//genesis // kkit Version 2 dumpfile // Saved on Tue Feb 18 09:54:45 1997 include kkit FASTDT = 0.01 SIMDT = 0.01 CONTROLDT = 5 PLOTDT = 1 MAXTIME = 4000 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 flags script fg ysquish do_slope wy simobjdump kpool CoTotal CoInit Co CoRemaining n nInit nTotal nMin vol \ slave_enable keepconc 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 kreac A B kf kb is_active notes editfunc xtree_fg_req \ xtree_textfg_req plotfield manageclass simobjdump kenz CoComplexInit CoComplex nComplexInit nComplex vol sA pA eA B \ k1 k2 k3 keepconc usecomplex ksum notes editfunc xtree_fg_req \ xtree_textfg_req plotfield manageclass link_to_manage simundump kpool /kinetics/X_prd 1 1 0 0.22662 0.77338 0.22662 0 1 0 1 0 0 "" \ blue black simundump kpool /kinetics/X_sub 1 1 1 1 0.87628 1 1 1 0 1 4 0 "" blue black simundump kreac /kinetics/degrade_X 1 0 0.011331 0.05 0 1 "" edit_reac white \ black A group simundump kpool /kinetics/X 1 1 1 0.022662 0.97734 0.022662 1 1 0 1 0 0 "" \ blue black simundump kenz /kinetics/X/X_enz 1 0 0 0 0.011331 0 0.011331 0.011331 \ 0.022662 0.022662 1 1 1 0 0 2 "" edit_enz red blue CoComplex kpool \ enzproto_to_pool_link simundump kpool /kinetics/X_inactive 1 1 0 0.99625 0.0037486 0.99625 0 1 0 1 \ 0 0 "" blue black simundump kpool /kinetics/Y 1 1 1 0.66304 0.33696 0.66304 1 1 0 1 0 0 "" red \ black simundump kenz /kinetics/Y/Y_enz 1 0 0 0 0.33152 0 0.33152 0.33152 0.66304 \ 0.66304 1 1 1 0 0 2 "" edit_enz red red CoComplex kpool \ enzproto_to_pool_link simundump kpool /kinetics/Y_sub 1 1 1 1 1 1 1 1 0 1 4 0 "" red black simundump kpool /kinetics/Y_prd 1 20 0 6.6304 13.37 6.6304 0 20 0 1 0 0 "" \ red black simundump kreac /kinetics/degrade_Y 1 0 0.33152 0.05 0 1 "" edit_reac white \ black A group simundump kpool /kinetics/Y_inactive 1 1 0 0.03405 0.96595 0.03405 0 1 0 1 0 \ 0 "" red black simundump kreac /kinetics/inactivate_Y 1 0.03405 0.03405 1 1 1 "" edit_reac \ white black A group simundump kreac /kinetics/inactivate_X 1 0.99625 0.99625 1 1 1 "" edit_reac \ white black A group simundump xtab /kinetics/xtab 1 0 1 1 1 0 "" edit_xtab white green output \ group 0 1 0.022727 2 loadtab /kinetics/xtab table 1 100 0 2000 \ 0 0 0 0 0 0 0 0 0 0 0 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.2 0.2 0.2 \ 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.4 0.4 \ 0.4 0.4 0.4 0.4 0.4 0.4 0.4 0.4 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.6 \ 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.7 0.7 0.7 0.7 0.7 0.7 0.7 0.7 0.7 0.7 \ 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8 1 1 1 1 1 1 1 1 1 1 simundump xgraph /graphs/conc1 0 0 4000 0 0.49091 0 simundump xgraph /graphs/conc2 0 0 4000 0 0.53528 0 simundump xplot /graphs/conc1/X.Co 3 524288 3 \ "delete_plot.w ; edit_plot.D " blue 0 0 1 simundump xplot /graphs/conc1/Y_prd.Co 3 524288 3 \ "delete_plot.w ; edit_plot.D " red 0 0 1 simundump xplot /graphs/conc2/Y.Co 3 524288 3 \ "delete_plot.w ; edit_plot.D " red 0 0 1 simundump xplot /graphs/conc2/X_prd.Co 3 524288 3 \ "delete_plot.w ; edit_plot.D " blue 0 0 1 simundump xgraph /moregraphs/conc3 0 0 4000 0 1 0 simundump xgraph /moregraphs/conc4 0 0 4000 0 1 0 simundump xcoredraw /edit/draw 0 -4.8515 4.8515 -4.8515 4.8515 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 \ "echo.p dragging to for product" "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 \ "echo.p dragging to for substrate" "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 UNDUMP 15 \ "/kinetics/X_prd" 2.2541 3.1157 0 \ "/kinetics/X_sub" -2.9303 3.097 0 \ "/kinetics/degrade_X" -0.30738 3.8806 0 \ "/kinetics/X" -0.51229 0.87687 0 \ "/kinetics/X/X_enz" -0.59426 1.95147 0 \ "/kinetics/X_inactive" -4.0574 0.22388 0 \ "/kinetics/Y" -0.51229 -0.6903 0 \ "/kinetics/Y/Y_enz" -0.47131 -2.0522 0 \ "/kinetics/Y_sub" 2.1926 -2.7612 0 \ "/kinetics/Y_prd" -2.9303 -2.8545 0 \ "/kinetics/degrade_Y" -0.59426 -3.7687 0 \ "/kinetics/Y_inactive" 3.738 0.018103 0 \ "/kinetics/inactivate_Y" 2.0679 -1.3758 0 \ "/kinetics/inactivate_X" -2.7638 1.6111 0 \ "/kinetics/xtab" 1.5111 1.9551 0 simundump xtext /file/notes 0 1 xtextload /file/notes \ "Here we do get bistability. It is" \ "just a matter of changing the rates" \ "of degradation of the products, so" \ "that the conc-eff curves are somewhat" \ "steeper." addmsg /kinetics/X/X_enz /kinetics/X_prd MM_PRD pA addmsg /kinetics/degrade_X /kinetics/X_prd REAC A B addmsg /kinetics/inactivate_Y /kinetics/X_prd REAC A B addmsg /kinetics/inactivate_Y /kinetics/X_prd REAC A B addmsg /kinetics/X/X_enz /kinetics/X_sub REAC sA B addmsg /kinetics/degrade_X /kinetics/X_sub REAC B A addmsg /kinetics/X_prd /kinetics/degrade_X SUBSTRATE n addmsg /kinetics/X_sub /kinetics/degrade_X PRODUCT n addmsg /kinetics/X/X_enz /kinetics/X REAC eA B addmsg /kinetics/inactivate_X /kinetics/X REAC A B addmsg /kinetics/xtab /kinetics/X SLAVE output addmsg /kinetics/X /kinetics/X/X_enz ENZYME n addmsg /kinetics/X_sub /kinetics/X/X_enz SUBSTRATE n addmsg /kinetics/inactivate_X /kinetics/X_inactive REAC B A addmsg /kinetics/Y/Y_enz /kinetics/Y REAC eA B addmsg /kinetics/inactivate_Y /kinetics/Y REAC A B addmsg /kinetics/Y /kinetics/Y/Y_enz ENZYME n addmsg /kinetics/Y_sub /kinetics/Y/Y_enz SUBSTRATE n addmsg /kinetics/Y/Y_enz /kinetics/Y_sub REAC sA B addmsg /kinetics/degrade_Y /kinetics/Y_sub REAC B A addmsg /kinetics/Y/Y_enz /kinetics/Y_prd MM_PRD pA addmsg /kinetics/degrade_Y /kinetics/Y_prd REAC A B addmsg /kinetics/inactivate_X /kinetics/Y_prd REAC A B addmsg /kinetics/inactivate_X /kinetics/Y_prd REAC A B addmsg /kinetics/Y_prd /kinetics/degrade_Y SUBSTRATE n addmsg /kinetics/Y_sub /kinetics/degrade_Y PRODUCT n addmsg /kinetics/inactivate_Y /kinetics/Y_inactive REAC B A addmsg /kinetics/X_prd /kinetics/inactivate_Y SUBSTRATE n addmsg /kinetics/X_prd /kinetics/inactivate_Y SUBSTRATE n addmsg /kinetics/Y /kinetics/inactivate_Y SUBSTRATE n addmsg /kinetics/Y_inactive /kinetics/inactivate_Y PRODUCT n addmsg /kinetics/Y_prd /kinetics/inactivate_X SUBSTRATE n addmsg /kinetics/Y_prd /kinetics/inactivate_X SUBSTRATE n addmsg /kinetics/X /kinetics/inactivate_X SUBSTRATE n addmsg /kinetics/X_inactive /kinetics/inactivate_X PRODUCT n addmsg /kinetics/X /graphs/conc1/X.Co PLOT Co *X.Co *blue addmsg /kinetics/Y_prd /graphs/conc1/Y_prd.Co PLOT Co *Y_prd.Co *red addmsg /kinetics/Y /graphs/conc2/Y.Co PLOT Co *Y.Co *red addmsg /kinetics/X_prd /graphs/conc2/X_prd.Co PLOT Co *X_prd.Co *blue enddump // End of dump call /edit/draw/tree RESET reset