 0 \ "echo.p dragging to for stimulus" "stim_to_pool_add.p " "stim_to_pool_drop.p " call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=stim] /kinetics/##[TYPE=stim] INPUT stim orange -1015 0 \ "echo.p dragging to for stim" "stim_to_stim_add.p " "stim_to_stim_drop.p " call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=xtab] /kinetics/##[TYPE=kpool] SLAVE kpool orange -1016 0 \ "echo.p dragging to for xtab" "xtab_to_pool_add.p " "xtab_to_pool_drop.p " call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=xtab] /kinetics/##[TYPE=xtab] INPUT xtab orange -1017 0 \ "echo.p dragging to for xtab" "xtab_to_xtab_add.p " "xtab_to_xtab_drop.p " call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=kpool] /kinetics/##[TYPE=xtab] INPUT xtab hotpink -1018 0 \ "echo.p dragging to for xtab" "pool_to_xtab_add.p " "pool_to_xtab_drop.p " call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=kchan] /kinetics/##[TYPE=kpool] REAC kpool none -1019 0 \ "echo.p dragging to for chan product" "chan_to_pool_add.p " "chan_to_pool_drop.p " call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=kpool] /kinetics/##[TYPE=kchan] PRODUCT kchan orange -1020 1 \ "" "" "" call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=kpool] /kinetics/##[TYPE=kchan] SUBSTRATE kchan orange -1021 0 \ "echo.p dragging to for chan substrate" "pool_to_chan_add.p " "pool_to_chan_drop.p " call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=transport] /kinetics/##[TYPE=kpool] MM_PRD kpool yellow -1022 0 \ "" "transport_to_pool_add.p " "transport_to_pool_drop.p " call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=kpool] /kinetics/##[TYPE=transport] SUBSTRATE transport yellow -1023 0 \ "" "pool_to_transport_add.p " "pool_to_transport_drop.p " call /edit/draw/tree UNDUMP 8 \ "/kinetics/epi" 0.73771 5.6893 0 \ "/kinetics/epi/xtab" -1.7623 6.3477 0 \ "/kinetics/epi/sub" -4.2418 4.2387 0 \ "/kinetics/epi/prd" -1.0246 4.2181 0 \ "/kinetics/epi/enz" -2.6844 2.3251 0 \ "/kinetics/epi/enz/kenz" -2.7254 3.2428 0 \ "/kinetics/epi/inhib" 1.0861 3.107 0 \ "/kinetics/epi/inhib-enz" 2.9713 4.3827 0 simundump xtext /file/notes 0 1 xtextload /file/notes \ "Some useful comments here." \ "Kkit tutorial file." addmsg /kinetics/epi/enz/kenz /kinetics/epi/sub REAC sA B addmsg /kinetics/epi/xtab /kinetics/epi/sub SLAVE output addmsg /kinetics/epi/enz/kenz /kinetics/epi/prd MM_PRD pA addmsg /kinetics/epi/inhib /kinetics/epi/prd REAC A B addmsg /kinetics/epi/enz/kenz /kinetics/epi/enz REAC eA B addmsg /kinetics/epi/inhib /kinetics/epi/enz REAC A B addmsg /kinetics/epi/enz /kinetics/epi/enz/kenz ENZYME n addmsg /kinetics/epi/sub /kinetics/epi/enz/kenz SUBSTRATE n addmsg /kinetics/epi/prd /kinetics/epi/inhib SUBSTRATE n addmsg /kinetics/epi/enz /kinetics/epi/inhib SUBSTRATE n addmsg /kinetics/epi/inhib-enz /kinetics/epi/inhib PRODUCT n addmsg /kinetics/epi/inhib /kinetics/epi/inhib-enz REAC B A enddump // End of dump call /edit/draw/tree RESET fix_transp_msgs reset