//genesis
// kkit Version 8 flat dumpfile
 
// Saved on Sat Dec 28 11:35:12 2002
 
include kkit {argv 1}
 
FASTDT = 0.0001
SIMDT = 0.005
CONTROLDT = 10
PLOTDT = 10
MAXTIME = 3000
TRANSIENT_TIME = 2
VARIABLE_DT_FLAG = 1
DEFAULT_VOL = 2e-08
VERSION = 8.0
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 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
simobjdump transport input output alloced step_mode stepsize dt delay clock \
  kf editfunc createfunc xtree_fg_req xtree_textfg_req plotfield manageclass \
  linkparms
simundump group /kinetics/Transcription 0 61 black x 1 0 "" Transcription \
  /home2/bhalla/scripts/modules/Transcription_0.g 0 0 0 29 0 0
simundump kreac /kinetics/Transcription/Complex_Formation 0 1.5167e-11 0 "" \
  white 61 23 -1 0
simundump kpool /kinetics/Transcription/RNAP 0 0.083333 0.0375 0.0375 4.5e+11 \
  4.5e+11 1e+12 0 1.2e+13 0 "" 16 61 22 -3 0
simundump kpool /kinetics/Transcription/TrRNAP 0 0 0 0 0 0 0 0 1.2e+13 0 "" \
  blue 61 24 1 0
simundump kreac /kinetics/Transcription/In_Transcription 0 3.75e-19 0 "" \
  white 61 25 -1 0
simundump kpool /kinetics/Transcription/N 0 1000 1000 1000 1.2e+16 1.2e+16 \
  1.2e+16 0 1.2e+13 0 "" blue 61 26 1 0
simundump kpool /kinetics/Transcription/P 0 0.025 0.025 0.025 3e+11 3e+11 \
  3e+11 0 1.2e+13 0 "" 15 61 24 -3 0
simundump kpool /kinetics/Transcription/mRNA 0 0 0 0 0 0 0 0 1.2e+13 0 "" \
  blue 61 22 -7 0
simundump transport /kinetics/Transcription/mRNA_synthesis 4 0 7.4282e+07 1 6 \
  0 0.25 425 4 0.0002 edit_transport transport_create_func yellow 61 output \
  group "kf dt delay"
loadtab /kinetics/Transcription/mRNA_synthesis table 1 1700 0 1700 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 
loadtab -continue \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 
loadtab -continue \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 
loadtab -continue \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 
loadtab -continue \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 
loadtab -continue \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 
loadtab -continue \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 
loadtab -continue \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 
loadtab -continue \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
simundump kreac /kinetics/Transcription/RNAPdecay 0 1e-05 0 "" white 61 21 -1 \
  0
simundump kreac /kinetics/Transcription/mRNA_Decay 0 1e-05 0 "" 15 61 21 -5 0
simundump kpool /kinetics/Transcription/decayed_mRNA 0 0 0 0 0 0 0 0 1.2e+13 \
  0 "" blue 61 20 -3 0
simundump kpool /kinetics/Transcription/decayed_RNAP 0 0 0 0 0 0 0 0 1.2e+13 \
  0 "" blue 61 22 1 0
simundump kpool /kinetics/Transcription/RBS 0 0 0 0 0 0 0 0 1.2e+13 0 "" 36 \
  61 26 -3 0
simundump kreac /kinetics/Transcription/RBS_Decay 0 1e-05 0 "" white 61 27 -5 \
  0
simundump kpool /kinetics/Transcription/decayed_RBS 0 0 0 0 0 0 0 0 1.2e+13 0 \
  "" blue 61 28 -3 0
simundump xtab /kinetics/noOligo 0 -10 0 1 2 0 "" edit_xtab white red 0 0 0 0 \
  30 -8 0
loadtab /kinetics/noOligo table 0 2500 0 2500 \
 16.25 15.4713 14.6926 13.9139 13.1352 13.396 13.8752 14.3544 14.8336 15.6647 \
 16.683 17.7013 18.7196 18.4177 16.6806 14.9435 13.2064 12.2013 12.8602 \
 13.5191 14.178 14.6473 13.8686 13.0899 12.3112 11.5325 11.3852 11.2654 \
 11.1456 11.0258 11.564 12.2828 13.0016 13.7204 13.4144 12.456 11.4976 \
 10.5392 10.2882 10.9471 11.606 12.2649 12.8764 13.3556 13.8348 14.314 \
 14.8094 15.4683 16.1272 16.7861 17.445 17.3902 17.2704 17.1506 17.0308 \
 15.7985 14.1812 12.5639 10.9466 10.6251 11.284 11.9429 12.6018 14.2324 \
 17.3472 20.462 23.5768 25.2153 21.6812 18.1471 14.613 11.2326 10.8732 \
 10.5138 10.1544 9.795 10.6932 11.7714 12.8496 13.9278 15.3 16.7975 18.295 \
 19.7925 19.8364 18.5785 17.3206 16.0627 15.674 16.872 18.07 19.268 20.0016 \
 18.6239 17.2462 15.8685 14.4976 14.1382 13.7788 13.4194 13.06 12.7006 \
 12.3412 11.9818 11.6224 11.579 11.6988 11.8186 11.9384 12 12 12 12 12.4488 \
 13.8864 15.324 16.7616 17.7925 16.295 14.7975 13.3 11.8025 14.062 16.458 \
 18.854 21.25 19.38 16.385 13.39 10.395 9.398 9.6376 9.8772 10.1168 10.25 \
 10.25 10.25 10.25 10.412 11.011 11.61 12.209 12.7384 12.6186 12.4988 12.379 \
 12.2592 12.25 12.25 12.25 12.25 12.0255 11.726 11.4265 11.127 12.2765 \
 14.4928 16.7091 18.9254 19.286 16.89 14.494 12.098 10.6199 12.2372 13.8545 \
 15.4718 16.934 15.736 14.538 13.34 12.142 11.736 11.4365 11.137 10.8375 \
 10.75 10.75 10.75 10.75 10.814 10.9338 11.0536 11.1734 11.5092 12.228 \
 12.9468 13.6656 14.1492 13.6101 13.071 12.5319 12.0088 12.6677 13.3266 \
 13.9855 14.6444 14.9009 15.0806 15.2603 
loadtab -continue \
 15.44 14.3828 12.7056 11.0284 9.3512 9.68 12.076 14.472 16.868 18.0225 \
 16.525 15.0275 13.53 12.337 12.936 13.535 14.134 14.733 13.2368 11.6794 \
 10.122 8.5646 8.5846 9.0039 9.4232 9.8425 11.0098 12.6271 14.2444 15.8617 \
 16.588 16.2286 15.8692 15.5098 15.0508 14.332 13.6132 12.8944 12.3802 \
 13.6381 14.896 16.1539 17.4118 18.0013 18.5404 19.0795 19.6186 18.7987 \
 17.5408 16.2829 15.025 13.9765 13.078 12.1795 11.281 11.6565 13.8728 16.0891 \
 18.3054 19.6052 17.928 16.2508 14.5736 13.0444 13.7632 14.482 15.2008 \
 15.9196 14.936 13.738 12.54 11.342 12.4124 14.3891 16.3658 18.3425 18.7964 \
 17.9578 17.1192 16.2806 15.354 14.2758 13.1976 12.1194 11.308 11.6075 11.907 \
 12.2065 12.5252 13.7831 15.041 16.2989 17.5568 16.4318 14.8744 13.317 \
 11.7596 11.5321 11.9514 12.3707 12.79 13.3887 14.1674 14.9461 15.7248 \
 16.1135 15.6942 15.2749 14.8556 14.4363 14.017 13.5977 13.1784 12.7591 12.75 \
 12.75 12.75 12.75 13.232 13.831 14.43 15.029 15.8926 16.9109 17.9292 18.9475 \
 18.404 16.008 13.612 11.216 9.755 10.6535 11.552 12.4505 13.2434 13.1835 \
 13.1236 13.0637 13.0038 12.8317 12.652 12.4723 12.2926 12.4785 12.778 \
 13.0775 13.377 13.3941 13.2144 13.0347 12.855 12.7998 12.9196 13.0394 \
 13.1592 13.3225 13.622 13.9215 14.221 14.5164 14.756 14.9956 15.2352 15.4748 \
 15.6608 15.8405 16.0202 16.1999 16.0772 15.8376 15.598 15.3584 14.4628 \
 13.0252 11.5876 10.15 9.6756 10.8137 11.9518 13.0899 13.916 13.4967 13.0774 \
 12.6581 12.29 13.7875 15.285 16.7825 18.28 17.2225 15.725 14.2275 12.73 \
 12.0465 11.747 11.4475 11.148 10.8788 10.6392 10.3996 
loadtab -continue \
 10.16 10.2786 11.1172 11.9558 12.7944 13.367 12.5284 11.6898 10.8512 10.0126 \
 9.941 9.8811 9.8212 9.7613 11.2566 13.1135 14.9704 16.8273 16.736 15.538 \
 14.34 13.142 12.639 12.9385 13.238 13.5375 14.0284 14.9868 15.9452 16.9036 \
 17.68 17.081 16.482 15.883 15.284 15.1935 15.1336 15.0737 15.0138 14.7695 \
 14.47 14.1705 13.871 13.4644 12.9852 12.506 12.0268 11.75 11.75 11.75 11.75 \
 11.6606 11.3012 10.9418 10.5824 10.3265 11.3448 12.3631 13.3814 14.3997 \
 16.012 17.6892 19.3664 21.0436 20.1048 18.188 16.2712 14.3544 14.1308 \
 15.2689 16.407 17.5451 17.8168 16.6787 15.5406 14.4025 13.4876 13.4277 \
 13.3678 13.3079 13.244 13.0643 12.8846 12.7049 12.5252 12.912 13.3912 \
 13.8704 14.3496 14.4178 14.298 14.1782 14.0584 13.693 13.094 12.495 11.896 \
 11.6218 11.9812 12.3406 12.7 12.9406 12.5812 12.2218 11.8624 11.503 12.8068 \
 14.1246 15.4424 16.7602 15.383 13.4063 11.4296 9.4529 9.2132 9.932 10.6508 \
 11.3696 11.9474 12.3667 12.786 13.2053 13.5356 13.6554 13.7752 13.895 \
 13.8964 13.0578 12.2192 11.3806 10.542 11.638 12.836 14.034 15.232 15.9185 \
 16.4576 16.9967 17.5358 17.1363 16.118 15.0997 14.0814 13.5514 13.6712 \
 13.791 13.9108 13.8623 13.3232 12.7841 12.245 11.7206 11.3612 11.0018 \
 10.6424 10.283 10.8484 11.5073 12.1662 12.8251 13.704 14.6624 15.6208 \
 16.5792 17.1008 17.2805 17.4602 17.6399 17.4948 16.8359 16.177 15.5181 \
 14.8976 14.4184 13.9392 13.46 12.9832 12.5639 12.1446 11.7253 11.306 11.6133 \
 12.0326 12.4519 12.8712 13.3735 13.9126 14.4517 14.9908 15.1256 14.886 \
 14.6464 14.4068 14.6019 15.6202 16.6385 17.6568 18.3455 17.447 16.5485 
loadtab -continue \
 15.65 14.7515 15.348 15.947 16.546 17.145 17.0524 16.8128 16.5732 16.3336 \
 16.016 15.6566 15.2972 14.9378 14.464 13.865 13.266 12.667 12.1408 11.7814 \
 11.422 11.0626 10.75 10.75 10.75 10.75 10.75 10.9792 11.2188 11.4584 11.698 \
 11.6562 11.5364 11.4166 11.2968 11.3595 11.5392 11.7189 11.8986 12.1566 \
 12.516 12.8754 13.2348 13.4058 13.0464 12.687 12.3276 12.0689 12.8476 \
 13.6263 14.405 15.1837 13.9348 12.4972 11.0596 9.622 10.0492 11.1274 12.2056 \
 13.2838 14.532 15.9097 17.2874 18.6651 18.8156 17.0785 15.3414 13.6043 \
 12.0784 11.2997 10.521 9.7423 9.1036 11.3199 13.5362 15.7525 17.9688 17.3086 \
 16.2304 15.1522 14.074 13.9595 14.259 14.5585 14.858 14.748 14.2688 13.7896 \
 13.3104 13.1055 13.405 13.7045 14.004 14.2928 14.5324 14.772 15.0116 15.2494 \
 15.1296 15.0098 14.89 14.7702 14.2022 13.5433 12.8844 12.2255 12.4334 \
 13.0923 13.7512 14.4101 14.866 15.1056 15.3452 15.5848 15.6942 15.5145 \
 15.3348 15.1551 14.9836 14.8638 14.744 14.6242 14.5044 13.7499 12.9712 \
 12.1925 11.4138 11.2027 11.1428 11.0829 11.023 11.4059 12.0648 12.7237 \
 13.3826 13.5645 13.1452 12.7259 12.3066 12.1932 12.912 13.6308 14.3496 \
 15.0855 15.984 16.8825 17.781 18.6795 18.5292 18.2896 18.05 17.8104 17.3468 \
 16.8077 16.2686 15.7295 15.0184 14.1798 13.3412 12.5026 12.768 14.6848 \
 16.6016 18.5184 19.8504 19.1915 18.5326 17.8737 17.186 15.988 14.79 13.592 \
 12.394 13.6202 15.1776 16.735 18.2924 18.2847 17.6258 16.9669 16.308 15.0749 \
 13.3378 11.6007 9.8636 9.18 10.378 11.576 12.774 13.9276 14.886 15.8444 \
 16.8028 17.7248 15.5684 13.412 11.2556 9.0992 10.5572 12.7136 
loadtab -continue \
 14.87 17.0264 17.3122 16.6533 15.9944 15.3355 14.5002 13.4819 12.4636 \
 11.4453 11.016 11.8546 12.6932 13.5318 14.25 14.25 14.25 14.25 14.25 13.9014 \
 13.542 13.1826 12.8232 13.4655 14.364 15.2625 16.161 15.8659 14.8476 13.8293 \
 12.811 12.6804 13.6388 14.5972 15.5556 16.2005 16.0208 15.8411 15.6614 \
 15.5671 16.226 16.8849 17.5438 18.2027 18.8616 19.5205 20.1794 20.8383 \
 20.548 19.949 19.35 18.751 17.63 16.1325 14.635 13.1375 12.3476 12.5872 \
 12.8268 13.0664 13.544 14.8019 16.0598 17.3177 18.4424 17.484 16.5256 \
 15.5672 14.6088 14.4469 14.387 14.3271 14.2672 14.1219 13.9422 13.7625 \
 13.5828 13.8553 14.5142 15.1731 15.832 16.1624 15.9228 15.6832 15.4436 \
 15.296 15.5356 15.7752 16.0148 16.2621 16.921 17.5799 18.2388 18.8977 \
 18.8482 18.6685 18.4888 18.3091 18.1294 17.9497 17.77 17.5903 17.3212 \
 16.9618 16.6024 16.243 15.8836 15.5242 15.1648 14.8054 14.536 14.7756 \
 15.0152 15.2548 15.4944 15.734 15.9736 16.2132 16.4528 17.5582 18.876 \
 20.1938 21.5116 21.246 20.048 18.85 17.652 17.3549 18.1336 18.9123 19.691 \
 20.1824 19.9428 19.7032 19.4636 19.1785 18.5196 17.8607 17.2018 16.5429 \
 17.956 19.5134 21.0708 22.6282 22.5896 22.0505 21.5114 20.9723 20.8204 \
 20.9402 21.06 21.1798 20.754 19.556 18.358 17.16 16.6244 18.1818 19.7392 \
 21.2966 22.722 22.3027 21.8834 21.4641 21.0448 20.358 19.6392 18.9204 \
 18.2016 19.724 22.12 24.516 26.912 27.019 25.222 23.425 21.628 20.8122 \
 21.6508 22.4894 23.328 24 24 24 24 23.9955 23.8158 23.6361 23.4564 23.2767 \
 24.066 25.0244 25.9828 26.9412 25.5042 22.9285 20.3528 17.7771 17.255 \
 18.7525 
loadtab -continue \
 20.25 21.7475 22.5124 21.7936 21.0748 20.356 20.032 21.829 23.626 25.423 \
 27.22 27.6034 27.9628 28.3222 28.6816 27.392 25.7148 24.0376 22.3604 22.6644 \
 24.102 25.5396 26.9772 27.5284 27.0492 26.57 26.0908 25.5943 25.0552 24.5161 \
 23.977 23.5069 23.5668 23.6267 23.6866 23.7465 23.3552 22.9359 22.5166 \
 22.0973 22.874 24.0121 25.1502 26.2883 26.928 27.2275 27.527 27.8265 27.8992 \
 27.6596 27.42 27.1804 27.1036 27.5229 27.9422 28.3615 28.7236 28.3642 \
 28.0048 27.6454 27.286 28.3819 29.6398 30.8977 32.1556 31.6735 30.5354 \
 29.3973 28.2592 27.8824 28.122 28.3616 28.6012 28.9543 29.4934 30.0325 \
 30.5716 31.369 33.166 34.963 36.76 38.4335 36.337 34.2405 32.144 30.0475 \
 29.9042 30.0839 30.2636 30.4433 31.074 31.9126 32.7512 33.5898 33.847 \
 33.5475 33.248 32.9485 32.8308 33.0704 33.31 33.5496 33.8284 34.3076 34.7868 \
 35.266 35.7452 34.9791 34.2004 33.4217 32.643 33.1357 33.9144 34.6931 \
 35.4718 36.7125 38.21 39.7075 41.205 41.0446 39.008 36.9714 34.9348 33.9602 \
 35.5176 37.075 38.6324 39.9197 39.2608 38.6019 37.943 37.2841 37.0228 \
 36.7832 36.5436 36.304 36.6676 37.2067 37.7458 38.2849 38.608 38.7877 \
 38.9674 39.1471 39.6596 40.618 41.5764 42.5348 43.4172 44.0761 44.735 \
 45.3939 45.8848 44.4472 43.0096 41.572 40.1344 41.2489 42.6266 44.0043 \
 45.382 45.4866 45.1272 44.7678 44.4084 44.6185 45.2774 45.9363 46.5952 \
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simundump group /kinetics/luciferase 0 yellow black x 0 0 "" x؏`ݎ��� \
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simundump xtext /file/notes 0 1
xtextload /file/notes \
"Based on B_binding6.g." \
"Fixed dumping of location of transporters." \
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""
addmsg /kinetics/Transcription/P /kinetics/Transcription/Complex_Formation SUBSTRATE n 
addmsg /kinetics/Transcription/RNAP /kinetics/Transcription/Complex_Formation SUBSTRATE n 
addmsg /kinetics/Transcription/TrRNAP /kinetics/Transcription/Complex_Formation PRODUCT n 
addmsg /kinetics/Transcription/Complex_Formation /kinetics/Transcription/RNAP REAC A B 
addmsg /kinetics/Transcription/RNAPdecay /kinetics/Transcription/RNAP REAC A B 
addmsg /kinetics/Transcription/mRNA_synthesis /kinetics/Transcription/RNAP MM_PRD output 
addmsg /kinetics/Transcription/In_Transcription /kinetics/Transcription/TrRNAP REAC A B 
addmsg /kinetics/Transcription/Complex_Formation /kinetics/Transcription/TrRNAP REAC B A 
addmsg /kinetics/Transcription/TrRNAP /kinetics/Transcription/In_Transcription SUBSTRATE n 
addmsg /kinetics/Transcription/N /kinetics/Transcription/In_Transcription SUBSTRATE n 
addmsg /kinetics/Transcription/P /kinetics/Transcription/In_Transcription PRODUCT n 
addmsg /kinetics/Transcription/RBS /kinetics/Transcription/In_Transcription PRODUCT n 
addmsg /kinetics/Transcription/In_Transcription /kinetics/Transcription/N REAC A B 
addmsg /kinetics/Transcription/Complex_Formation /kinetics/Transcription/P REAC A B 
addmsg /kinetics/Transcription/In_Transcription /kinetics/Transcription/P REAC B A 
addmsg /kinetics/Transcription/mRNA_Decay /kinetics/Transcription/mRNA REAC A B 
addmsg /kinetics/Transcription/mRNA_synthesis /kinetics/Transcription/mRNA MM_PRD output 
addmsg /kinetics/Translation/Rib_RNA_Complex /kinetics/Transcription/mRNA REAC A B 
addmsg /kinetics/Translation/Prot_synthesis /kinetics/Transcription/mRNA MM_PRD output 
addmsg /kinetics/Translation/Rib_mRNA-decay /kinetics/Transcription/mRNA REAC B A 
addmsg /kinetics/Transcription/RBS /kinetics/Transcription/mRNA_synthesis SUBSTRATE n 
addmsg /kinetics/Transcription/RNAP /kinetics/Transcription/RNAPdecay SUBSTRATE n 
addmsg /kinetics/Transcription/decayed_RNAP /kinetics/Transcription/RNAPdecay PRODUCT n 
addmsg /kinetics/Transcription/mRNA /kinetics/Transcription/mRNA_Decay SUBSTRATE n 
addmsg /kinetics/Transcription/decayed_mRNA /kinetics/Transcription/mRNA_Decay PRODUCT n 
addmsg /kinetics/Transcription/mRNA_Decay /kinetics/Transcription/decayed_mRNA REAC B A 
addmsg /kinetics/Transcription/RNAPdecay /kinetics/Transcription/decayed_RNAP REAC B A 
addmsg /kinetics/Transcription/In_Transcription /kinetics/Transcription/RBS REAC B A 
addmsg /kinetics/Transcription/RBS_Decay /kinetics/Transcription/RBS REAC A B 
addmsg /kinetics/Transcription/RBS /kinetics/Transcription/RBS_Decay SUBSTRATE n 
addmsg /kinetics/Transcription/decayed_RBS /kinetics/Transcription/RBS_Decay PRODUCT n 
addmsg /kinetics/Transcription/RBS_Decay /kinetics/Transcription/decayed_RBS REAC B A 
addmsg /kinetics/luciferase/k5 /kinetics/luciferase/E.S1_in REAC B A 
addmsg /kinetics/luciferase/E.S1 /kinetics/luciferase/k5 SUBSTRATE n 
addmsg /kinetics/luciferase/E.S1_in /kinetics/luciferase/k5 PRODUCT n 
addmsg /kinetics/luciferase/k5 /kinetics/luciferase/E.S1 REAC A B 
addmsg /kinetics/luciferase/k1 /kinetics/luciferase/E.S1 REAC B A 
addmsg /kinetics/luciferase/k1_prime /kinetics/luciferase/E.S1 REAC A B 
addmsg /kinetics/luciferase/k1 /kinetics/luciferase/S1 REAC A B 
addmsg /kinetics/luciferase/k1_2 /kinetics/luciferase/S1 REAC A B 
addmsg /kinetics/luciferase/E /kinetics/luciferase/k1 SUBSTRATE n 
addmsg /kinetics/luciferase/E.S1 /kinetics/luciferase/k1 PRODUCT n 
addmsg /kinetics/luciferase/S1 /kinetics/luciferase/k1 SUBSTRATE n 
addmsg /kinetics/luciferase/k1 /kinetics/luciferase/E REAC A B 
addmsg /kinetics/luciferase/k1_prime_2 /kinetics/luciferase/E REAC A B 
addmsg /kinetics/luciferase/k5_2 /kinetics/luciferase/E REAC A B 
addmsg /kinetics/luciferase/k4 /kinetics/luciferase/E REAC B A 
addmsg /kinetics/Translation/Prot_synthesis /kinetics/luciferase/E MM_PRD output 
addmsg /kinetics/Translation/Protein_Decay /kinetics/luciferase/E REAC A B 
addmsg /kinetics/luciferase/E.S1 /kinetics/luciferase/k1_prime SUBSTRATE n 
addmsg /kinetics/luciferase/E.S1.S2 /kinetics/luciferase/k1_prime PRODUCT n 
addmsg /kinetics/luciferase/S2 /kinetics/luciferase/k1_prime SUBSTRATE n 
addmsg /kinetics/luciferase/k1_prime /kinetics/luciferase/S2 REAC A B 
addmsg /kinetics/luciferase/k1_prime_2 /kinetics/luciferase/S2 REAC A B 
addmsg /kinetics/luciferase/E.P /kinetics/luciferase/k4 SUBSTRATE n 
addmsg /kinetics/luciferase/P /kinetics/luciferase/k4 PRODUCT n 
addmsg /kinetics/luciferase/E /kinetics/luciferase/k4 PRODUCT n 
addmsg /kinetics/luciferase/k1_prime /kinetics/luciferase/E.S1.S2 REAC B A 
addmsg /kinetics/luciferase/k5_4 /kinetics/luciferase/E.S1.S2 REAC A B 
addmsg /kinetics/luciferase/k2 /kinetics/luciferase/E.S1.S2 REAC A B 
addmsg /kinetics/luciferase/k1_2 /kinetics/luciferase/E.S1.S2 REAC B A 
addmsg /kinetics/luciferase/E.S1.S2 /kinetics/luciferase/k2 SUBSTRATE n 
addmsg /kinetics/luciferase/E.P1 /kinetics/luciferase/k2 PRODUCT n 
addmsg /kinetics/luciferase/AMP /kinetics/luciferase/k2 PRODUCT n 
addmsg /kinetics/luciferase/k2 /kinetics/luciferase/E.P1 REAC B A 
addmsg /kinetics/luciferase/k3 /kinetics/luciferase/E.P1 REAC A B 
addmsg /kinetics/luciferase/E.P1 /kinetics/luciferase/k3 SUBSTRATE n 
addmsg /kinetics/luciferase/E.P /kinetics/luciferase/k3 PRODUCT n 
addmsg /kinetics/luciferase/photon /kinetics/luciferase/k3 PRODUCT n 
addmsg /kinetics/luciferase/k3 /kinetics/luciferase/E.P REAC B A 
addmsg /kinetics/luciferase/k6 /kinetics/luciferase/E.P REAC A B 
addmsg /kinetics/luciferase/k4 /kinetics/luciferase/E.P REAC A B 
addmsg /kinetics/luciferase/k4 /kinetics/luciferase/P REAC B A 
addmsg /kinetics/luciferase/E /kinetics/luciferase/k1_prime_2 SUBSTRATE n 
addmsg /kinetics/luciferase/E.S2 /kinetics/luciferase/k1_prime_2 PRODUCT n 
addmsg /kinetics/luciferase/S2 /kinetics/luciferase/k1_prime_2 SUBSTRATE n 
addmsg /kinetics/luciferase/E.S2 /kinetics/luciferase/k1_2 SUBSTRATE n 
addmsg /kinetics/luciferase/E.S1.S2 /kinetics/luciferase/k1_2 PRODUCT n 
addmsg /kinetics/luciferase/S1 /kinetics/luciferase/k1_2 SUBSTRATE n 
addmsg /kinetics/luciferase/k1_prime_2 /kinetics/luciferase/E.S2 REAC B A 
addmsg /kinetics/luciferase/k5_3 /kinetics/luciferase/E.S2 REAC A B 
addmsg /kinetics/luciferase/k1_2 /kinetics/luciferase/E.S2 REAC A B 
addmsg /kinetics/luciferase/k2 /kinetics/luciferase/AMP REAC B A 
addmsg /kinetics/luciferase/k3 /kinetics/luciferase/photon REAC B A 
addmsg /kinetics/luciferase/E /kinetics/luciferase/k5_2 SUBSTRATE n 
addmsg /kinetics/luciferase/E_in /kinetics/luciferase/k5_2 PRODUCT n 
addmsg /kinetics/luciferase/E.S2 /kinetics/luciferase/k5_3 SUBSTRATE n 
addmsg /kinetics/luciferase/E.S2_in /kinetics/luciferase/k5_3 PRODUCT n 
addmsg /kinetics/luciferase/E.S1.S2 /kinetics/luciferase/k5_4 SUBSTRATE n 
addmsg /kinetics/luciferase/E.S1.S2_in /kinetics/luciferase/k5_4 PRODUCT n 
addmsg /kinetics/luciferase/photon /kinetics/luciferase/num_photons SUMTOTAL n nInit 
addmsg /kinetics/luciferase/photon /kinetics/luciferase/PMT_count SUMTOTAL n nInit 
addmsg /kinetics/luciferase/E.P /kinetics/luciferase/k6 SUBSTRATE n 
addmsg /kinetics/luciferase/E.P_in /kinetics/luciferase/k6 PRODUCT n 
addmsg /kinetics/luciferase/k6 /kinetics/luciferase/E.P_in REAC B A 
addmsg /kinetics/luciferase/k5_4 /kinetics/luciferase/E.S1.S2_in REAC B A 
addmsg /kinetics/luciferase/k5_3 /kinetics/luciferase/E.S2_in REAC B A 
addmsg /kinetics/luciferase/k5_2 /kinetics/luciferase/E_in REAC B A 
addmsg /kinetics/Translation/Rib_RNA_Complex /kinetics/Translation/Ribosome REAC A B 
addmsg /kinetics/Translation/RibosomeDecay /kinetics/Translation/Ribosome REAC A B 
addmsg /kinetics/Translation/Prot_synthesis /kinetics/Translation/Ribosome MM_PRD output 
addmsg /kinetics/Translation/Ribosome /kinetics/Translation/Rib_RNA_Complex SUBSTRATE n 
addmsg /kinetics/Transcription/mRNA /kinetics/Translation/Rib_RNA_Complex SUBSTRATE n 
addmsg /kinetics/Translation/Rib_mRNA /kinetics/Translation/Rib_RNA_Complex PRODUCT n 
addmsg /kinetics/Translation/Rib_RNA_Complex /kinetics/Translation/Rib_mRNA REAC B A 
addmsg /kinetics/Translation/Rib_mRNA-decay /kinetics/Translation/Rib_mRNA REAC A B 
addmsg /kinetics/Translation/B-subunit-bind-to_ribosome /kinetics/Translation/Rib_mRNA REAC A B 
addmsg /kinetics/Translation/decayed_Rib_mRNA /kinetics/Translation/Rib_mRNA-decay PRODUCT n 
addmsg /kinetics/Transcription/mRNA /kinetics/Translation/Rib_mRNA-decay PRODUCT n 
addmsg /kinetics/Translation/Rib_mRNA /kinetics/Translation/Rib_mRNA-decay SUBSTRATE n 
addmsg /kinetics/Translation/Ribosome /kinetics/Translation/RibosomeDecay SUBSTRATE n 
addmsg /kinetics/Translation/decayed_Ribosome /kinetics/Translation/RibosomeDecay PRODUCT n 
addmsg /kinetics/Translation/RibosomeDecay /kinetics/Translation/decayed_Ribosome REAC B A 
addmsg /kinetics/Translation/B-subunit /kinetics/Translation/B-subunit-bind-to_ribosome SUBSTRATE n 
addmsg /kinetics/Translation/Rib_mRNA /kinetics/Translation/B-subunit-bind-to_ribosome SUBSTRATE n 
addmsg /kinetics/Translation/primed-mRNA /kinetics/Translation/B-subunit-bind-to_ribosome PRODUCT n 
addmsg /kinetics/Translation/B-subunit-bind-to_ribosome /kinetics/Translation/primed-mRNA REAC B A 
addmsg /kinetics/Translation/Rib_mRNA-decay /kinetics/Translation/decayed_Rib_mRNA REAC B A 
addmsg /kinetics/Translation/decayed_protein /kinetics/Translation/Protein_Decay PRODUCT n 
addmsg /kinetics/luciferase/E /kinetics/Translation/Protein_Decay SUBSTRATE n 
addmsg /kinetics/Translation/Protein_Decay /kinetics/Translation/decayed_protein REAC B A 
addmsg /kinetics/Translation/B-subunit-bind-to_ribosome /kinetics/Translation/B-subunit REAC A B 
addmsg /kinetics/Translation/primed-mRNA /kinetics/Translation/Prot_synthesis SUBSTRATE n 
addmsg /kinetics/luciferase/PMT_count /graphs/conc1/PMT_count.Co PLOT Co *PMT_count.Co *51 
addmsg /kinetics/noOligo /graphs/conc1/noOligo.output PLOT output *noOligo.output *white 
addmsg /kinetics/Transcription/mRNA /graphs/conc2/mRNA.Co PLOT Co *mRNA.Co *blue 
addmsg /kinetics/luciferase/E /graphs/conc2/E.Co PLOT Co *E.Co *54 
enddump
// End of dump

call /kinetics/Transcription/Complex_Formation/notes LOAD \
"Smita Patel et al." \
"Biochemistery 2002,41, 3586-3595"
call /kinetics/Transcription/TrRNAP/notes LOAD \
"Open complex of DNA and RNApolymerase"
call /kinetics/Transcription/In_Transcription/notes LOAD \
"Initiation Of Transcription" \
"The forward rate is 0.45 nucleotides/second." \
"We are assuming that this step represents 100 nucleotides." \
"We are considering that there are 1.2e16 nucleotides to get" \
"the kf = 3.33e-17"
call /kinetics/Transcription/N/notes LOAD \
"nucleotide "
call /kinetics/Transcription/P/notes LOAD \
"Promotor." \
"Assume conc of promoter is 25 nM."
call /kinetics/Transcription/mRNA_synthesis/notes LOAD \
"I scale down the input rate to 2/sec assuming that the space between" \
"successive RNA Pols is 20 bases." \
"The mRNA is 1700 bases long." \
"Promega says that the amount of mRNA" \
"produced after 1 hour should be about" \
"equal to the amount of DNA originally added." \
"Temperature dependence means that the actual" \
"amount will be less."
call /kinetics/Transcription/mRNA_Decay/notes LOAD \
"There are inhibitors in the reaction mix, so decay rate is 1e-6/sec"
call /kinetics/Transcription/RBS_Decay/notes LOAD \
"Same as mRNA decay"
call /kinetics/luciferase/E.S1/notes LOAD \
"S1 is ATP. E.S1 is luciferase.ATP"
call /kinetics/luciferase/S1/notes LOAD \
"S1 is ATP" \
"Conc as specified by Promega."
call /kinetics/luciferase/S2/notes LOAD \
"S2 = LH2 = luciferin." \
""
call /kinetics/luciferase/E.S2/notes LOAD \
"S2 is Luciferin."
call /kinetics/luciferase/PMT_count/notes LOAD \
"Volume is scaled so that 1 photon gives a Co equivalent of 0.0031," \
"which is the collection efficiency." \
"" \
"vol = 1.6667e-21 / 0.0031 = 5.37e-19" \
""
call /kinetics/Translation/Rib_RNA_Complex/notes LOAD \
"Formation Of RBS and Ribosome Complex" \
"Rate taken from Kierzek et al." \
"Kf=100" \
"Kb=2.25"
call /kinetics/Translation/Protein_Decay/notes LOAD \
"Assuming same rate as Kierzek et al." \
""
call /kinetics/Translation/Prot_synthesis/notes LOAD \
"The synthesis rate is assumed at 15 nucleotides (5 AAs) per second." \
"This gives a total synthesis time of 120 sec as" \
"600 AAs/5 per sec." \
"" \
"The open parameter is input rate, which defines how closely spaced the " \
"ribosomes are upon the mRNA. At a rate of 0.1, there are 150 nucleotides" \
"between ribomes (1/(0.067 * 0.1))" \
""
complete_loading