//genesis // kkit Version 8 dumpfile // Saved on Sun Jan 21 01:10:24 2001 include kkit {argv 1} FASTDT = 0.0001 SIMDT = 0.01 CONTROLDT = 5 PLOTDT = 0.1 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 modout nmsgr nreac nenz notes xtree_fg_req xtree_textfg_req simobjdump modin nmsgr nreac nenz nenzsub nenzprd nreacsub nreacprd notes \ xtree_fg_req xtree_textfg_req simobjdump kreac A B kf kb stoch_flag is_active oldmsgmode notes editfunc \ xtree_fg_req xtree_textfg_req plotfield manageclass simundump kpool /kinetics/B 0 0 0 0 0 0 0 0 0 1 0 "" blue black simundump kpool /kinetics/C 0 0 0 1 -1 1 0 0 0 1 0 "" 28 black simundump kpool /kinetics/A 0 1 1 0 1 0 1 1 0 1 0 "" 1 black simundump kreac /kinetics/DA 0 0 0 0.1 0.1 1 0 0 "" edit_reac 1 black A group simundump kpool /kinetics/D 0 0 0 0 0 0 0 0 0 1 0 "" 61 black simundump kreac /kinetics/CD 0 0 0 0.1 0.1 1 0 0 "" edit_reac white black A \ group simundump kreac /kinetics/BC 0 0 0 0.1 0.1 1 0 0 "" edit_reac white black A \ group simundump kreac /kinetics/AB 0 0 0 0.1 0.1 1 0 0 "" edit_reac white black A \ group simundump xgraph /graphs/conc1 0 0 100 0 1.1454 0 simundump xgraph /graphs/conc2 0 0 100 0 1 0 simundump xplot /graphs/conc1/A.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 1 0 0 1 simundump xplot /graphs/conc1/B.Co 3 524288 \ "delete_plot.w ; edit_plot.D " blue 0 0 1 simundump xplot /graphs/conc1/C.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 28 0 0 1 simundump xplot /graphs/conc1/D.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 61 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 -5 5 -5 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 ADDMSGARROW \ /kinetics/##[TYPE=modout] /kinetics/##[TYPE=modin] INPUT modin red -1024 0 \ "echo.p dragging to for interacting modules" "modout_to_modin_add.p " "modout_to_modin_drop.p " call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=kpool] /kinetics/##[TYPE=modout] DUMMY modout none -1025 0 \ "msgr_to_modout.p " "" "" call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=kenz] /kinetics/##[TYPE=modout] DUMMY modout none -1026 0 \ "enz_to_modout.p " "" "" call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=kreac] /kinetics/##[TYPE=modout] DUMMY modout none -1027 0 \ "reac_to_modout.p " "" "" call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=kpool] /kinetics/##[TYPE=modin] DUMMY modin none -1028 0 \ "msgr_to_modin.p " "" "" call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=kenz] /kinetics/##[TYPE=modin] DUMMY modin none -1029 0 \ "enz_to_modin.p " "" "" call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=kreac] /kinetics/##[TYPE=modin] DUMMY modin none -1030 0 \ "reac_to_modin.p " "" "" call /edit/draw/tree UNDUMP 8 \ "/kinetics/B" 2.1926 2.5514 0 \ "/kinetics/C" 2.0492 -1.5638 0 \ "/kinetics/A" -2.459 2.5514 0 \ "/kinetics/DA" -3.9754 0.84362 0 \ "/kinetics/D" -2.2541 -1.7078 0 \ "/kinetics/CD" -0.32787 -3.0247 0 \ "/kinetics/BC" 3.8525 0.26749 0 \ "/kinetics/AB" -0.14344 3.6831 0 simundump xtext /file/notes 0 1 xtextload /file/notes \ "Example of stochastic transitions" \ "among a molecule which can exist" \ "in 4 states." addmsg /kinetics/AB /kinetics/B REAC B A addmsg /kinetics/BC /kinetics/B REAC A B addmsg /kinetics/BC /kinetics/C REAC B A addmsg /kinetics/CD /kinetics/C REAC A B addmsg /kinetics/DA /kinetics/A REAC B A addmsg /kinetics/AB /kinetics/A REAC A B addmsg /kinetics/A /kinetics/DA PRODUCT n addmsg /kinetics/D /kinetics/DA SUBSTRATE n addmsg /kinetics/CD /kinetics/D REAC B A addmsg /kinetics/DA /kinetics/D REAC A B addmsg /kinetics/C /kinetics/CD SUBSTRATE n addmsg /kinetics/D /kinetics/CD PRODUCT n addmsg /kinetics/B /kinetics/BC SUBSTRATE n addmsg /kinetics/C /kinetics/BC PRODUCT n addmsg /kinetics/A /kinetics/AB SUBSTRATE n addmsg /kinetics/B /kinetics/AB PRODUCT n addmsg /kinetics/A /graphs/conc1/A.Co PLOT Co *A.Co *1 addmsg /kinetics/B /graphs/conc1/B.Co PLOT Co *B.Co *blue addmsg /kinetics/C /graphs/conc1/C.Co PLOT Co *C.Co *28 addmsg /kinetics/D /graphs/conc1/D.Co PLOT Co *D.Co *61 enddump // End of dump call /edit/draw/tree RESET fix_transp_msgs reset