//genesis // kkit Version 11 flat dumpfile // Saved on Thu Feb 12 16:54:22 2009 include kkit {argv 1} FASTDT = 2e-06 SIMDT = 0.001 CONTROLDT = 1 PLOTDT = 10 MAXTIME = 1000 TRANSIENT_TIME = 2 VARIABLE_DT_FLAG = 1 DEFAULT_VOL = 1e-15 VERSION = 11.0 setfield /file/modpath value /home2/bhalla/scripts/modules kparms //genesis initdump -version 3 -ignoreorphans 1 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 simobjdump doqcsinfo filename accessname accesstype transcriber developer \ citation species tissue cellcompartment methodology sources \ model_implementation model_validation editfunc simundump geometry /kinetics/geometry 0 1e-15 3 sphere "" white black 49 32 0 simundump text /kinetics/notes 0 "" call /kinetics/notes LOAD \ "" simundump text /kinetics/geometry/notes 0 "" call /kinetics/geometry/notes LOAD \ "" simundump kpool /kinetics/40S 0 0 0 0 0 0 0 0 6e+05 0 /kinetics/geometry 7 \ black 43 41 0 simundump text /kinetics/40S/notes 0 "Activated form of S6\n" call /kinetics/40S/notes LOAD \ "Activated form of S6" \ "" simundump kpool /kinetics/eIF4F-mRNA_clx 0 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry 59 black 45 55 0 simundump text /kinetics/eIF4F-mRNA_clx/notes 0 "" call /kinetics/eIF4F-mRNA_clx/notes LOAD \ "" simundump group /kinetics/43S_complex 0 yellow black x 0 0 "" 43S_complex \ defaultfile.g 0 0 0 45 68 0 simundump text /kinetics/43S_complex/notes 0 "" call /kinetics/43S_complex/notes LOAD \ "" simundump kreac /kinetics/43S_complex/Q_binds_R 0 8e-07 0.5 "" white yellow \ 41 72 0 simundump text /kinetics/43S_complex/Q_binds_R/notes 0 "" call /kinetics/43S_complex/Q_binds_R/notes LOAD \ "" simundump kpool /kinetics/43S_complex/Q.R 0 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry blue yellow 50 70 0 simundump text /kinetics/43S_complex/Q.R/notes 0 \ "Q.R= Quaternary complex.Ribosome\n" call /kinetics/43S_complex/Q.R/notes LOAD \ "Q.R= Quaternary complex.Ribosome" \ "" simundump kreac /kinetics/43S_complex/QR_binds_M 0 8.1667e-07 0.0045 "" white \ yellow 46 63 0 simundump text /kinetics/43S_complex/QR_binds_M/notes 0 "" call /kinetics/43S_complex/QR_binds_M/notes LOAD \ "" simundump kreac /kinetics/43S_complex/R_binds_M 0 2.1333e-06 0.719 "" white \ yellow 44 46 0 simundump text /kinetics/43S_complex/R_binds_M/notes 0 "" call /kinetics/43S_complex/R_binds_M/notes LOAD \ "" simundump kpool /kinetics/43S_complex/RM 0 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry pink yellow 38 52 0 simundump text /kinetics/43S_complex/RM/notes 0 "" call /kinetics/43S_complex/RM/notes LOAD \ "" simundump kreac /kinetics/43S_complex/RM_binds_Q 0 1.6333e-07 0.00169 "" \ white yellow 35 57 0 simundump text /kinetics/43S_complex/RM_binds_Q/notes 0 "" call /kinetics/43S_complex/RM_binds_Q/notes LOAD \ "" simundump kpool /kinetics/43S_complex/Quaternary_clx 0 0 0.047 0.047 28200 \ 28200 0 0 6e+05 0 /kinetics/geometry 28 yellow 38 65 0 simundump text /kinetics/43S_complex/Quaternary_clx/notes 0 \ "Q= Quaternary complex\n" call /kinetics/43S_complex/Quaternary_clx/notes LOAD \ "Q= Quaternary complex" \ "" simundump kpool /kinetics/eEF2 0 0 0.5 0.5 3e+05 3e+05 0 0 6e+05 0 \ /kinetics/geometry 27 black 62 68 0 simundump text /kinetics/eEF2/notes 0 "" call /kinetics/eEF2/notes LOAD \ "" simundump kpool /kinetics/60S_R 0 0 0.068 0.068 40800 40800 0 0 6e+05 4 \ /kinetics/geometry 46 black 65 69 0 simundump text /kinetics/60S_R/notes 0 "" call /kinetics/60S_R/notes LOAD \ "" simundump kpool /kinetics/Translation_clx 0 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry 52 black 57 50 0 simundump text /kinetics/Translation_clx/notes 0 "" call /kinetics/Translation_clx/notes LOAD \ "" simundump kenz /kinetics/Translation_clx/pro_syn 0 0 0 0 0 6e+05 3.0304e-06 \ 0.08 0.02 0 0 "" red 52 "" 57 49 0 simundump text /kinetics/Translation_clx/pro_syn/notes 0 "" call /kinetics/Translation_clx/pro_syn/notes LOAD \ "" simundump kenz /kinetics/Translation_clx/rad_pro_syn 0 0 0 0 0 6e+05 \ 2.7778e-06 0.08 0.02 0 0 "" red 52 "" 57 52 0 simundump text /kinetics/Translation_clx/rad_pro_syn/notes 0 "" call /kinetics/Translation_clx/rad_pro_syn/notes LOAD \ "" simundump kpool /kinetics/AA 0 0 0.1 0.1 60000 60000 0 0 6e+05 4 \ /kinetics/geometry cyan black 62 49 0 simundump text /kinetics/AA/notes 0 "" call /kinetics/AA/notes LOAD \ "" simundump kpool /kinetics/peptide 0 0 0 0 0 0 0 0 6e+05 0 /kinetics/geometry \ brown black 56 44 0 simundump text /kinetics/peptide/notes 0 "" call /kinetics/peptide/notes LOAD \ "" simundump kreac /kinetics/elongation 0 6.6667e-05 10 "" white black 65 52 0 simundump text /kinetics/elongation/notes 0 "" call /kinetics/elongation/notes LOAD \ "" simundump kreac /kinetics/activation 0 1.6667e-06 0.9 "" white black 63 60 0 simundump text /kinetics/activation/notes 0 "" call /kinetics/activation/notes LOAD \ "" simundump kpool /kinetics/degraded_protein 0 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry white black 65 32 0 simundump text /kinetics/degraded_protein/notes 0 "" call /kinetics/degraded_protein/notes LOAD \ "" simundump kpool /kinetics/protein 0 0 0 0 0 0 0 0 6e+05 0 /kinetics/geometry \ red black 56 32 0 simundump text /kinetics/protein/notes 0 "" call /kinetics/protein/notes LOAD \ "" simundump kpool /kinetics/80S_ribos_clx 0 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry blue black 59 57 0 simundump text /kinetics/80S_ribos_clx/notes 0 "" call /kinetics/80S_ribos_clx/notes LOAD \ "" simundump kpool /kinetics/43Scomplex 0 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry hotpink black 58 63 0 simundump text /kinetics/43Scomplex/notes 0 \ "40S_complex consist of Quaternary complex, mRNA complex, \n40S Ribosomes." call /kinetics/43Scomplex/notes LOAD \ "40S_complex consist of Quaternary complex, mRNA complex, " \ "40S Ribosomes." simundump kreac /kinetics/pep_elongation 0 0.1 0.001 "" white black 56 39 0 simundump text /kinetics/pep_elongation/notes 0 "" call /kinetics/pep_elongation/notes LOAD \ "" simundump kreac /kinetics/protein_deg 0 1 0 "" white black 60 33 0 simundump text /kinetics/protein_deg/notes 0 "" call /kinetics/protein_deg/notes LOAD \ "" simundump kpool /kinetics/Basal_Translation 0 0 0.0002 0.0002 120 120 0 0 \ 6e+05 0 /kinetics/geometry 53 black 62 43 0 simundump text /kinetics/Basal_Translation/notes 0 \ "It will contribute to mTOR independent translation." call /kinetics/Basal_Translation/notes LOAD \ "It will contribute to mTOR independent translation." simundump kenz /kinetics/Basal_Translation/basal_syn 0 0 0 0 0 1 3.0303e-06 \ 0.08 0.02 0 0 "" red 53 "" 63 44 0 simundump text /kinetics/Basal_Translation/basal_syn/notes 0 "" call /kinetics/Basal_Translation/basal_syn/notes LOAD \ "" simundump kenz /kinetics/Basal_Translation/rad_basal_syn 0 0 0 0 0 6e+05 \ 3.0303e-06 0.08 0.02 0 0 "" red 53 "" 67 39 0 simundump text /kinetics/Basal_Translation/rad_basal_syn/notes 0 "" call /kinetics/Basal_Translation/rad_basal_syn/notes LOAD \ "" simundump kpool /kinetics/rad_AA 0 0 0 0 0 0 0 0 6e+05 0 /kinetics/geometry \ 45 black 67 46 0 simundump text /kinetics/rad_AA/notes 0 "" call /kinetics/rad_AA/notes LOAD \ "" simundump kpool /kinetics/rad_peptide 0 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry 1 black 58 42 0 simundump text /kinetics/rad_peptide/notes 0 "" call /kinetics/rad_peptide/notes LOAD \ "" simundump kreac /kinetics/rad_pep_elongation 0 0.1 0.001 "" white black 62 40 \ 0 simundump text /kinetics/rad_pep_elongation/notes 0 "" call /kinetics/rad_pep_elongation/notes LOAD \ "" simundump kpool /kinetics/rad_protein 0 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry 47 black 59 36 0 simundump text /kinetics/rad_protein/notes 0 "" call /kinetics/rad_protein/notes LOAD \ "" simundump kreac /kinetics/rad_protein_deg 0 1 0 "" white black 63 36 0 simundump text /kinetics/rad_protein_deg/notes 0 "" call /kinetics/rad_protein_deg/notes LOAD \ "" simundump kpool /kinetics/rad_deg_pro 0 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry 2 black 67 36 0 simundump text /kinetics/rad_deg_pro/notes 0 "" call /kinetics/rad_deg_pro/notes LOAD \ "" simundump kreac /kinetics/labelling 0 0 0 "" white black 67 51 0 simundump text /kinetics/labelling/notes 0 "" call /kinetics/labelling/notes LOAD \ "" simundump doqcsinfo /kinetics/doqcsinfo 0 Protein_synthesis.g \ Protein_synthesis Network "Pragati Jain, NCBS" "Pragati Jain, NCBS" \ "citation here" "General Mammalian" - "Cell membrane, Cytosol" \ "Quantitative match to experiments, Hypothetical" \ "Jain P, and Bhalla, U.S. PLoS Comput Biol. 2009 Feb;5(2). ( Peer-reviewed publication )" \ "Exact GENESIS implementation" \ "Replicates original data , Approximates original data " show_dumpdb simundump text /kinetics/doqcsinfo/notes 0 \ "40S, the eIF4F-mRNA complex, and eEF2 bind to form the translation complex, leading to \nprotein synthesis." call /kinetics/doqcsinfo/notes LOAD \ "40S, the eIF4F-mRNA complex, and eEF2 bind to form the translation complex, leading to " \ "protein synthesis." simundump xgraph /graphs/conc1 0 0 10070 0 0.88766 0 simundump xgraph /graphs/conc2 0 0 7890 0 0.47175 0 simundump xplot /graphs/conc1/40S.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 50 0 0 1 simundump xplot /graphs/conc1/protein.Co 3 524288 \ "delete_plot.w ; edit_plot.D " red 0 0 1 simundump xplot /graphs/conc1/eIF4F-mRNA_clx.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 59 0 0 1 simundump xplot /graphs/conc1/eEF2.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 27 0 0 1 simundump xplot /graphs/conc2/43Scomplex.Co 3 524288 \ "delete_plot.w ; edit_plot.D " hotpink 0 0 1 simundump xplot /graphs/conc2/degraded_protein.Co 3 524288 \ "delete_plot.w ; edit_plot.D " white 0 0 1 simundump xplot /graphs/conc2/peptide.Co 3 524288 \ "delete_plot.w ; edit_plot.D " brown 0 0 1 simundump xplot /graphs/conc2/rad_protein.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 47 0 0 1 simundump xplot /graphs/conc2/rad_deg_pro.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 2 0 0 1 simundump xgraph /moregraphs/conc3 0 0 12000 0 0.25 0 simundump xgraph /moregraphs/conc4 0 0 12000 0 0.71395 0 simundump xcoredraw /edit/draw 0 -2 69 -2 74 simundump xtree /edit/draw/tree 0 \ /kinetics/#[],/kinetics/#[]/#[],/kinetics/#[]/#[]/#[][TYPE!=proto],/kinetics/#[]/#[]/#[][TYPE!=linkinfo]/##[] \ "edit_elm.D ; drag_from_edit.w " auto 0.6 simundump xtext /file/notes 0 1 xtextload /file/notes \ "" \ "" \ " " addmsg /kinetics/43S_complex/Q_binds_R /kinetics/40S REAC A B addmsg /kinetics/43S_complex/R_binds_M /kinetics/40S REAC A B addmsg /kinetics/43S_complex/R_binds_M /kinetics/eIF4F-mRNA_clx REAC A B addmsg /kinetics/43S_complex/QR_binds_M /kinetics/eIF4F-mRNA_clx REAC A B addmsg /kinetics/40S /kinetics/43S_complex/Q_binds_R SUBSTRATE n addmsg /kinetics/43S_complex/Quaternary_clx /kinetics/43S_complex/Q_binds_R SUBSTRATE n addmsg /kinetics/43S_complex/Q.R /kinetics/43S_complex/Q_binds_R PRODUCT n addmsg /kinetics/43S_complex/Q_binds_R /kinetics/43S_complex/Q.R REAC B A addmsg /kinetics/43S_complex/QR_binds_M /kinetics/43S_complex/Q.R REAC A B addmsg /kinetics/43S_complex/Q.R /kinetics/43S_complex/QR_binds_M SUBSTRATE n addmsg /kinetics/eIF4F-mRNA_clx /kinetics/43S_complex/QR_binds_M SUBSTRATE n addmsg /kinetics/43Scomplex /kinetics/43S_complex/QR_binds_M PRODUCT n addmsg /kinetics/eIF4F-mRNA_clx /kinetics/43S_complex/R_binds_M SUBSTRATE n addmsg /kinetics/43S_complex/RM /kinetics/43S_complex/R_binds_M PRODUCT n addmsg /kinetics/40S /kinetics/43S_complex/R_binds_M SUBSTRATE n addmsg /kinetics/43S_complex/R_binds_M /kinetics/43S_complex/RM REAC B A addmsg /kinetics/43S_complex/RM_binds_Q /kinetics/43S_complex/RM REAC A B addmsg /kinetics/43S_complex/RM /kinetics/43S_complex/RM_binds_Q SUBSTRATE n addmsg /kinetics/43Scomplex /kinetics/43S_complex/RM_binds_Q PRODUCT n addmsg /kinetics/43S_complex/Quaternary_clx /kinetics/43S_complex/RM_binds_Q SUBSTRATE n addmsg /kinetics/43S_complex/Q_binds_R /kinetics/43S_complex/Quaternary_clx REAC A B addmsg /kinetics/43S_complex/RM_binds_Q /kinetics/43S_complex/Quaternary_clx REAC A B addmsg /kinetics/elongation /kinetics/eEF2 REAC A B addmsg /kinetics/activation /kinetics/60S_R REAC A B addmsg /kinetics/Translation_clx/pro_syn /kinetics/Translation_clx REAC eA B addmsg /kinetics/elongation /kinetics/Translation_clx REAC B A addmsg /kinetics/Translation_clx/rad_pro_syn /kinetics/Translation_clx REAC eA B addmsg /kinetics/Translation_clx /kinetics/Translation_clx/pro_syn ENZYME n addmsg /kinetics/AA /kinetics/Translation_clx/pro_syn SUBSTRATE n addmsg /kinetics/Translation_clx /kinetics/Translation_clx/rad_pro_syn ENZYME n addmsg /kinetics/rad_AA /kinetics/Translation_clx/rad_pro_syn SUBSTRATE n addmsg /kinetics/Translation_clx/pro_syn /kinetics/AA REAC sA B addmsg /kinetics/Basal_Translation/basal_syn /kinetics/AA REAC sA B addmsg /kinetics/labelling /kinetics/AA REAC A B addmsg /kinetics/Translation_clx/pro_syn /kinetics/peptide MM_PRD pA addmsg /kinetics/pep_elongation /kinetics/peptide REAC A B addmsg /kinetics/Basal_Translation/basal_syn /kinetics/peptide MM_PRD pA addmsg /kinetics/Basal_Translation/rad_basal_syn /kinetics/peptide MM_PRD pA addmsg /kinetics/eEF2 /kinetics/elongation SUBSTRATE n addmsg /kinetics/80S_ribos_clx /kinetics/elongation SUBSTRATE n addmsg /kinetics/Translation_clx /kinetics/elongation PRODUCT n addmsg /kinetics/60S_R /kinetics/activation SUBSTRATE n addmsg /kinetics/43Scomplex /kinetics/activation SUBSTRATE n addmsg /kinetics/80S_ribos_clx /kinetics/activation PRODUCT n addmsg /kinetics/protein_deg /kinetics/degraded_protein REAC B A addmsg /kinetics/pep_elongation /kinetics/protein REAC B A addmsg /kinetics/protein_deg /kinetics/protein REAC A B addmsg /kinetics/activation /kinetics/80S_ribos_clx REAC B A addmsg /kinetics/elongation /kinetics/80S_ribos_clx REAC A B addmsg /kinetics/43S_complex/QR_binds_M /kinetics/43Scomplex REAC B A addmsg /kinetics/43S_complex/RM_binds_Q /kinetics/43Scomplex REAC B A addmsg /kinetics/activation /kinetics/43Scomplex REAC A B addmsg /kinetics/protein /kinetics/pep_elongation PRODUCT n addmsg /kinetics/peptide /kinetics/pep_elongation SUBSTRATE n addmsg /kinetics/degraded_protein /kinetics/protein_deg PRODUCT n addmsg /kinetics/protein /kinetics/protein_deg SUBSTRATE n addmsg /kinetics/Basal_Translation/basal_syn /kinetics/Basal_Translation REAC eA B addmsg /kinetics/Basal_Translation/rad_basal_syn /kinetics/Basal_Translation REAC eA B addmsg /kinetics/Basal_Translation /kinetics/Basal_Translation/basal_syn ENZYME n addmsg /kinetics/AA /kinetics/Basal_Translation/basal_syn SUBSTRATE n addmsg /kinetics/Basal_Translation /kinetics/Basal_Translation/rad_basal_syn ENZYME n addmsg /kinetics/rad_AA /kinetics/Basal_Translation/rad_basal_syn SUBSTRATE n addmsg /kinetics/labelling /kinetics/rad_AA REAC B A addmsg /kinetics/Translation_clx/rad_pro_syn /kinetics/rad_AA REAC sA B addmsg /kinetics/Basal_Translation/rad_basal_syn /kinetics/rad_AA REAC sA B addmsg /kinetics/Translation_clx/rad_pro_syn /kinetics/rad_peptide MM_PRD pA addmsg /kinetics/rad_pep_elongation /kinetics/rad_peptide REAC A B addmsg /kinetics/rad_peptide /kinetics/rad_pep_elongation SUBSTRATE n addmsg /kinetics/rad_protein /kinetics/rad_pep_elongation PRODUCT n addmsg /kinetics/rad_pep_elongation /kinetics/rad_protein REAC B A addmsg /kinetics/rad_protein_deg /kinetics/rad_protein REAC A B addmsg /kinetics/rad_protein /kinetics/rad_protein_deg SUBSTRATE n addmsg /kinetics/rad_deg_pro /kinetics/rad_protein_deg PRODUCT n addmsg /kinetics/rad_protein_deg /kinetics/rad_deg_pro REAC B A addmsg /kinetics/AA /kinetics/labelling SUBSTRATE n addmsg /kinetics/rad_AA /kinetics/labelling PRODUCT n addmsg /kinetics/40S /graphs/conc1/40S.Co PLOT Co *40S.Co *50 addmsg /kinetics/protein /graphs/conc1/protein.Co PLOT Co *protein.Co *red addmsg /kinetics/eIF4F-mRNA_clx /graphs/conc1/eIF4F-mRNA_clx.Co PLOT Co *eIF4F-mRNA_clx.Co *59 addmsg /kinetics/eEF2 /graphs/conc1/eEF2.Co PLOT Co *eEF2.Co *27 addmsg /kinetics/43Scomplex /graphs/conc2/43Scomplex.Co PLOT Co *43Scomplex.Co *hotpink addmsg /kinetics/degraded_protein /graphs/conc2/degraded_protein.Co PLOT Co *degraded_protein.Co *white addmsg /kinetics/peptide /graphs/conc2/peptide.Co PLOT Co *peptide.Co *brown addmsg /kinetics/rad_protein /graphs/conc2/rad_protein.Co PLOT Co *rad_protein.Co *47 addmsg /kinetics/rad_deg_pro /graphs/conc2/rad_deg_pro.Co PLOT Co *rad_deg_pro.Co *2 enddump // End of dump call /kinetics/40S/notes LOAD \ "Activated form of S6" \ "" call /kinetics/43S_complex/Q.R/notes LOAD \ "Q.R= Quaternary complex.Ribosome" \ "" call /kinetics/43S_complex/Quaternary_clx/notes LOAD \ "Q= Quaternary complex" \ "" call /kinetics/43Scomplex/notes LOAD \ "40S_complex consist of Quaternary complex, mRNA complex, " \ "40S Ribosomes." call /kinetics/Basal_Translation/notes LOAD \ "It will contribute to mTOR independent translation." call /kinetics/doqcsinfo/notes LOAD \ "40S, the eIF4F-mRNA complex, and eEF2 bind to form the translation complex, leading to " \ "protein synthesis." complete_loading