//genesis // kkit Version 9 flat dumpfile // Saved on Wed Jan 21 00:46:00 2004 include kkit {argv 1} FASTDT = 5e-05 SIMDT = 0.01 CONTROLDT = 60 PLOTDT = 60 MAXTIME = 10000 TRANSIENT_TIME = 2 VARIABLE_DT_FLAG = 1 DEFAULT_VOL = 3e-18 VERSION = 9.0 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 kpool CoTotal CoInit Co n nInit nTotal nMin vol slave_enable notes \ 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 linkinfo xtree_fg_req xtree_textfg_req uplink downlink x y z simobjdump uplink xtree_fg_req xtree_textfg_req x y z simobjdump downlink xtree_fg_req xtree_textfg_req x y z simobjdump mirror notes xtree_fg_req x y z simundump group /kinetics/lac_gene 0 yellow black x 0 0 "" lac_gene \ /home2/bhalla/scripts/modules/lac_gene_0.g 0 0 0 27 0 0 simundump kpool /kinetics/lac_gene/l_op_2nd_bound[1] 0 0 0 0.034504 62.108 0 \ 0 0 1800 0 "" 52 yellow 26 -12 0 simundump kenz /kinetics/lac_gene/l_op_2nd_bound[1]/lac_transcription1 0 0 \ 0.017416 0 31.348 1800 0.0024998 0.002 0.0005 0 1 "" red 52 "" 26 -11 0 simundump kreac /kinetics/lac_gene/inhib_reac[1] 0 0.55556 9 "" white yellow \ 30 -13 0 simundump kpool /kinetics/lac_gene/l_op_1rst_bound 0 0 0 0.00040076 0.72137 0 \ 0 0 1800 0 "" 2 yellow 33 -12 0 simundump kenz /kinetics/lac_gene/l_op_1rst_bound/lac_transcription 0 0 \ 0.00018179 0 0.32722 1800 0.0024998 0.002 0.0005 0 1 "" red 2 "" 33 -10 0 simundump kreac /kinetics/lac_gene/inhib_reac 0 0.55556 224 "" white yellow \ 36 -13 0 simundump kpool /kinetics/lac_gene/lac_operator 0 40 0.022222 0.00011585 \ 0.20853 40 72000 0 1800 0 "" 36 yellow 40 -12 0 simundump kenz /kinetics/lac_gene/lac_operator/lac_transcription2 0 0 \ 5.7831e-05 0 0.1041 1800 2.4998 2 0.5 0 1 "" red 36 "" 40 -11 0 simundump kpool /kinetics/lac_gene/lac_mRNA 0 0 0 0.010511 18.92 0 0 0 1800 0 \ "" 12 yellow 26 -8 0 simundump kenz /kinetics/lac_gene/lac_mRNA/lac_translation 0 0 0.0052622 0 \ 9.472 1800 0.83494 0.668 0.167 0 1 "" red 12 "" 20 -10 0 simundump kpool /kinetics/lac_gene/lac 0 250 0 0.072258 130.06 0 4.5e+05 0 \ 1800 0 "" 62 yellow 20 -15 0 simundump kpool /kinetics/lac_gene/degraded_lac 0 0 0 70.729 1.2731e+05 0 0 0 \ 1800 0 "" 2 yellow 20 -19 0 simundump kpool /kinetics/lac_gene/degraded_lac_mRNA 0 0 0 4.8997 8819.5 0 0 \ 0 1800 0 "" 1 yellow 33 -8 0 simundump kreac /kinetics/lac_gene/lac_mRNA_degradation 0 0.005775 0 "" white \ yellow 29 -7 0 simundump kreac /kinetics/lac_gene/lac_degradation 0 0.016666 0 "" white \ yellow 20 -17 0 simundump kpool /kinetics/lac_gene/AminoAcids 0 1 0.00055555 0.00055555 \ 0.99999 0.99999 1800 0 1800 4 "" 52 yellow 20 -8 0 simundump kpool /kinetics/lac_gene/Nucleotides 0 1 0.00055555 0.00055555 \ 0.99999 0.99999 1800 0 1800 4 "" 6 yellow 40 -8 0 simundump group /kinetics/TetR_gene 0 61 black x 0 0 "" TetR_gene \ /home2/bhalla/scripts/modules/TetR_gene_0.g 0 0 0 -2 0 0 simundump kpool /kinetics/TetR_gene/l_op_2nd_bound[1] 0 0 0 0.014175 25.514 0 \ 0 0 1800 0 "" 46 61 -3 -12 0 simundump kenz /kinetics/TetR_gene/l_op_2nd_bound[1]/TetR_transcription1 0 0 \ 0.010572 0 19.03 1800 0.0024998 0.002 0.0005 0 1 "" red 46 "" -3 -11 0 simundump kreac /kinetics/TetR_gene/inhib_reac[1] 0 0.55556 9 "" white 61 1 \ -13 0 simundump kpool /kinetics/TetR_gene/l_op_1rst_bound 0 0 0 0.001765 3.1769 0 0 \ 0 1800 0 "" 2 61 4 -12 0 simundump kenz /kinetics/TetR_gene/l_op_1rst_bound/TetR_transcription 0 0 \ 0.00061998 0 1.116 1800 0.0024998 0.002 0.0005 0 1 "" red 2 "" 4 -10 0 simundump kreac /kinetics/TetR_gene/inhib_reac 0 0.55556 224 "" white 61 7 \ -13 0 simundump kpool /kinetics/TetR_gene/TetR 0 250 0 0.42162 758.91 0 4.5e+05 0 \ 1800 0 "" 11 61 -9 -15 0 simundump kpool /kinetics/TetR_gene/degraded_TetR 0 0 0 64.423 1.1596e+05 0 0 \ 0 1800 0 "" 2 61 -9 -19 0 simundump kreac /kinetics/TetR_gene/TetR_degradation 0 0.01666 0 "" white 61 \ -9 -17 0 simundump kpool /kinetics/TetR_gene/TetR_mRNA 0 0 0 0.11853 213.35 0 0 0 1800 \ 0 "" 12 61 -3 -8 0 simundump kenz /kinetics/TetR_gene/TetR_mRNA/TetR_translation 0 0 0.059056 0 \ 106.3 1800 0.83494 0.668 0.167 0 1 "" red 12 "" -9 -10 0 simundump kreac /kinetics/TetR_gene/TetR_mRNA_degradation 0 0.005775 0 "" \ white 61 1 -7 0 simundump kpool /kinetics/TetR_gene/degraded_TetR_mRNA 0 0 0 4.4901 8082.1 0 \ 0 0 1800 0 "" 1 61 4 -8 0 simundump kpool /kinetics/TetR_gene/TetR_operator 0 40 0.022222 0.0054709 \ 9.8477 40 72000 0 1800 0 "" 36 61 11 -12 0 simundump kenz /kinetics/TetR_gene/TetR_operator/TetR_transcription2 0 0 \ 0.002733 0 4.9194 1800 2.4998 2 0.5 0 1 "" red 36 "" 11 -11 0 simundump kpool /kinetics/TetR_gene/Nucleotides 0 1 0.00055555 0.00055555 \ 0.99999 0.99999 1800 0 1800 4 "" blue 61 11 -8 0 simundump kpool /kinetics/TetR_gene/AminoAcids 0 1 0.00055555 0.00055555 \ 0.99999 0.99999 1800 0 1800 4 "" blue 61 -9 -8 0 simundump group /kinetics/Lcl 0 15 black x 0 0 "" yellow \ /home2/bhalla/scripts/modules/yellow_0.g 0 0 0 56 0 0 simundump kpool /kinetics/Lcl/l_op_2nd_bound[1] 0 0 0 0.028262 50.872 0 0 0 \ 1800 0 "" 52 15 55 -12 0 simundump kenz /kinetics/Lcl/l_op_2nd_bound[1]/Lcl_transcription1 0 0 \ 0.010336 0 18.605 1800 0.0024998 0.002 0.0005 0 1 "" red 52 "" 55 -11 0 simundump kreac /kinetics/Lcl/inhib_reac[1] 0 0.55556 9 "" white 15 59 -13 0 simundump kpool /kinetics/Lcl/l_op_1rst_bound 0 0 0 0.00060338 1.0861 0 0 0 \ 1800 0 "" 2 15 62 -12 0 simundump kenz /kinetics/Lcl/l_op_1rst_bound/Lcl_transcription 0 0 0.00060341 \ 0 1.0861 1800 0.0024998 0.002 0.0005 0 1 "" red 2 "" 62 -10 0 simundump kreac /kinetics/Lcl/inhib_reac 0 0.55556 224 "" white 15 65 -13 0 simundump kpool /kinetics/Lcl/AminoAcids 0 1 0.00055555 0.00055555 0.99999 \ 0.99999 1800 0 1800 4 "" 52 15 48 -8 0 simundump kpool /kinetics/Lcl/Nucleotides 0 1 0.00055555 0.00055555 0.99999 \ 0.99999 1800 0 1800 4 "" 6 15 69 -8 0 simundump kreac /kinetics/Lcl/Lcl_mRNA_degradation 0 0.005775 0 "" white 15 \ 58 -7 0 simundump kpool /kinetics/Lcl/Lcl_mRNA 0 0 0 0.11492 206.86 0 0 0 1800 0 "" 5 \ 15 55 -8 0 simundump kenz /kinetics/Lcl/Lcl_mRNA/Lcl_translation 0 0 0.057633 0 103.74 \ 1800 0.83494 0.668 0.167 0 1 "" red 5 "" 48 -10 0 simundump kpool /kinetics/Lcl/Lcl 0 0.055555 0.055555 0.77482 1394.7 99.999 \ 99.999 0 1800 0 "" 24 15 48 -15 0 simundump kreac /kinetics/Lcl/Lcl_degradation 0 0.016666 0 "" white 15 48 -17 \ 0 simundump kpool /kinetics/Lcl/degraded_Lcl 0 0 0 73.308 1.3195e+05 0 0 0 1800 \ 0 "" 2 15 48 -19 0 simundump kpool /kinetics/Lcl/degraded_Lcl_mRNA 0 0 0 5.1256 9226 0 0 0 1800 \ 0 "" 1 15 62 -8 0 simundump kpool /kinetics/Lcl/Lcl_operator 0 40 0.022222 0.0003206 0.57708 40 \ 72000 0 1800 0 "" 36 15 69 -12 0 simundump kenz /kinetics/Lcl/Lcl_operator/Lcl_transcription2 0 0 0.00016068 0 \ 0.28923 1800 2.4998 2 0.5 0 1 "" red 36 "" 69 -11 0 simundump xgraph /graphs/conc1 0 0 10000 0 2.0691 0 simundump xgraph /graphs/conc2 0 0 10000 0 3.33 0 simundump xplot /graphs/conc1/TetR.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 11 0 0 1 simundump xplot /graphs/conc1/lac.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 62 0 0 1 simundump xplot /graphs/conc1/Lcl.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 24 0 0 1 simundump xgraph /moregraphs/conc3 0 0 10000 0 95.756 0 simundump xgraph /moregraphs/conc4 0 0 10000 0 1 0 simundump xcoredraw /edit/draw 0 -11 71 -21 2 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 \ "Repressilator model: A synthetic oscillatory network" \ "of transcriptional regulators designed by Michael B. Elowitz and" \ "Stanislas Leibler 2000 Nature 403(6767):335-338" addmsg /kinetics/lac_gene/inhib_reac[1] /kinetics/lac_gene/l_op_2nd_bound[1] REAC B A addmsg /kinetics/lac_gene/l_op_2nd_bound[1] /kinetics/lac_gene/l_op_2nd_bound[1]/lac_transcription1 ENZYME n addmsg /kinetics/lac_gene/Nucleotides /kinetics/lac_gene/l_op_2nd_bound[1]/lac_transcription1 SUBSTRATE n addmsg /kinetics/lac_gene/l_op_1rst_bound /kinetics/lac_gene/inhib_reac[1] SUBSTRATE n addmsg /kinetics/lac_gene/l_op_2nd_bound[1] /kinetics/lac_gene/inhib_reac[1] PRODUCT n addmsg /kinetics/Lcl/Lcl /kinetics/lac_gene/inhib_reac[1] SUBSTRATE n addmsg /kinetics/lac_gene/inhib_reac /kinetics/lac_gene/l_op_1rst_bound REAC B A addmsg /kinetics/lac_gene/inhib_reac[1] /kinetics/lac_gene/l_op_1rst_bound REAC A B addmsg /kinetics/lac_gene/l_op_1rst_bound /kinetics/lac_gene/l_op_1rst_bound/lac_transcription ENZYME n addmsg /kinetics/lac_gene/Nucleotides /kinetics/lac_gene/l_op_1rst_bound/lac_transcription SUBSTRATE n addmsg /kinetics/lac_gene/lac_operator /kinetics/lac_gene/inhib_reac SUBSTRATE n addmsg /kinetics/lac_gene/l_op_1rst_bound /kinetics/lac_gene/inhib_reac PRODUCT n addmsg /kinetics/Lcl/Lcl /kinetics/lac_gene/inhib_reac SUBSTRATE n addmsg /kinetics/lac_gene/inhib_reac /kinetics/lac_gene/lac_operator REAC A B addmsg /kinetics/lac_gene/lac_operator /kinetics/lac_gene/lac_operator/lac_transcription2 ENZYME n addmsg /kinetics/lac_gene/Nucleotides /kinetics/lac_gene/lac_operator/lac_transcription2 SUBSTRATE n addmsg /kinetics/lac_gene/lac_mRNA_degradation /kinetics/lac_gene/lac_mRNA REAC A B addmsg /kinetics/lac_gene/lac_operator/lac_transcription2 /kinetics/lac_gene/lac_mRNA MM_PRD pA addmsg /kinetics/lac_gene/l_op_2nd_bound[1]/lac_transcription1 /kinetics/lac_gene/lac_mRNA MM_PRD pA addmsg /kinetics/lac_gene/l_op_1rst_bound/lac_transcription /kinetics/lac_gene/lac_mRNA MM_PRD pA addmsg /kinetics/lac_gene/lac_mRNA /kinetics/lac_gene/lac_mRNA/lac_translation ENZYME n addmsg /kinetics/lac_gene/AminoAcids /kinetics/lac_gene/lac_mRNA/lac_translation SUBSTRATE n addmsg /kinetics/lac_gene/lac_degradation /kinetics/lac_gene/lac REAC A B addmsg /kinetics/lac_gene/lac_mRNA/lac_translation /kinetics/lac_gene/lac MM_PRD pA addmsg /kinetics/TetR_gene/inhib_reac /kinetics/lac_gene/lac REAC A B addmsg /kinetics/TetR_gene/inhib_reac[1] /kinetics/lac_gene/lac REAC A B addmsg /kinetics/lac_gene/lac_degradation /kinetics/lac_gene/degraded_lac REAC B A addmsg /kinetics/lac_gene/lac_mRNA_degradation /kinetics/lac_gene/degraded_lac_mRNA REAC B A addmsg /kinetics/lac_gene/lac_mRNA /kinetics/lac_gene/lac_mRNA_degradation SUBSTRATE n addmsg /kinetics/lac_gene/degraded_lac_mRNA /kinetics/lac_gene/lac_mRNA_degradation PRODUCT n addmsg /kinetics/lac_gene/degraded_lac /kinetics/lac_gene/lac_degradation PRODUCT n addmsg /kinetics/lac_gene/lac /kinetics/lac_gene/lac_degradation SUBSTRATE n addmsg /kinetics/lac_gene/lac_mRNA/lac_translation /kinetics/lac_gene/AminoAcids REAC sA B addmsg /kinetics/lac_gene/lac_operator/lac_transcription2 /kinetics/lac_gene/Nucleotides REAC sA B addmsg /kinetics/lac_gene/l_op_2nd_bound[1]/lac_transcription1 /kinetics/lac_gene/Nucleotides REAC sA B addmsg /kinetics/lac_gene/l_op_1rst_bound/lac_transcription /kinetics/lac_gene/Nucleotides REAC sA B addmsg /kinetics/TetR_gene/inhib_reac[1] /kinetics/TetR_gene/l_op_2nd_bound[1] REAC B A addmsg /kinetics/TetR_gene/l_op_2nd_bound[1] /kinetics/TetR_gene/l_op_2nd_bound[1]/TetR_transcription1 ENZYME n addmsg /kinetics/TetR_gene/Nucleotides /kinetics/TetR_gene/l_op_2nd_bound[1]/TetR_transcription1 SUBSTRATE n addmsg /kinetics/TetR_gene/l_op_2nd_bound[1] /kinetics/TetR_gene/inhib_reac[1] PRODUCT n addmsg /kinetics/TetR_gene/l_op_1rst_bound /kinetics/TetR_gene/inhib_reac[1] SUBSTRATE n addmsg /kinetics/lac_gene/lac /kinetics/TetR_gene/inhib_reac[1] SUBSTRATE n addmsg /kinetics/TetR_gene/inhib_reac[1] /kinetics/TetR_gene/l_op_1rst_bound REAC A B addmsg /kinetics/TetR_gene/inhib_reac /kinetics/TetR_gene/l_op_1rst_bound REAC B A addmsg /kinetics/TetR_gene/l_op_1rst_bound /kinetics/TetR_gene/l_op_1rst_bound/TetR_transcription ENZYME n addmsg /kinetics/TetR_gene/Nucleotides /kinetics/TetR_gene/l_op_1rst_bound/TetR_transcription SUBSTRATE n addmsg /kinetics/TetR_gene/l_op_1rst_bound /kinetics/TetR_gene/inhib_reac PRODUCT n addmsg /kinetics/TetR_gene/TetR_operator /kinetics/TetR_gene/inhib_reac SUBSTRATE n addmsg /kinetics/lac_gene/lac /kinetics/TetR_gene/inhib_reac SUBSTRATE n addmsg /kinetics/TetR_gene/TetR_mRNA/TetR_translation /kinetics/TetR_gene/TetR MM_PRD pA addmsg /kinetics/TetR_gene/TetR_degradation /kinetics/TetR_gene/TetR REAC A B addmsg /kinetics/Lcl/inhib_reac[1] /kinetics/TetR_gene/TetR REAC A B addmsg /kinetics/Lcl/inhib_reac /kinetics/TetR_gene/TetR REAC A B addmsg /kinetics/TetR_gene/TetR_degradation /kinetics/TetR_gene/degraded_TetR REAC B A addmsg /kinetics/TetR_gene/TetR /kinetics/TetR_gene/TetR_degradation SUBSTRATE n addmsg /kinetics/TetR_gene/degraded_TetR /kinetics/TetR_gene/TetR_degradation PRODUCT n addmsg /kinetics/TetR_gene/l_op_2nd_bound[1]/TetR_transcription1 /kinetics/TetR_gene/TetR_mRNA MM_PRD pA addmsg /kinetics/TetR_gene/l_op_1rst_bound/TetR_transcription /kinetics/TetR_gene/TetR_mRNA MM_PRD pA addmsg /kinetics/TetR_gene/TetR_operator/TetR_transcription2 /kinetics/TetR_gene/TetR_mRNA MM_PRD pA addmsg /kinetics/TetR_gene/TetR_mRNA_degradation /kinetics/TetR_gene/TetR_mRNA REAC A B addmsg /kinetics/TetR_gene/TetR_mRNA /kinetics/TetR_gene/TetR_mRNA/TetR_translation ENZYME n addmsg /kinetics/TetR_gene/AminoAcids /kinetics/TetR_gene/TetR_mRNA/TetR_translation SUBSTRATE n addmsg /kinetics/TetR_gene/TetR_mRNA /kinetics/TetR_gene/TetR_mRNA_degradation SUBSTRATE n addmsg /kinetics/TetR_gene/degraded_TetR_mRNA /kinetics/TetR_gene/TetR_mRNA_degradation PRODUCT n addmsg /kinetics/TetR_gene/TetR_mRNA_degradation /kinetics/TetR_gene/degraded_TetR_mRNA REAC B A addmsg /kinetics/TetR_gene/inhib_reac /kinetics/TetR_gene/TetR_operator REAC A B addmsg /kinetics/TetR_gene/TetR_operator /kinetics/TetR_gene/TetR_operator/TetR_transcription2 ENZYME n addmsg /kinetics/TetR_gene/Nucleotides /kinetics/TetR_gene/TetR_operator/TetR_transcription2 SUBSTRATE n addmsg /kinetics/TetR_gene/TetR_operator/TetR_transcription2 /kinetics/TetR_gene/Nucleotides REAC sA B addmsg /kinetics/TetR_gene/l_op_1rst_bound/TetR_transcription /kinetics/TetR_gene/Nucleotides REAC sA B addmsg /kinetics/TetR_gene/l_op_2nd_bound[1]/TetR_transcription1 /kinetics/TetR_gene/Nucleotides REAC sA B addmsg /kinetics/TetR_gene/TetR_mRNA/TetR_translation /kinetics/TetR_gene/AminoAcids REAC sA B addmsg /kinetics/Lcl/inhib_reac[1] /kinetics/Lcl/l_op_2nd_bound[1] REAC B A addmsg /kinetics/Lcl/l_op_2nd_bound[1] /kinetics/Lcl/l_op_2nd_bound[1]/Lcl_transcription1 ENZYME n addmsg /kinetics/Lcl/Nucleotides /kinetics/Lcl/l_op_2nd_bound[1]/Lcl_transcription1 SUBSTRATE n addmsg /kinetics/Lcl/l_op_2nd_bound[1] /kinetics/Lcl/inhib_reac[1] PRODUCT n addmsg /kinetics/Lcl/l_op_1rst_bound /kinetics/Lcl/inhib_reac[1] SUBSTRATE n addmsg /kinetics/TetR_gene/TetR /kinetics/Lcl/inhib_reac[1] SUBSTRATE n addmsg /kinetics/Lcl/inhib_reac[1] /kinetics/Lcl/l_op_1rst_bound REAC A B addmsg /kinetics/Lcl/inhib_reac /kinetics/Lcl/l_op_1rst_bound REAC B A addmsg /kinetics/Lcl/l_op_1rst_bound /kinetics/Lcl/l_op_1rst_bound/Lcl_transcription ENZYME n addmsg /kinetics/Lcl/Nucleotides /kinetics/Lcl/l_op_1rst_bound/Lcl_transcription SUBSTRATE n addmsg /kinetics/Lcl/l_op_1rst_bound /kinetics/Lcl/inhib_reac PRODUCT n addmsg /kinetics/Lcl/Lcl_operator /kinetics/Lcl/inhib_reac SUBSTRATE n addmsg /kinetics/TetR_gene/TetR /kinetics/Lcl/inhib_reac SUBSTRATE n addmsg /kinetics/Lcl/Lcl_mRNA/Lcl_translation /kinetics/Lcl/AminoAcids REAC sA B addmsg /kinetics/Lcl/l_op_2nd_bound[1]/Lcl_transcription1 /kinetics/Lcl/Nucleotides REAC sA B addmsg /kinetics/Lcl/l_op_1rst_bound/Lcl_transcription /kinetics/Lcl/Nucleotides REAC sA B addmsg /kinetics/Lcl/Lcl_operator/Lcl_transcription2 /kinetics/Lcl/Nucleotides REAC sA B addmsg /kinetics/Lcl/Lcl_mRNA /kinetics/Lcl/Lcl_mRNA_degradation SUBSTRATE n addmsg /kinetics/Lcl/degraded_Lcl_mRNA /kinetics/Lcl/Lcl_mRNA_degradation PRODUCT n addmsg /kinetics/Lcl/l_op_2nd_bound[1]/Lcl_transcription1 /kinetics/Lcl/Lcl_mRNA MM_PRD pA addmsg /kinetics/Lcl/l_op_1rst_bound/Lcl_transcription /kinetics/Lcl/Lcl_mRNA MM_PRD pA addmsg /kinetics/Lcl/Lcl_operator/Lcl_transcription2 /kinetics/Lcl/Lcl_mRNA MM_PRD pA addmsg /kinetics/Lcl/Lcl_mRNA_degradation /kinetics/Lcl/Lcl_mRNA REAC A B addmsg /kinetics/Lcl/Lcl_mRNA /kinetics/Lcl/Lcl_mRNA/Lcl_translation ENZYME n addmsg /kinetics/Lcl/AminoAcids /kinetics/Lcl/Lcl_mRNA/Lcl_translation SUBSTRATE n addmsg /kinetics/Lcl/Lcl_mRNA/Lcl_translation /kinetics/Lcl/Lcl MM_PRD pA addmsg /kinetics/Lcl/Lcl_degradation /kinetics/Lcl/Lcl REAC A B addmsg /kinetics/lac_gene/inhib_reac /kinetics/Lcl/Lcl REAC A B addmsg /kinetics/lac_gene/inhib_reac[1] /kinetics/Lcl/Lcl REAC A B addmsg /kinetics/Lcl/Lcl /kinetics/Lcl/Lcl_degradation SUBSTRATE n addmsg /kinetics/Lcl/degraded_Lcl /kinetics/Lcl/Lcl_degradation PRODUCT n addmsg /kinetics/Lcl/Lcl_degradation /kinetics/Lcl/degraded_Lcl REAC B A addmsg /kinetics/Lcl/Lcl_mRNA_degradation /kinetics/Lcl/degraded_Lcl_mRNA REAC B A addmsg /kinetics/Lcl/inhib_reac /kinetics/Lcl/Lcl_operator REAC A B addmsg /kinetics/Lcl/Lcl_operator /kinetics/Lcl/Lcl_operator/Lcl_transcription2 ENZYME n addmsg /kinetics/Lcl/Nucleotides /kinetics/Lcl/Lcl_operator/Lcl_transcription2 SUBSTRATE n addmsg /kinetics/TetR_gene/TetR /graphs/conc1/TetR.Co PLOT Co *TetR.Co *11 addmsg /kinetics/lac_gene/lac /graphs/conc1/lac.Co PLOT Co *lac.Co *62 addmsg /kinetics/Lcl/Lcl /graphs/conc1/Lcl.Co PLOT Co *Lcl.Co *24 enddump // End of dump call /kinetics/lac_gene/notes LOAD \ "This is a group of reactions resulting in the production" \ "of Lac" call /kinetics/lac_gene/l_op_2nd_bound[1]/notes LOAD \ "it represents the promotor with both of its sites" \ " bound by the inhibitor" call /kinetics/lac_gene/l_op_2nd_bound[1]/lac_transcription1/notes LOAD \ "Rates from" \ "Box 1 Elowitz et al Nature (2000)" \ "403: 335-338" call /kinetics/lac_gene/inhib_reac[1]/notes LOAD \ "It signifies the first binding of the repressor" \ " with the operator" \ "" \ "Kf=1 /nM/sec" \ "Kb=9 /sec" \ "" \ "Box 1 Elowitz et al Nature 2000 vol 403:335-338" call /kinetics/lac_gene/l_op_1rst_bound/notes LOAD \ "it represents the promotor with one of its sites" \ " bound by the inhibitor" call /kinetics/lac_gene/l_op_1rst_bound/lac_transcription/notes LOAD \ "Rates from" \ "Box 1 Elowitz et al Nature 2000" \ "403: 335-338" call /kinetics/lac_gene/inhib_reac/notes LOAD \ "It signifies the first binding of the repressor" \ " with the operator" \ "" \ "Kf = 1 /nM/sec" \ "Kb = 224 /sec" \ "" \ "Box 1 Elowitz et al Nature 2000 vol 403:335-338" call /kinetics/lac_gene/lac_operator/notes LOAD \ "The lac operator under normal conditions" \ " drives transcription of lac" \ "" \ "Elowitz et al Nature 2000 Vol 403:335-338" call /kinetics/lac_gene/lac_operator/lac_transcription2/notes LOAD \ "Rates from" \ "Box 1 Elowitz et al (2000)" \ "403:335-338" call /kinetics/lac_gene/lac_mRNA/notes LOAD \ "The m-RNA transcribed by the lac operator" \ "" \ "Elowitz et al Nature 2000 Vol 403:335-338" call /kinetics/lac_gene/lac_mRNA/lac_translation/notes LOAD \ "Rates from " \ "Box 1 Elowitz et al Nature (2000)" \ "403: 335-338" call /kinetics/lac_gene/lac/notes LOAD \ "Lac translated from lac m-RNA" \ "Derived from Figure 1(c) stochastic version" \ "" \ "Elowitz et al Nature 2000 Vol 403:335-338" call /kinetics/lac_gene/degraded_lac/notes LOAD \ "Degradation product of lac protein" call /kinetics/lac_gene/degraded_lac_mRNA/notes LOAD \ "Degradation product of lac m-RNA" call /kinetics/lac_gene/lac_mRNA_degradation/notes LOAD \ "This reaction denotes the degradation of the Lac m-RNA," \ " the half life of which is two minutes." \ "t1/2=.693/k where k denotes kf" call /kinetics/lac_gene/lac_degradation/notes LOAD \ "This reaction denotes the degradation of the Lac" \ " the half life of which is ten minutes." \ "t1/2=.693/k where k denotes kf" \ "" \ "Note: Rates had to scaled by approx 1.4 to get desired levels" \ "" \ "Elowitz et al Nature 2000. Vol403 335-338" call /kinetics/TetR_gene/notes LOAD \ "This is a group of reactions resulting in the production" \ "of Tet R" call /kinetics/TetR_gene/l_op_2nd_bound[1]/notes LOAD \ "it represents the promotor with both of its sites" \ " bound by the inhibitor" call /kinetics/TetR_gene/l_op_2nd_bound[1]/TetR_transcription1/notes LOAD \ "Rates from " \ "Box 1 Elowitz et al (2000)" \ "Nature 403:335-338" call /kinetics/TetR_gene/inhib_reac[1]/notes LOAD \ "It signifies the first binding of the repressor" \ " with the operator" \ "" \ "Kf = 1 /nM/sec" \ "Kb = 9 /sec" \ "" \ "Box 1 Elowitz et al Nature 2000 vol 403:335-338" call /kinetics/TetR_gene/l_op_1rst_bound/notes LOAD \ "it represents the promotor with one of its sites" \ " bound by the inhibitor" call /kinetics/TetR_gene/l_op_1rst_bound/TetR_transcription/notes LOAD \ "Rates from " \ "Box 1 Elowitz et al (2000)" \ "Nature 403:335-338" call /kinetics/TetR_gene/inhib_reac/notes LOAD \ "It signifies the first binding of the repressor" \ " with the operator" \ "" \ "Kf=1 /nM/sec" \ "Kb=224 /sec" \ "" \ "Box1 Elowitz etal Nature 2000 vol 403:335-338" call /kinetics/TetR_gene/TetR/notes LOAD \ "Lac translated from lac m-RNA" \ "Derived from Figure 1(c) stochastic version" \ "" \ "Elowitz etal Nature 2000 Vol 403:335-338" call /kinetics/TetR_gene/degraded_TetR/notes LOAD \ "Degradation product of lac protein" call /kinetics/TetR_gene/TetR_degradation/notes LOAD \ "This reaction denotes the degradation of the Lac" \ " the half life of which is ten minutes." \ "t1/2=.693/k where k denotes kf" \ "" \ "Note: Rates had to be scaled by 1.4 to get appropriate levels" \ "" \ "Elowitz etal Nature 2000. Vol403 335-338" call /kinetics/TetR_gene/TetR_mRNA/notes LOAD \ "The m-RNA transcribed by the lac operator" \ "" \ "Elowitz etal Nature 2000 Vol 403:335-338" call /kinetics/TetR_gene/TetR_mRNA/TetR_translation/notes LOAD \ "Rates from" \ "Box 1 Elowitz et al (2000)" \ "Nature 403:335-338" call /kinetics/TetR_gene/TetR_mRNA_degradation/notes LOAD \ "This reaction denotes the degradation of the Lac m-RNA," \ " the half life of which is two minutes." \ "t1/2=.693/k where k denotes kf" call /kinetics/TetR_gene/degraded_TetR_mRNA/notes LOAD \ "Degradation product of lac m-RNA" call /kinetics/TetR_gene/TetR_operator/notes LOAD \ "The lac operator under normal conditions" \ " drives transcription of lac" \ "" \ "Elowitz etal Nature 2000 Vol 403:335-338" call /kinetics/TetR_gene/TetR_operator/TetR_transcription2/notes LOAD \ "Rates from" \ "Box 1 Elowitz et al (2000)" \ "Nature 403:335-338" call /kinetics/Lcl/notes LOAD \ "This is a group of reactions resulting in the production" \ "of Lambda cl" call /kinetics/Lcl/l_op_2nd_bound[1]/notes LOAD \ "it represents the promotor with both of its sites" \ " bound by the inhibitor" call /kinetics/Lcl/inhib_reac[1]/notes LOAD \ "It signifies the first binding of the repressor" \ " with the operator" \ "" \ "Kf=1 /nM/sec" \ "Kb=9 /sec" \ "" \ "Box1 Elowitz etal Nature 2000 vol 403:335-338" call /kinetics/Lcl/l_op_1rst_bound/notes LOAD \ "it represents the promotor with one of its sites" \ " bound by the inhibitor" call /kinetics/Lcl/l_op_1rst_bound/Lcl_transcription/notes LOAD \ "Rates from" \ "Box 1 Elowitz et al (2000)" \ "Nature 403:335-338" call /kinetics/Lcl/inhib_reac/notes LOAD \ "It signifies the first binding of the repressor" \ " with the operator" \ "" \ "Kf=1 /nM/sec" \ "Kb=224 /sec" \ "" \ "Box1 Elowitz etal Nature 2000 vol 403:335-338" call /kinetics/Lcl/Lcl_mRNA_degradation/notes LOAD \ "This reaction denotes the degradation of the Lac m-RNA," \ " the half life of which is two minutes." \ "t1/2=.693/k where k denotes kf" call /kinetics/Lcl/Lcl_mRNA/notes LOAD \ "The m-RNA transcribed by the lac operator" \ "" \ "Elowitz etal Nature 2000 Vol 403:335-338" call /kinetics/Lcl/Lcl_mRNA/Lcl_translation/notes LOAD \ "Rates from" \ "Box 1 Elowitz et al (2003)" \ "Nature 403:335-338" call /kinetics/Lcl/Lcl/notes LOAD \ "Lac translated from lac m-RNA" \ "Derived from Figure 1(c) stochastic version" \ "" \ "Elowitz et al Nature 2000 Vol 403:335-338" call /kinetics/Lcl/Lcl_degradation/notes LOAD \ "This reaction denotes the degradation of the Lac" \ " the half life of which is ten minutes." \ "t1/2=.693/k where k denotes kf" \ "" \ "Note: Rates had to be scaled by 1.4 to get the desired levels" \ "" \ "Elowitz etal Nature 2000. Vol403 335-338" call /kinetics/Lcl/degraded_Lcl/notes LOAD \ "Degradation product of lac protein" call /kinetics/Lcl/degraded_Lcl_mRNA/notes LOAD \ "Degradation product of lac m-RNA" call /kinetics/Lcl/Lcl_operator/notes LOAD \ "The lac operator under normal conditions" \ " drives transcription of lac" \ "" \ "Elowitz etal Nature 2000 Vol 403:335-338" call /kinetics/Lcl/Lcl_operator/Lcl_transcription2/notes LOAD \ "Rates from" \ "Box 1 Elowitz et al (2003)" \ "Nature 403:335-338" complete_loading