//genesis // kkit Version 8 flat dumpfile // Saved on Tue Jan 28 10:46:49 2003 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 1.7418e-06 \ 2.0901e+07 4.5e+11 1e+12 0 1.2e+13 0 "" 16 61 22 -3 0 simundump kpool /kinetics/Transcription/TrRNAP 0 0 0 0.0014471 1.7365e+10 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 999.95 1.1999e+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 0.020501 2.4601e+11 \ 3e+11 3e+11 0 1.2e+13 0 "" 15 61 24 -3 0 simundump kpool /kinetics/Transcription/mRNA 0 0 0 0.015401 1.8481e+11 0 0 0 \ 1.2e+13 0 "" blue 61 22 -7 0 simundump transport /kinetics/Transcription/mRNA_synthesis 4 101 7.7987e+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 \ 7.77113e+07 7.77111e+07 7.7711e+07 7.77108e+07 7.77106e+07 7.77104e+07 \ 7.77103e+07 7.77101e+07 7.77099e+07 7.77098e+07 7.77096e+07 7.77094e+07 \ 7.77092e+07 7.77091e+07 7.77089e+07 7.77087e+07 7.77086e+07 7.77084e+07 \ 7.77082e+07 7.7708e+07 7.77079e+07 7.77077e+07 7.77075e+07 7.77074e+07 \ 7.77072e+07 7.7707e+07 7.77068e+07 7.77067e+07 7.77065e+07 7.77063e+07 \ 7.77061e+07 7.7706e+07 7.77058e+07 7.77056e+07 7.77055e+07 7.77053e+07 \ 7.77051e+07 7.77049e+07 7.77048e+07 7.77046e+07 7.77044e+07 7.77043e+07 \ 7.77041e+07 7.77039e+07 7.77037e+07 7.77036e+07 7.77034e+07 7.77032e+07 \ 7.77031e+07 7.77029e+07 7.77027e+07 7.77025e+07 7.77024e+07 7.77022e+07 \ 7.7702e+07 7.77019e+07 7.77017e+07 7.77015e+07 7.77013e+07 7.77012e+07 \ 7.7701e+07 7.77008e+07 7.77006e+07 7.77005e+07 7.77003e+07 7.77001e+07 \ 7.77e+07 7.76998e+07 7.76996e+07 7.76994e+07 7.76993e+07 7.76991e+07 \ 7.76989e+07 7.76988e+07 7.76986e+07 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7.79773e+07 7.79771e+07 7.79769e+07 7.79767e+07 7.79766e+07 7.79764e+07 \ 7.79762e+07 7.7976e+07 7.79759e+07 7.79757e+07 7.79755e+07 7.79754e+07 \ 7.79752e+07 7.7975e+07 7.79748e+07 7.79747e+07 7.79745e+07 7.79743e+07 \ 7.79741e+07 7.7974e+07 7.79738e+07 7.79736e+07 7.79735e+07 7.79733e+07 \ 7.79731e+07 7.79729e+07 7.79728e+07 7.79726e+07 7.79724e+07 7.79722e+07 \ 7.79721e+07 7.79719e+07 7.79717e+07 7.79716e+07 7.79714e+07 7.79712e+07 \ 7.7971e+07 7.79709e+07 7.79707e+07 7.79705e+07 7.79704e+07 7.79702e+07 \ 7.797e+07 7.79698e+07 loadtab -continue \ 7.79697e+07 7.79695e+07 7.79693e+07 7.79691e+07 7.7969e+07 7.79688e+07 \ 7.79686e+07 7.79685e+07 7.79683e+07 7.79681e+07 7.79679e+07 7.79678e+07 \ 7.79676e+07 7.79674e+07 7.79672e+07 7.79671e+07 7.79669e+07 7.79667e+07 \ 7.79666e+07 7.79664e+07 7.79662e+07 7.7966e+07 7.79659e+07 7.79657e+07 \ 7.79655e+07 7.79653e+07 7.79652e+07 7.7965e+07 7.79648e+07 7.79647e+07 \ 7.79645e+07 7.79643e+07 7.79641e+07 7.7964e+07 7.79638e+07 7.79636e+07 \ 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7.79353e+07 loadtab -continue \ 7.79352e+07 7.7935e+07 7.79348e+07 7.79346e+07 7.79345e+07 7.79343e+07 \ 7.79341e+07 7.7934e+07 7.79338e+07 7.79336e+07 7.79334e+07 7.79333e+07 \ 7.79331e+07 7.79329e+07 7.79328e+07 7.79326e+07 7.79324e+07 7.79322e+07 \ 7.79321e+07 7.79319e+07 7.79317e+07 7.79315e+07 7.79314e+07 7.79312e+07 \ 7.7931e+07 7.79309e+07 7.79307e+07 7.79305e+07 7.79303e+07 7.79302e+07 \ 7.793e+07 7.79298e+07 7.79296e+07 7.79295e+07 7.79293e+07 7.79291e+07 \ 7.7929e+07 7.79288e+07 7.79286e+07 7.79284e+07 7.79283e+07 7.79281e+07 \ 7.79279e+07 7.79277e+07 7.79276e+07 7.79274e+07 7.79272e+07 7.79271e+07 \ 7.79269e+07 7.79267e+07 7.79265e+07 7.79264e+07 7.79262e+07 7.7926e+07 \ 7.79259e+07 7.79257e+07 7.79255e+07 7.79253e+07 7.79252e+07 7.7925e+07 \ 7.79248e+07 7.79246e+07 7.79245e+07 7.79243e+07 7.79241e+07 7.7924e+07 \ 7.79238e+07 7.79236e+07 7.79234e+07 7.79233e+07 7.79231e+07 7.79229e+07 \ 7.79227e+07 7.79226e+07 7.79224e+07 7.79222e+07 7.79221e+07 7.79219e+07 \ 7.79217e+07 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7.79074e+07 \ 7.79072e+07 7.79071e+07 7.79069e+07 7.79067e+07 7.79065e+07 7.79064e+07 \ 7.79062e+07 7.7906e+07 7.79059e+07 7.79057e+07 7.79055e+07 7.79053e+07 \ 7.79052e+07 7.7905e+07 7.79048e+07 7.79046e+07 7.79045e+07 7.79043e+07 \ 7.79041e+07 7.7904e+07 7.79038e+07 7.79036e+07 7.79034e+07 7.79033e+07 \ 7.79031e+07 7.79029e+07 7.79028e+07 7.79026e+07 7.79024e+07 7.79022e+07 \ 7.79021e+07 7.79019e+07 7.79017e+07 7.79015e+07 7.79014e+07 7.79012e+07 \ 7.7901e+07 7.79009e+07 loadtab -continue \ 7.79007e+07 7.79005e+07 7.79003e+07 7.79002e+07 7.79e+07 7.78998e+07 \ 7.78996e+07 7.78995e+07 7.78993e+07 7.78991e+07 7.7899e+07 7.78988e+07 \ 7.78986e+07 7.78984e+07 7.78983e+07 7.78981e+07 7.78979e+07 7.78978e+07 \ 7.78976e+07 7.78974e+07 7.78972e+07 7.78971e+07 7.78969e+07 7.78967e+07 \ 7.78965e+07 7.78964e+07 7.78962e+07 7.7896e+07 7.78959e+07 7.78957e+07 \ 7.78955e+07 7.78953e+07 7.78952e+07 7.7895e+07 7.78948e+07 7.78947e+07 \ 7.78945e+07 7.78943e+07 7.78941e+07 7.7894e+07 7.78938e+07 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7.78797e+07 7.78795e+07 7.78793e+07 7.78791e+07 \ 7.7879e+07 7.78788e+07 7.78786e+07 7.78785e+07 7.78783e+07 7.78781e+07 \ 7.78779e+07 7.78778e+07 7.78776e+07 7.78774e+07 7.78772e+07 7.78771e+07 \ 7.78769e+07 7.78767e+07 7.78766e+07 7.78764e+07 7.78762e+07 7.7876e+07 \ 7.78759e+07 7.78757e+07 7.78755e+07 7.78753e+07 7.78752e+07 7.7875e+07 \ 7.78748e+07 7.78747e+07 7.78745e+07 7.78743e+07 7.78741e+07 7.7874e+07 \ 7.78738e+07 7.78736e+07 7.78735e+07 7.78733e+07 7.78731e+07 7.78729e+07 \ 7.78728e+07 7.78726e+07 7.78724e+07 7.78722e+07 7.78721e+07 7.78719e+07 \ 7.78717e+07 7.78716e+07 7.78714e+07 7.78712e+07 7.7871e+07 7.78709e+07 \ 7.78707e+07 7.78705e+07 7.78704e+07 7.78702e+07 7.787e+07 7.78698e+07 \ 7.78697e+07 7.78695e+07 7.78693e+07 7.78691e+07 7.7869e+07 7.78688e+07 \ 7.78686e+07 7.78685e+07 7.78683e+07 7.78681e+07 7.78679e+07 7.78678e+07 \ 7.78676e+07 7.78674e+07 7.78673e+07 7.78671e+07 7.78669e+07 7.78667e+07 \ 7.78666e+07 7.78664e+07 loadtab -continue \ 7.78662e+07 7.7866e+07 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\ 7.78517e+07 7.78516e+07 7.78514e+07 7.78512e+07 7.78511e+07 7.78509e+07 \ 7.78507e+07 7.78505e+07 7.78504e+07 7.78502e+07 7.785e+07 7.78499e+07 \ 7.78497e+07 7.78495e+07 7.78493e+07 7.78492e+07 7.7849e+07 7.78488e+07 \ 7.78486e+07 7.78485e+07 7.78483e+07 7.78481e+07 7.7848e+07 7.78478e+07 \ 7.78476e+07 7.78474e+07 7.78473e+07 7.78471e+07 7.78469e+07 7.78468e+07 \ 7.78466e+07 7.78464e+07 7.78462e+07 7.78461e+07 7.78459e+07 7.78457e+07 \ 7.78455e+07 7.78454e+07 7.78452e+07 7.7845e+07 7.78449e+07 7.78447e+07 \ 7.78445e+07 7.78443e+07 7.78442e+07 7.7844e+07 7.78438e+07 7.78437e+07 \ 7.78435e+07 7.78433e+07 7.78431e+07 7.7843e+07 7.78428e+07 7.78426e+07 \ 7.78424e+07 7.78423e+07 7.78421e+07 7.78419e+07 7.78418e+07 7.78416e+07 \ 7.78414e+07 7.78412e+07 7.78411e+07 7.78409e+07 7.78407e+07 7.78405e+07 \ 7.78404e+07 7.78402e+07 7.784e+07 7.78399e+07 7.78397e+07 7.78395e+07 \ 7.78393e+07 7.78392e+07 7.7839e+07 7.78388e+07 7.78387e+07 7.78385e+07 \ 7.78383e+07 7.78381e+07 7.7838e+07 7.78378e+07 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7.78238e+07 7.78237e+07 \ 7.78235e+07 7.78233e+07 7.78232e+07 7.7823e+07 7.78228e+07 7.78226e+07 \ 7.78225e+07 7.78223e+07 7.78221e+07 7.7822e+07 7.78218e+07 7.78216e+07 \ 7.78214e+07 7.78213e+07 7.78211e+07 7.78209e+07 7.78207e+07 7.78206e+07 \ 7.78204e+07 7.78202e+07 7.78201e+07 7.78199e+07 7.78197e+07 7.78195e+07 \ 7.78194e+07 7.78192e+07 7.7819e+07 7.78189e+07 7.78187e+07 7.78185e+07 \ 7.78183e+07 7.78182e+07 7.7818e+07 7.78178e+07 7.78176e+07 7.78175e+07 \ 7.78173e+07 7.78171e+07 7.7817e+07 7.78168e+07 7.78166e+07 7.78164e+07 \ 7.78163e+07 7.78161e+07 7.78159e+07 7.78158e+07 7.78156e+07 7.78154e+07 \ 7.78152e+07 7.78151e+07 7.78149e+07 7.78147e+07 7.78145e+07 7.78144e+07 \ 7.78142e+07 7.7814e+07 7.78139e+07 7.78137e+07 7.78135e+07 7.78133e+07 \ 7.78132e+07 7.7813e+07 7.78128e+07 7.78127e+07 7.78125e+07 7.78123e+07 \ 7.78121e+07 7.7812e+07 7.78118e+07 7.78116e+07 7.78114e+07 7.78113e+07 \ 7.78111e+07 7.78109e+07 7.78108e+07 7.78106e+07 7.78104e+07 7.78102e+07 \ 7.78101e+07 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7.77822e+07 7.7782e+07 \ 7.77818e+07 7.77817e+07 7.77815e+07 7.77813e+07 7.77812e+07 7.7781e+07 \ 7.77808e+07 7.77806e+07 7.77805e+07 7.77803e+07 7.77801e+07 7.77799e+07 \ 7.77798e+07 7.77796e+07 7.77794e+07 7.77793e+07 7.77791e+07 7.77789e+07 \ 7.77787e+07 7.77786e+07 7.77784e+07 7.77782e+07 7.77781e+07 7.77779e+07 \ 7.77777e+07 7.77775e+07 7.77774e+07 7.77772e+07 7.7777e+07 7.77768e+07 \ 7.77767e+07 7.77765e+07 7.77763e+07 7.77762e+07 7.7776e+07 7.77758e+07 \ 7.77756e+07 7.77755e+07 7.77753e+07 7.77751e+07 7.7775e+07 7.77748e+07 \ 7.77746e+07 7.77744e+07 7.77743e+07 7.77741e+07 7.77739e+07 7.77738e+07 \ 7.77736e+07 7.77734e+07 7.77732e+07 7.77731e+07 7.77729e+07 7.77727e+07 \ 7.77725e+07 7.77724e+07 7.77722e+07 7.7772e+07 7.77719e+07 7.77717e+07 \ 7.77715e+07 7.77713e+07 7.77712e+07 7.7771e+07 7.77708e+07 7.77707e+07 \ 7.77705e+07 7.77703e+07 7.77701e+07 7.777e+07 7.77698e+07 7.77696e+07 \ 7.77694e+07 7.77693e+07 7.77691e+07 7.77689e+07 7.77688e+07 7.77686e+07 \ 7.77684e+07 7.77682e+07 7.77681e+07 7.77679e+07 7.77677e+07 7.77676e+07 \ 7.77674e+07 7.77672e+07 7.7767e+07 7.77669e+07 7.77667e+07 7.77665e+07 \ 7.77664e+07 7.77662e+07 7.7766e+07 7.77658e+07 7.77657e+07 7.77655e+07 \ 7.77653e+07 7.77651e+07 7.7765e+07 7.77648e+07 7.77646e+07 7.77645e+07 \ 7.77643e+07 7.77641e+07 7.77639e+07 7.77638e+07 7.77636e+07 7.77634e+07 \ 7.77633e+07 7.77631e+07 loadtab -continue \ 7.77629e+07 7.77627e+07 7.77626e+07 7.77624e+07 7.77622e+07 7.77621e+07 \ 7.77619e+07 7.77617e+07 7.77615e+07 7.77614e+07 7.77612e+07 7.7761e+07 \ 7.77608e+07 7.77607e+07 7.77605e+07 7.77603e+07 7.77602e+07 7.776e+07 \ 7.77598e+07 7.77596e+07 7.77595e+07 7.77593e+07 7.77591e+07 7.7759e+07 \ 7.77588e+07 7.77586e+07 7.77584e+07 7.77583e+07 7.77581e+07 7.77579e+07 \ 7.77577e+07 7.77576e+07 7.77574e+07 7.77572e+07 7.77571e+07 7.77569e+07 \ 7.77567e+07 7.77565e+07 7.77564e+07 7.77562e+07 7.7756e+07 7.77559e+07 \ 7.77557e+07 7.77555e+07 7.77553e+07 7.77552e+07 7.7755e+07 7.77548e+07 \ 7.77547e+07 7.77545e+07 7.77543e+07 7.77541e+07 7.7754e+07 7.77538e+07 \ 7.77536e+07 7.77534e+07 7.77533e+07 7.77531e+07 7.77529e+07 7.77528e+07 \ 7.77526e+07 7.77524e+07 7.77522e+07 7.77521e+07 7.77519e+07 7.77517e+07 \ 7.77516e+07 7.77514e+07 7.77512e+07 7.7751e+07 7.77509e+07 7.77507e+07 \ 7.77505e+07 7.77504e+07 7.77502e+07 7.775e+07 7.77498e+07 7.77497e+07 \ 7.77495e+07 7.77493e+07 7.77491e+07 7.7749e+07 7.77488e+07 7.77486e+07 \ 7.77485e+07 7.77483e+07 7.77481e+07 7.77479e+07 7.77478e+07 7.77476e+07 \ 7.77474e+07 7.77473e+07 7.77471e+07 7.77469e+07 7.77467e+07 7.77466e+07 \ 7.77464e+07 7.77462e+07 7.7746e+07 7.77459e+07 7.77457e+07 7.77455e+07 \ 7.77454e+07 7.77452e+07 7.7745e+07 7.77448e+07 7.77447e+07 7.77445e+07 \ 7.77443e+07 7.77442e+07 7.7744e+07 7.77438e+07 7.77436e+07 7.77435e+07 \ 7.77433e+07 7.77431e+07 7.7743e+07 7.77428e+07 7.77426e+07 7.77424e+07 \ 7.77423e+07 7.77421e+07 7.77419e+07 7.77417e+07 7.77416e+07 7.77414e+07 \ 7.77412e+07 7.77411e+07 7.77409e+07 7.77407e+07 7.77405e+07 7.77404e+07 \ 7.77402e+07 7.774e+07 7.77399e+07 7.77397e+07 7.77395e+07 7.77393e+07 \ 7.77392e+07 7.7739e+07 7.77388e+07 7.77387e+07 7.77385e+07 7.77383e+07 \ 7.77381e+07 7.7738e+07 7.77378e+07 7.77376e+07 7.77374e+07 7.77373e+07 \ 7.77371e+07 7.77369e+07 7.77368e+07 7.77366e+07 7.77364e+07 7.77362e+07 \ 7.77361e+07 7.77359e+07 7.77357e+07 7.77356e+07 7.77354e+07 7.77352e+07 \ 7.7735e+07 7.77349e+07 7.77347e+07 7.77345e+07 7.77344e+07 7.77342e+07 \ 7.7734e+07 7.77338e+07 7.77337e+07 7.77335e+07 7.77333e+07 7.77331e+07 \ 7.7733e+07 7.77328e+07 7.77326e+07 7.77325e+07 7.77323e+07 7.77321e+07 \ 7.77319e+07 7.77318e+07 7.77316e+07 7.77314e+07 7.77313e+07 7.77311e+07 \ 7.77309e+07 7.77307e+07 7.77306e+07 7.77304e+07 7.77302e+07 7.77301e+07 \ 7.77299e+07 7.77297e+07 7.77295e+07 7.77294e+07 7.77292e+07 7.7729e+07 \ 7.77288e+07 7.77287e+07 loadtab -continue \ 7.77285e+07 7.77283e+07 7.77282e+07 7.7728e+07 7.77278e+07 7.77276e+07 \ 7.77275e+07 7.77273e+07 7.77271e+07 7.7727e+07 7.77268e+07 7.77266e+07 \ 7.77264e+07 7.77263e+07 7.77261e+07 7.77259e+07 7.77258e+07 7.77256e+07 \ 7.77254e+07 7.77252e+07 7.77251e+07 7.77249e+07 7.77247e+07 7.77245e+07 \ 7.77244e+07 7.77242e+07 7.7724e+07 7.77239e+07 7.77237e+07 7.77235e+07 \ 7.77233e+07 7.77232e+07 7.7723e+07 7.77228e+07 7.77227e+07 7.77225e+07 \ 7.77223e+07 7.77221e+07 7.7722e+07 7.77218e+07 7.77216e+07 7.77215e+07 \ 7.77213e+07 7.77211e+07 7.77209e+07 7.77208e+07 7.77206e+07 7.77204e+07 \ 7.77203e+07 7.77201e+07 7.77199e+07 7.77197e+07 7.77196e+07 7.77194e+07 \ 7.77192e+07 7.7719e+07 7.77189e+07 7.77187e+07 7.77185e+07 7.77184e+07 \ 7.77182e+07 7.7718e+07 7.77178e+07 7.77177e+07 7.77175e+07 7.77173e+07 \ 7.77172e+07 7.7717e+07 7.77168e+07 7.77166e+07 7.77165e+07 7.77163e+07 \ 7.77161e+07 7.7716e+07 7.77158e+07 7.77156e+07 7.77154e+07 7.77153e+07 \ 7.77151e+07 7.77149e+07 7.77147e+07 7.77146e+07 7.77144e+07 7.77142e+07 \ 7.77141e+07 7.77139e+07 7.77137e+07 7.77135e+07 7.77134e+07 7.77132e+07 \ 7.7713e+07 7.77129e+07 7.77127e+07 7.77125e+07 7.77123e+07 7.77122e+07 \ 7.7712e+07 7.77118e+07 7.77117e+07 7.77115e+07 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 0.00018429 \ 2.2114e+09 0 0 0 1.2e+13 0 "" blue 61 20 -3 0 simundump kpool /kinetics/Transcription/decayed_RNAP 0 0 0 7.2948e-06 \ 8.7538e+07 0 0 0 1.2e+13 0 "" blue 61 22 1 0 simundump kpool /kinetics/Transcription/RBS 0 0 0 0.032373 3.8847e+11 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 0.00091772 \ 1.1013e+10 0 0 0 1.2e+13 0 "" blue 61 28 -3 0 simundump xtab /kinetics/noOligo 0 -550 2635.6 1 2 0 "" edit_xtab white red 0 \ 0 0 0 36 -9 0 loadtab /kinetics/noOligo table 0 3000 0 3000 \ 17 16.5507 16.1015 15.6522 15.203 14.8857 15.0965 15.4459 15.7953 16.1448 \ 16.3508 16.3037 16.104 15.9043 15.7047 15.5768 15.5487 15.5986 15.6485 \ 15.6984 15.7849 15.943 16.1427 16.3423 16.542 16.7943 17.324 17.923 18.522 \ 19.121 19.72 19.745 19.75 19.75 19.75 19.6403 19.092 18.3932 17.6943 16.9955 \ 16.5163 16.4363 16.636 16.8357 17.0353 17.0516 16.7883 16.2892 15.79 15.2908 \ 14.8443 14.5213 14.2717 14.0221 13.7725 13.6759 14.8147 16.2623 17.7098 \ 19.1574 20.605 19.0788 17.336 15.539 13.742 12.3233 12.4175 13.1663 13.915 \ 14.6637 15.3443 15.8967 16.346 16.7952 17.2445 17.5752 17.7063 17.6564 \ 17.6065 17.5566 17.4889 17.3702 17.2205 17.0707 16.921 16.7712 16.6215 \ 16.4718 16.322 16.1722 16.0225 16.0911 16.1847 16.2845 16.3843 16.4772 \ 16.542 16.5919 16.6418 16.6917 16.8049 17.0411 17.3905 17.7399 18.0893 \ 18.3116 18.2942 18.0446 17.795 17.5454 17.303 17.087 16.8873 16.6877 16.488 \ 16.2967 17.097 18.1453 19.1935 20.2417 21.29 20.5502 19.5237 18.4255 17.3273 \ 16.3279 15.7235 15.3741 15.0247 14.6753 14.5101 14.719 15.318 15.917 16.516 \ 16.9654 17.0953 16.8957 16.696 16.4963 16.3409 16.403 16.6027 16.8023 17.002 \ 17.2017 17.3628 17.5133 17.663 17.8127 17.9625 18.2703 18.6113 18.9607 \ 19.3102 19.6041 19.676 19.5762 19.4763 19.3765 19.0905 18.4086 17.2605 \ 16.1124 14.9643 14.1402 14.1148 14.9634 15.812 16.6606 17.3622 16.9992 \ 15.951 14.9028 13.8545 12.8063 13.4907 14.7165 16.0143 17.3122 18.61 19.0472 \ 19.2545 19.4043 19.554 19.5255 18.784 17.3863 15.9887 14.591 13.5147 13.159 \ 13.758 14.357 14.956 15.555 16.154 16.753 17.352 17.951 loadtab -continue \ 18.5324 18.883 19.0827 19.2823 19.482 19.6817 18.9661 17.9295 16.8313 \ 15.7332 14.635 14.1728 13.9207 13.721 13.5213 13.4657 13.986 15.1341 16.2822 \ 17.4303 18.2543 18.3052 17.207 16.1088 15.0107 14.1085 13.9052 14.5541 \ 15.203 15.8519 16.496 16.873 17.0727 17.2723 17.472 17.6717 17.1671 16.3857 \ 15.5372 14.6886 13.84 13.6897 13.8193 14.019 14.2187 14.4528 14.8245 15.3736 \ 15.9227 16.4717 17.1036 17.948 19.146 20.344 21.542 22.5225 22.5047 21.2068 \ 19.909 18.6112 17.3133 17.0049 17.3753 17.7747 18.174 18.5733 18.0167 \ 17.0395 15.9413 14.8432 13.745 13.4572 13.5593 13.759 13.9587 14.2933 15.168 \ 16.8652 18.5623 20.2595 21.6191 22.0323 20.6845 19.3368 17.989 16.7281 \ 16.0262 16.0761 16.126 16.1759 16.2258 16.2758 16.3257 16.3756 16.4255 \ 16.4754 17.6125 19.2842 21.1312 22.9781 24.825 24.8978 23.954 22.756 21.558 \ 20.5356 20.2155 21.1639 22.1123 23.0607 23.8212 23.9942 22.946 21.8977 \ 20.8495 19.8863 19.8417 21.0896 22.3375 23.5854 24.8333 25.7621 26.4512 \ 27.1001 27.749 28.3979 28.8471 29.1865 29.486 29.7855 30.085 30.7625 31.6967 \ 32.695 33.6933 34.7173 35.844 37.1918 38.5395 39.8873 41.2969 42.9281 \ 45.0745 47.2209 49.3673 51.467 52.0092 50.2621 48.515 46.7679 45.0208 \ 44.8455 45.908 47.2558 48.6035 49.9512 51.8363 54.0517 56.3978 58.7439 61.09 \ 63.6354 66.3408 69.0863 71.8317 74.4243 76.406 76.8053 77.2047 77.604 \ 78.1884 79.5668 83.011 86.4553 89.8995 93.3438 96.202 98.1748 100.122 \ 102.068 104.015 105.673 107.09 108.438 109.786 111.134 113.414 116.336 \ 119.531 122.725 125.92 128.704 131.097 133.394 135.69 137.898 139.755 \ 140.504 141.253 142.001 loadtab -continue \ 142.897 144.61 148.703 152.796 156.889 160.982 164.384 166.724 168.97 \ 171.216 173.462 177.194 182.223 187.714 193.205 198.696 202.916 206.154 \ 208.949 211.745 214.54 216.858 218.639 220.287 221.934 223.734 226.142 \ 230.934 235.726 240.518 245.261 249.595 252.59 255.585 258.58 261.575 265.07 \ 269.345 273.738 278.131 282.523 286.7 290.677 294.571 298.464 302.358 305.07 \ 306.756 307.954 309.152 310.35 313.359 318.792 324.832 330.872 336.816 \ 342.376 346.02 349.664 353.308 356.912 359.738 359.688 359.639 359.589 \ 359.539 362.385 369.823 378.259 386.695 395.131 400.86 403.934 405.731 \ 407.528 409.325 411.304 413.461 415.707 417.954 420.2 423.375 428.043 \ 433.085 438.126 443.063 447.582 449.33 451.077 452.824 454.571 457.026 \ 462.313 467.654 472.995 478.336 484.066 490.424 496.963 503.503 510.042 \ 514.575 517.012 518.31 519.608 520.906 522.704 525.061 527.706 530.352 \ 532.997 535.614 538.174 540.72 543.265 545.879 548.763 554.204 559.645 \ 565.086 570.527 575.61 579.261 582.806 586.35 589.894 592.593 593.897 \ 594.696 595.495 596.293 597.503 599.171 601.118 603.064 605.011 608.948 \ 615.424 623.261 631.098 638.935 646.412 653.019 659.408 665.797 672.064 \ 677.843 676.095 674.348 672.601 670.854 670.808 677.566 685.253 692.94 \ 700.628 706.643 709.84 711.787 713.733 715.68 718.042 720.903 724.097 \ 727.292 730.487 733.59 736.559 739.455 742.35 745.245 748.988 755.327 \ 762.315 769.303 776.267 783.132 786.427 789.721 793.016 796.31 799.613 \ 802.951 806.295 809.639 812.984 816.616 820.745 825.138 829.531 833.923 \ 835.829 834.501 830.807 827.113 823.419 823.555 830.252 840.685 851.117 loadtab -continue \ 861.55 870.564 873.844 875.691 877.538 879.385 881.232 879.168 877.078 \ 874.982 872.885 871.858 875.111 879.554 883.996 888.439 892.766 896.887 \ 900.88 904.873 908.867 913.382 918.636 924.476 930.316 936.156 941.641 \ 946.404 950.747 955.09 959.433 963.029 962.391 960.693 958.996 957.299 \ 955.602 959.073 962.763 966.506 970.25 973.839 976.808 979.553 982.298 \ 985.044 987.909 990.995 994.24 997.485 1000.73 1001.66 998.998 993.258 \ 987.517 981.777 978.842 982.74 990.727 998.713 1006.7 1014.53 1020.97 \ 1027.06 1033.15 1039.24 1045.33 1050.15 1054.87 1059.56 1064.25 1068.36 \ 1070.16 1070.91 1071.66 1072.41 1073.6 1075.65 1078.39 1081.14 1083.88 \ 1087.79 1093.69 1101.43 1109.17 1116.9 1122.41 1121.22 1115.93 1110.64 \ 1105.35 1100.32 1100.31 1101.56 1102.8 1104.05 1105.3 1112.65 1120.74 \ 1129.03 1137.32 1145.01 1150.32 1154.31 1158.31 1162.3 1165.87 1168.6 \ 1170.55 1172.5 1174.44 1175.76 1175.86 1174.76 1173.66 1172.56 1172.33 \ 1175.48 1180.72 1185.96 1191.2 1196.44 1199.97 1203.06 1206.16 1209.25 \ 1212.35 1210.96 1208.8 1206.46 1204.11 1203.58 1210.34 1221.97 1233.6 \ 1245.23 1255.4 1262.59 1266.58 1270.57 1274.57 1277.14 1276.6 1272.81 \ 1269.01 1265.22 1262.49 1265.33 1271.72 1278.11 1284.5 1290.89 1298.96 \ 1307.51 1316.09 1324.68 1333.26 1332.16 1328.9 1325.11 1321.31 1318.56 \ 1319.97 1324.71 1329.45 1334.19 1338.61 1342.34 1345.24 1348.13 1351.03 \ 1353.08 1353 1350.56 1348.11 1345.66 1343.64 1344.93 1348.38 1351.82 1355.27 \ 1358.71 1359.16 1358.65 1358 1357.35 1356.7 1366.04 1378.17 1391 1403.83 \ 1415.19 1420.65 1420.5 1420.35 1420.2 1421.18 1424.74 1431.77 1438.81 loadtab -continue \ 1445.85 1450.57 1448.25 1437.72 1427.19 1416.65 1406.82 1407.81 1415.89 \ 1423.98 1432.07 1440.15 1443.98 1446.29 1448.29 1450.28 1452.28 1454.52 \ 1456.85 1459.19 1461.54 1463.4 1463.3 1461 1458.71 1456.41 1455.32 1457.14 \ 1463.38 1469.61 1475.85 1481.35 1484.07 1483.37 1482.67 1481.97 1481.28 \ 1481.97 1483.57 1485.16 1486.76 1488.36 1497.19 1508.94 1521.42 1533.9 \ 1546.37 1553.34 1558.01 1562.1 1566.19 1569.86 1571.83 1571.53 1571.23 \ 1570.93 1570.74 1570.84 1571.44 1572.04 1572.64 1572.98 1572.06 1569.52 \ 1566.97 1564.43 1561.88 1561.24 1561.92 1562.66 1563.41 1564.16 1568.13 \ 1573.54 1579.38 1585.22 1591.06 1590.84 1587.6 1583.61 1579.62 1576.06 \ 1574.28 1575.28 1576.28 1577.28 1580.38 1589.52 1610.14 1630.75 1651.37 \ 1670.39 1678.28 1671.04 1663.8 1656.56 1649.33 1646.73 1647.48 1648.63 \ 1649.77 1650.92 1652.13 1653.37 1654.62 1655.86 1657.11 1656.76 1655.45 \ 1653.9 1652.35 1651.2 1651.66 1655.1 1658.54 1661.99 1665.3 1668.17 1670.12 \ 1672.06 1674.01 1675.98 1678.25 1680.95 1683.64 1686.34 1689.03 1692.41 \ 1696.31 1700.31 1704.3 1708.29 1712.77 1717.51 1722.35 1727.19 1732.03 \ 1737.19 1742.58 1748.02 1753.46 1758.17 1759.96 1755.22 1750.47 1745.73 \ 1741.73 1740.44 1745.63 1750.83 1756.02 1761.17 1764.39 1764.74 1765.09 \ 1765.44 1765.79 1766.84 1768.46 1770.2 1771.95 1773.7 1771.89 1767.84 1762.9 \ 1757.96 1753.02 1753.66 1758.94 1765.38 1771.82 1777.6 1780.71 1776.67 \ 1772.62 1768.58 1765.2 1764.79 1772.27 1779.76 1787.25 1794.74 1798.89 1798 \ 1796.9 1795.81 1794.71 1795.71 1798.47 1801.76 1805.06 1808.35 1813.58 \ 1820.18 1827.37 1834.56 1841.75 1842.3 1836.34 1828.75 loadtab -continue \ 1821.17 1814.49 1811.45 1820.39 1829.32 1838.26 1846.92 1853.99 1856.29 \ 1858.58 1860.88 1863.17 1866.99 1873.14 1879.53 1885.92 1892.31 1895.06 \ 1894.6 1892.95 1891.3 1889.66 1891.35 1895.69 1901.23 1906.77 1912.31 \ 1917.61 1922.62 1927.56 1932.5 1936.84 1938.77 1930.84 1922.9 1914.96 \ 1907.16 1900.54 1897.95 1895.35 1892.76 1890.16 1890.34 1894.87 1900.11 \ 1905.36 1910.6 1913.3 1913.62 1912.92 1912.23 1911.53 1911.58 1912.31 \ 1913.36 1914.4 1915.45 1919.04 1926.14 1934.13 1942.12 1950.08 1957.95 \ 1965.34 1972.73 1980.12 1987.43 1992.81 1990.81 1988.81 1986.82 1984.82 \ 1985.08 1988.94 1993.64 1998.33 2003.02 2003.83 2000.79 1995.85 1990.91 \ 1985.97 1981.44 1977.34 1973.45 1969.55 1965.66 1966.03 1973.54 1982.82 \ 1992.11 2001 2008.33 2004.64 2000.95 1997.25 1993.56 1990.78 1991.67 1992.67 \ 1993.67 1994.66 1997.54 2003.46 2010.3 2017.13 2023.97 2027.74 2028.25 \ 2026.95 2025.66 2024.36 2025.92 2030.75 2037.29 2043.83 2050.37 2053.72 \ 2050.6 2045.86 2041.12 2036.64 2033.24 2040.83 2048.41 2056 2063.59 2068.98 \ 2065.6 2061.46 2057.32 2053.17 2051.96 2055.61 2061.1 2066.6 2072.09 2076.43 \ 2079.48 2081.73 2083.98 2086.22 2089.79 2095.09 2101.33 2107.57 2113.81 \ 2117.1 2112.93 2106.89 2100.85 2094.95 2089.63 2094.43 2099.22 2104.01 \ 2108.8 2111.09 2103.35 2094.12 2084.88 2075.65 2072.45 2079.47 2091.21 \ 2102.94 2114.67 2122.73 2126.33 2126.88 2127.43 2127.98 2129.39 2132.11 \ 2135.55 2138.99 2142.44 2145.01 2144.77 2143.82 2142.87 2141.88 2140.72 \ 2131.39 2122.05 2112.72 2103.38 2097.33 2104.4 2114.33 2124.27 2134.2 \ 2142.79 2149.06 2154.05 2159.04 2164.03 2166.34 2165.09 2161.19 loadtab -continue \ 2157.3 2153.41 2151.84 2154.38 2159.27 2164.16 2169.05 2173.48 2175.92 \ 2177.87 2179.82 2181.76 2183.71 2186.39 2189.09 2191.78 2194.48 2197.18 \ 2199.92 2202.66 2205.41 2208.15 2210.95 2213.84 2216.78 2219.73 2222.67 \ 2223.57 2221.51 2217.07 2212.62 2208.18 2206 2208.56 2213.9 2219.24 2224.58 \ 2227.98 2219.43 2207.9 2196.37 2184.84 2173.31 2181.19 2190.03 2199.12 \ 2208.2 2215.67 2216.67 2215.22 2213.77 2212.32 2210.97 2209.79 2208.74 \ 2207.7 2206.65 2210.39 2221.71 2239.63 2257.55 2275.48 2288.67 2289.88 \ 2283.89 2277.9 2271.91 2266.35 2265.12 2264.97 2264.82 2264.67 2264.52 \ 2259.52 2254.08 2248.54 2243 2239.3 2242.97 2250.11 2257.25 2264.38 2270.4 \ 2274.27 2276.31 2278.36 2280.41 2280.81 2278.31 2273.12 2267.93 2262.74 \ 2258.57 2257.64 2258.69 2259.73 2260.78 2261.72 2259.91 2257.41 2254.92 \ 2252.42 2249.92 2258.65 2268.86 2279.45 2290.03 2299.1 2302.13 2301.68 \ 2301.23 2300.78 2298.8 2293.8 2285.86 2277.92 2269.99 2266.61 2272.23 2286.8 \ 2301.38 2315.96 2328.06 2330.04 2325.7 2321.36 2317.01 2312.67 2309.28 \ 2306.13 2302.98 2299.84 2296.69 2303.21 2311.46 2320.14 2328.83 2334.7 \ 2329.3 2316.07 2302.84 2289.61 2281.16 2282.58 2294.81 2307.04 2319.27 \ 2328.85 2332.47 2329.77 2327.07 2324.38 2322.27 2323.46 2326.75 2330.05 \ 2333.34 2336.64 2335.31 2332.64 2329.85 2327.05 2324.26 2323.9 2324.1 \ 2324.45 2324.8 2325.27 2326.19 2327.48 2328.78 2330.08 2332.27 2336.41 \ 2342.95 2349.49 2356.03 2361.27 2363.09 2361.1 2359.1 2357.1 2354.68 2348.49 \ 2339.85 2331.22 2322.58 2313.95 2317 2323.89 2331.38 2338.86 2346.35 2347.8 \ 2347.49 2346.74 2346 2344.98 2342.89 2339.74 loadtab -continue \ 2336.6 2333.46 2331.21 2331.04 2333.73 2336.43 2339.12 2341.13 2340.95 \ 2338.21 2335.46 2332.72 2329.81 2323.74 2315.61 2307.47 2299.33 2291.2 \ 2290.31 2292.09 2294.44 2296.78 2299.13 2311.03 2326.35 2342.53 2358.7 \ 2372.62 2377.53 2371.94 2366.35 2360.76 2356.06 2353.55 2354.45 2355.35 \ 2356.25 2356.57 2354.66 2349.97 2345.28 2340.59 2335.9 2337.56 2343.48 \ 2349.42 2355.36 2361.3 2356.43 2347.11 2336.62 2326.14 2315.66 2316.1 \ 2321.26 2327.6 2333.94 2340.21 2346.19 2351.78 2357.37 2362.96 2367.19 \ 2367.8 2362.11 2356.42 2350.73 2345.63 2343.58 2345.53 2347.47 2349.42 \ 2351.37 2354.06 2357.27 2360.51 2363.76 2367 2364.28 2358.83 2352.54 2346.25 \ 2339.96 2339.62 2342.34 2345.84 2349.33 2351.79 2350.08 2341.59 2333.11 \ 2324.62 2318.25 2318.04 2329.82 2341.6 2353.38 2364.23 2367.98 2361.99 2356 \ 2350.01 2344.02 2342.73 2344.88 2347.48 2350.07 2352.67 2359.64 2368.85 \ 2378.83 2388.82 2398.8 2399.15 2393.59 2386.55 2379.51 2372.85 2367.69 \ 2365.45 2363.2 2360.95 2358.82 2357.06 2356.11 2355.16 2354.22 2353.37 \ 2354.06 2356.96 2359.86 2362.75 2365.65 2365.07 2361.84 2358.09 2354.35 \ 2350.61 2355.92 2366.44 2378.92 2391.4 2403.87 2406.18 2401.08 2394.15 \ 2387.21 2380.68 2375.79 2374.69 2373.59 2372.49 2371.28 2369.64 2366.94 \ 2364.25 2361.55 2358.86 2357.39 2357.74 2358.09 2358.44 2358.79 2358.34 \ 2357.26 2356.01 2354.76 2353.51 2358.71 2368.05 2379.09 2390.12 2401.15 \ 2408.33 2412.2 2415.24 2418.29 2421.08 2422.88 2421.88 2420.88 2419.88 \ 2418.48 2415.14 2406.55 2397.97 2389.38 2380.8 2379.45 2389.1 2399.34 \ 2409.57 2419.8 2426.69 2430.73 2433.88 2437.02 2440.17 2437.91 2431.77 loadtab -continue \ 2423.93 2416.1 2408.26 2403.04 2400.48 2398.58 2396.69 2394.81 2393 2391.46 \ 2389.91 2388.36 2387.3 2389.32 2400.75 2412.18 2423.61 2435.04 2441.59 \ 2440.59 2438.74 2436.9 2435.05 2433.49 2432.2 2431 2429.8 2428.6 2428.94 \ 2430.51 2432.66 2434.81 2436.95 2434.96 2427.97 2419.73 2411.49 2403.77 \ 2398.11 2401.31 2404.5 2407.7 2410.98 2415.25 2422.89 2430.53 2438.16 2445.8 \ 2448.34 2442.86 2435.98 2429.09 2422.2 2419.68 2421.29 2424.73 2428.18 \ 2431.62 2435 2438.33 2441.62 2444.91 2448.21 2448.1 2443.08 2436.84 2430.6 \ 2424.37 2418.16 2412.07 2405.98 2399.89 2393.9 2393.07 2412.29 2431.51 \ 2450.73 2469.95 2479.43 2473.35 2463.47 2453.59 2443.7 2442.3 2449.41 \ 2460.84 2472.28 2483.71 2489.53 2489.56 2486.67 2483.77 2480.88 2480.69 \ 2485.21 2490.9 2496.59 2501.79 2505.02 2493.39 2481.76 2470.13 2458.5 \ 2449.29 2449.79 2450.69 2451.59 2452.49 2454.72 2459.12 2464.22 2469.31 \ 2474.4 2476.44 2475.21 2472.11 2469.02 2465.92 2464.13 2463.87 2464.42 \ 2464.97 2465.52 2467.3 2471.69 2476.73 2481.77 2486.64 2490.81 2487.17 \ 2483.52 2479.88 2476.24 2473.03 2471.56 2470.26 2468.96 2467.66 2469.64 \ 2477.08 2486.66 2496.24 2505.83 2508.51 2503.24 2492.96 2482.67 2472.39 \ 2466.3 2465.88 2468.52 2471.17 2473.81 2477.91 2485.83 2494.72 2503.6 \ 2512.24 2519.87 2507.4 2494.92 2482.44 2469.96 2460.94 2465.78 2472.86 \ 2479.95 2487.04 2491.18 2490.28 2486.99 2483.69 2480.4 2478.29 2477.67 \ 2478.07 2478.47 2478.87 2484.86 2499.59 2519.2 2538.82 2558.44 2572.58 \ 2568.05 2558.87 2549.69 2540.55 2531.6 2536.8 2541.99 2547.18 2552.37 \ 2555.91 2552.85 2548.26 2543.67 2539.08 2532.29 2521.68 loadtab -continue \ 2508.9 2496.12 2483.34 2479.95 2489.17 2507.94 2526.71 2545.48 2554.9 \ 2547.21 2529.69 2512.17 2494.65 2480.87 2484.22 2491.86 2499.5 2507.13 \ 2514.77 2521 2527.19 2533.38 2539.57 2543.94 2541.01 2535.82 2530.63 2525.43 \ 2522.11 2522.14 2524.39 2526.63 2528.88 2534.2 2544.03 2557.56 2571.09 \ 2584.61 2591.96 2585.86 2571.84 2557.81 2543.78 2531.4 2530.05 2531.45 \ 2532.84 2534.24 2535.64 2539.83 2544.18 2548.58 2552.97 2557 2559.57 2561.57 \ 2563.56 2565.56 2564.26 2556.84 2544.76 2532.68 2520.6 2512.39 2510.42 \ 2513.97 2517.51 2521.05 2523.41 2522.61 2519.92 2517.22 2514.52 2512.14 \ 2513.38 2515.53 2517.68 2519.82 2521.97 2527.32 2532.98 2538.72 2544.46 \ 2550.4 2557.11 2564.19 2571.28 2578.37 2583.7 2585.65 2584.65 2583.65 \ 2582.65 2581.42 2579.77 2577.72 2575.68 2573.63 2570.47 2563.61 2554.47 \ 2545.34 2536.21 2527.42 2530.29 2536.09 2541.88 2547.67 2553.46 2555.43 \ 2556.86 2558.16 2559.46 2559.64 2555.37 2548.43 2541.49 2534.56 2530.46 \ 2532.02 2539.21 2546.4 2553.59 2561.67 2571.57 2583.3 2595.03 2606.76 \ 2615.64 2612.17 2600.94 2589.71 2578.48 2567.24 2561.58 2557.38 2553.24 \ 2549.1 2544.95 2547.55 2551.42 2555.61 2559.81 2563.89 2567.55 2570.89 \ 2574.23 2577.58 2578.97 2576.3 2569.06 2561.82 2554.59 2548.74 2546.13 \ 2546.98 2547.83 2548.68 2550.35 2557.06 2567 2576.93 2586.86 2596.8 2600.12 \ 2601.48 2602.63 2603.78 2604.93 2590.47 2572.2 2552.99 2533.77 2517.06 \ 2510.42 2512.42 2514.41 2516.41 2520.71 2530.05 2545.78 2561.5 2577.22 \ 2589.59 2592.83 2585.74 2578.65 2571.56 2565.18 2565.85 2571.09 2576.33 \ 2581.57 2586.81 2590.15 2592.86 2595.45 2598.05 2600.64 2597.56 loadtab -continue \ 2592.75 2587.51 2582.27 2577.22 2572.97 2569.53 2566.08 2562.64 2561.3 \ 2564.84 2575.33 2585.81 2596.29 2605.05 2608.18 2604.59 2601 2597.4 2593.75 \ 2588.75 2582.86 2576.97 2571.08 2565.19 2562.62 2561.29 2560.25 2559.2 \ 2558.15 2563.78 2571.9 2580.63 2589.37 2596.79 2598.97 2594.83 2590.68 \ 2586.54 2583.49 2583.19 2587.23 2591.27 2595.32 2599.41 2603.73 2608.32 \ 2612.91 2617.51 2622.1 2612.78 2594.08 2575.21 2556.34 2537.47 2535.13 \ 2539.74 2546.23 2552.72 2559.2 2565.53 2571.79 2578.03 2584.27 2589.98 \ 2593.59 2594.18 2594.78 2595.38 2595.7 2595.26 2593.46 2591.66 2589.87 \ 2588.61 2590.32 2595.96 2601.6 2607.24 2612.88 2611.95 2606.38 2600.44 \ 2594.5 2588.56 2584.81 2582.09 2579.69 2577.3 2574.9 2575.56 2577.84 2580.54 \ 2583.24 2585.59 2586.59 2585.29 2583.99 2582.69 2581.99 2583.06 2587.65 \ 2592.24 2596.83 2601.22 2603.87 2604.12 2604.37 2604.62 2604.87 2602.14 \ 2597.21 2591.97 2586.73 2581.49 2576.8 2572.41 2568.11 2563.82 2559.53 \ 2560.3 2564.29 2569.08 2573.87 2578.37 2581.69 2582.64 2583.58 2584.53 \ 2586.01 2589.3 2596.58 2603.87 2611.16 2618.39 2624.56 2629.2 2633.85 \ 2638.49 2643.13 2641.52 2635.07 2627.63 2620.2 2612.76 2608.07 2605.01 \ 2602.56 2600.12 2597.67 2597.75 2599.72 2602.17 2604.61 2607.43 2611.74 \ 2619.63 2627.51 2635.4 2642.02 2643.64 2632.81 2621.98 2611.15 2600.31 \ 2596.73 2604.05 2611.44 2618.82 2626.21 2628.51 2626.67 2623.72 2620.78 \ 2617.83 2611.94 2604.11 2595.47 2586.84 2578.2 2580.71 2593.11 2607.99 \ 2622.86 2636.57 2645.59 2641 2636.41 2631.82 2626.8 2619.66 2606.63 2593.6 \ 2580.58 2567.55 2565.33 2579.59 2594.92 2610.24 2625.57 2630.15 loadtab -continue \ 2625.55 2617.91 2610.28 2602.64 2602.6 2608.17 2616.2 2624.24 2632.28 \ 2636.25 2635.97 2634.62 2633.28 2631.78 2629.71 2625.57 2621.43 2617.28 \ 2613.45 2611.76 2616.75 2621.74 2626.73 2631.72 2632.59 2627.05 2620.71 \ 2614.37 2608.03 2604.41 2603.24 2603.04 2602.84 2602.64 2603.1 2604.09 \ 2605.34 2606.59 2607.84 2609.34 2611.16 2613.05 2614.95 2616.88 2618.93 \ 2621.52 2624.12 2626.71 2629.06 2628.31 2616.62 2604.94 2593.26 2581.58 \ 2575.88 2579.58 2585.07 2590.56 2596.05 2598.64 2598.46 2597.01 2595.57 \ 2594.12 2599.47 2611.19 2626.02 2640.84 2655.67 2662.24 2656.48 2647.65 \ 2638.81 2629.86 2620.47 2608.44 2596.41 2584.38 2572.36 2564.52 2573.31 \ 2582.1 2590.88 2599.67 2605.33 2605.98 2605.33 2604.68 2604.03 2602.91 \ 2601.31 2599.46 2597.62 2595.77 2594.9 2595.07 2595.77 2596.47 2597.17 \ 2600.47 2608.48 2617.67 2626.85 2635.62 2642.71 2636.22 2629.73 2623.24 \ 2616.75 2612.85 2619.3 2626.29 2633.28 2640.27 2642.67 2637.57 2629.99 \ 2622.4 2614.81 2611.02 2611.37 2614.11 2616.86 2619.6 2619.6 2616.26 2611.17 \ 2606.08 2600.99 2598.39 2601.3 2605.59 2609.89 2614.07 2617.82 2616.23 \ 2614.63 2613.03 2611.43 2610.37 2611.43 2612.73 2614.03 2615.32 2614.81 \ 2611.26 2606.47 2601.68 2596.88 2594.96 2596.4 2599.99 2603.59 2607.18 \ 2608.27 2605.88 2601.58 2597.29 2593 2595.06 2614.76 2638.87 2662.98 2686.61 \ 2708.29 2684.09 2659.88 2635.67 2611.46 2591.49 2588.5 2588.5 2588.5 2588.5 \ 2590.45 2595.74 2602.68 2609.62 2616.55 2618.01 2612.55 2602.22 2591.89 \ 2581.56 2576.21 2578.88 2586.07 2593.26 2600.44 2607.15 2612.13 2616.67 \ 2621.21 2625.74 2630.22 2626.77 2623.33 2619.88 2616.44 2612.99 loadtab -continue \ 2609.55 2606.11 2602.66 2599.22 2597.07 2597.19 2598.64 2600.08 2601.53 \ 2605.62 2613.33 2623.81 2634.29 2644.77 2652.25 2654.04 2652.54 2651.04 \ 2649.54 2647.71 2644.23 2640.34 2636.44 2632.55 2628.66 2629.68 2630.85 \ 2632.05 2633.24 2633.21 2628.28 2621.74 2615.2 2608.66 2606.08 2610.65 \ 2620.08 2629.52 2638.95 2646.92 2652.69 2656.63 2660.57 2664.52 2666.13 \ 2662.51 2655.77 2649.03 2642.29 2635.63 2629.55 2623.61 2617.67 2611.73 \ 2605.79 2604.05 2602.58 2601.18 2599.79 2599.38 2602.93 2608.12 2613.31 \ 2618.5 2621.09 2618.81 2612.72 2606.63 2600.54 2596.96 2597.5 2601.75 \ 2605.99 2610.23 2613.63 2614.69 2614.34 2613.99 2613.65 2613.78 2620.36 \ 2628.54 2636.73 2644.92 2653.1 2642.42 2629.74 2616.56 2603.39 2591.72 \ 2586.12 2583.63 2581.13 2578.64 2578.44 2582.69 2590.93 2599.17 2607.4 \ 2613.96 2617.42 2617.92 2618.41 2618.91 2618.35 2614.1 2607.56 2601.02 \ 2594.48 2588.08 2588.91 2591.56 2594.21 2596.85 2599.5 2600.42 2601.08 \ 2601.68 2602.28 2601.47 2595 2585.02 2575.03 2565.05 2557.64 2555.41 2558.46 \ 2561.5 2564.55 2568.01 2572.32 2577.51 2582.71 2587.9 2592.84 2596.61 \ 2599.66 2602.7 2605.75 2608.79 2609.43 2609.41 2609.36 2609.31 2609.26 \ 2601.71 2592.65 2583.22 2573.78 2566.73 2569.2 2578.78 2588.37 2597.95 \ 2606.33 2612.19 2615.13 2618.08 2621.02 2623.93 2626.73 2629.43 2632.12 \ 2634.82 2636.95 2635.31 2631.27 2627.23 2623.18 2619.14 2612.08 2604.11 \ 2596.02 2587.94 2579.85 2587.27 2598.66 2611.04 2623.42 2633.54 2634.63 \ 2627.7 2620.76 2613.82 2607.44 2602.29 2598.75 2595.21 2591.66 2588.57 \ 2586.73 2586.33 2585.93 2585.53 2585.27 2586.59 2588.93 2591.28 2593.62 \ 2595.97 loadtab -continue \ 2598.39 2600.83 2603.28 2605.72 2608.17 2603.75 2597.15 2590.02 2582.88 \ 2576.68 2574.26 2575.8 2577.35 2578.9 2580.17 2580.78 2580.43 2580.08 \ 2579.73 2579.18 2577.95 2575.91 2573.86 2571.81 2569.93 2573.81 2581.5 \ 2589.19 2596.87 2604.56 2604.83 2602.25 2599.01 2595.76 2592.52 2587.59 \ 2582.01 2576.27 2570.53 2566.55 2569.58 2581.36 2593.14 2604.92 2614.68 \ 2619.31 2615.62 2611.92 2608.23 2604.93 2603.35 2603.95 2604.55 2605.15 \ 2605.75 2604.2 2601.2 2598.16 2595.11 2592.07 2591.24 2591.38 2591.78 \ 2592.17 2592.57 2594.39 2596.88 2599.52 2602.17 2603.79 2601.35 2592.92 \ 2584.48 2576.04 2569.1 2566.27 2570.91 2575.55 2580.2 2584.98 2590.63 \ 2597.42 2604.2 2610.99 2617.78 2615.75 2607.44 2598.56 2589.67 2580.79 \ 2581.61 2587.11 2594.09 2601.08 2608.07 2612.43 2615.34 2617.89 2620.43 \ 2621.28 2615.32 2597.5 2579.68 2561.86 2545.33 2532.74 2528.15 2523.55 \ 2518.96 2514.93 2516.28 2525.11 2533.95 2542.78 2551.62 2558.17 2563.03 \ 2567.62 2572.21 2576.8 2578.8 2579.4 2579.5 2579.6 2579.7 2583.61 2590.02 \ 2597.06 2604.1 2609.85 2610.45 2600.37 2590.29 2580.21 2571.23 2566.09 \ 2569.68 2573.28 2576.87 2580.33 2580.66 2576.42 2572.17 2567.93 2563.69 \ 2561.44 2560.75 2560.4 2560.05 2559.7 2560.85 2562.9 2565.29 2567.69 2570.08 \ 2569.47 2566.51 2562.96 2559.42 2556.73 2557.49 2566.82 2576.16 2585.49 \ 2594.16 2600.05 2598.9 2597.75 2596.61 2595.46 2590.82 2580.93 2570.95 \ 2560.97 2550.98 2549.67 2555.46 2563.25 2571.04 2578.82 2584.06 2587.57 \ 2590.37 2593.16 2595.96 2593.43 2586.01 2577.38 2568.74 2560.66 2554.78 \ 2555.58 2556.38 2557.18 2558.01 2559 2560.44 2561.89 2563.34 2564.79 loadtab -continue \ 2563.57 2558.29 2552.7 2547.11 2541.52 2538.77 2538.48 2539.03 2539.58 \ 2540.13 2536.5 2529.72 2521.53 2513.34 2505.16 2504.72 2512.7 2522.78 \ 2532.86 2542.79 2552.08 2559.02 2565.96 2572.9 2579.51 2583.67 2579.98 \ 2576.28 2572.59 2568.9 2567.6 2570.03 2572.98 2575.92 2578.87 2579.6 2578.33 \ 2576.23 2574.13 2572.04 2571.85 2573.28 2575.48 2577.68 2579.87 2580.1 \ 2577.79 2574.85 2571.9 2569.02 2566.36 2564.82 2563.27 2561.72 2560.16 \ 2558.46 2556.21 2553.96 2551.72 2549.47 2548.69 2550.21 2552.21 2554.21 \ 2556.2 2557.23 2557.32 2556.97 2556.62 2556.27 2554.34 2550.9 2546.7 2542.51 \ 2538.32 2536.08 2536.87 2538.42 2539.97 2541.63 2543.76 2548.8 2553.84 \ 2558.88 2563.93 2567.61 2565.86 2564.06 2562.26 2560.47 2560.55 2563.67 \ 2567.61 2571.55 2575.5 2575.67 2571.94 2566.15 2560.36 2554.57 2552.05 \ 2553.07 2555.92 2558.76 2561.61 2561.84 2557.18 2551.29 2545.4 2539.76 \ 2535.17 2539.61 2544.05 2548.5 2552.94 2555.06 2547.91 2540.18 2532.44 \ 2524.7 2520.29 2521.34 2524.28 2527.23 2530.17 2531.76 2531.85 2531.05 \ 2530.25 2529.46 2528.64 2527.8 2526.95 2526.11 2525.26 2523.96 2521.62 \ 2519.03 2516.43 2513.83 2511.24 2508.59 2505.94 2503.3 2500.65 2499.35 \ 2503.43 2508.17 2512.91 2517.65 2521.03 2522.11 2522.21 2522.31 2522.41 \ 2524.63 2529.37 2535.76 2542.15 2548.54 2552.38 2552.58 2550.79 2548.99 \ 2547.19 2545.3 2543.12 2540.88 2538.63 2536.45 2534.53 2540.12 2545.71 \ 2551.3 2556.89 2560.35 2555.28 2548.59 2541.9 2535.22 2532.69 2537.31 2545.6 \ 2553.89 2562.17 2562.24 2551.78 2533.76 2515.74 2497.72 2486.47 2486.45 \ 2492.78 2499.12 2505.46 2510.94 2513.16 2514.56 2515.95 2517.35 loadtab -continue \ 2518.75 simundump group /kinetics/luciferase 0 yellow black x 0 0 "" x؏`ݎ \ /home2/bhalla/scripts/modules/x؏`ݎ_0.g 0 0 0 29 -20 0 simundump kpool /kinetics/luciferase/E.S1_in 0 0 0 1.1043e-12 13.252 0 0 0 \ 1.2e+13 0 "" blue yellow 23 -20 0 simundump kreac /kinetics/luciferase/k5 0 2.6e-05 0 "" white yellow 23 -22 0 simundump kpool /kinetics/luciferase/E.S1 0 0 0 2.5812e-11 309.74 0 0 0 \ 1.2e+13 0 "" blue yellow 23 -24 0 simundump kpool /kinetics/luciferase/S1 0 1e+05 600 600 7.2e+15 7.2e+15 \ 1.2e+18 0 1.2e+13 0 "" blue yellow 23 -26 0 simundump kreac /kinetics/luciferase/k1 0 1.6667e-15 6 "" white yellow 21 -25 \ 0 simundump kpool /kinetics/luciferase/E 0 10 0 1.4267e-10 1712 0 1.2e+14 0 \ 1.2e+13 0 "" 54 yellow 19 -26 0 simundump kreac /kinetics/luciferase/k1_prime 0 8.3335e-14 10 "" white yellow \ 25 -25 0 simundump kpool /kinetics/luciferase/S2 0 1000 1000 1000 1.2e+16 1.2e+16 \ 1.2e+16 0 1.2e+13 0 "" blue yellow 27 -25 0 simundump kreac /kinetics/luciferase/k4 0 0.09 8.3335e-14 "" white yellow 35 \ -22 0 simundump kpool /kinetics/luciferase/E.S1.S2 0 0 0 2.4255e-09 29106 0 0 0 \ 1.2e+13 0 "" 26 yellow 27 -26 0 simundump kreac /kinetics/luciferase/k2 0 30 0 "" white yellow 29 -26 0 simundump kpool /kinetics/luciferase/E.P1 0 0 0 7.2766e-09 87320 0 0 0 \ 1.2e+13 0 "" 1 yellow 31 -26 0 simundump kreac /kinetics/luciferase/k3 0 10 0 "" white yellow 33 -26 0 simundump kpool /kinetics/luciferase/E.P 0 0 0 8.0685e-07 9.6823e+06 0 0 0 \ 1.2e+13 0 "" 58 yellow 35 -26 0 simundump kpool /kinetics/luciferase/P 0 0 0 0.00011853 1.4223e+09 0 0 0 \ 1.2e+13 0 "" blue yellow 37 -26 0 simundump kreac /kinetics/luciferase/k1_prime_2 0 8.3335e-14 10 "" white \ yellow 21 -27 0 simundump kreac /kinetics/luciferase/k1_2 0 1.6667e-15 6 "" white yellow 25 \ -27 0 simundump kpool /kinetics/luciferase/E.S2 0 0 0 7.1466e-09 85759 0 0 0 \ 1.2e+13 0 "" 47 yellow 23 -28 0 simundump kpool /kinetics/luciferase/AMP 0 0 0 0.00011974 1.4368e+09 0 0 0 \ 1.2e+13 0 "" blue yellow 29 -28 0 simundump kpool /kinetics/luciferase/photon 0 0 0 0.00011973 1.4367e+09 0 0 0 \ 1.2e+13 0 "" blue yellow 33 -28 0 simundump kreac /kinetics/luciferase/k5_2 0 2.6e-05 0 "" white yellow 19 -30 \ 0 simundump kreac /kinetics/luciferase/k5_3 0 2.6e-05 0 "" white yellow 23 -30 \ 0 simundump kreac /kinetics/luciferase/k5_4 0 2.6e-05 0 "" white yellow 27 -30 \ 0 simundump kpool /kinetics/luciferase/num_photons 0 0 0 1.4367e+09 1.4367e+09 \ 0 1.4367e+09 0 1 0 "" 62 yellow 30 -30 0 simundump kpool /kinetics/luciferase/PMT_count 0 0 0 4.4592e+06 1.4367e+09 0 \ 1.4367e+09 0 322.2 0 "" 51 yellow 33 -30 0 simundump kreac /kinetics/luciferase/k6 0 0.0003 0 "" white yellow 35 -30 0 simundump kpool /kinetics/luciferase/E.P_in 0 0 0 3.9509e-07 4.7411e+06 0 0 0 \ 1.2e+13 0 "" blue yellow 35 -32 0 simundump kpool /kinetics/luciferase/E.S1.S2_in 0 0 0 1.0377e-10 1245.3 0 0 0 \ 1.2e+13 0 "" blue yellow 27 -32 0 simundump kpool /kinetics/luciferase/E.S2_in 0 0 0 3.0576e-10 3669.2 0 0 0 \ 1.2e+13 0 "" blue yellow 23 -32 0 simundump kpool /kinetics/luciferase/E_in 0 0 0 6.1043e-12 73.252 0 0 0 \ 1.2e+13 0 "" blue yellow 19 -32 0 simundump group /kinetics/Translation 0 16 black x 0 0 "" Translation \ /home2/bhalla/scripts/modules/Translation_0.g 0 0 0 29 -13 0 simundump kpool /kinetics/Translation/Ribosome 0 0.0375 0.00375 1.5138e-05 \ 1.8166e+08 4.5e+10 4.5e+11 0 1.2e+13 0 "" 60 16 24 -13 0 simundump kreac /kinetics/Translation/Rib_RNA_Complex 0 8.3333e-12 2.25 "" \ white 16 23 -11 0 simundump kpool /kinetics/Translation/Rib_mRNA 0 0 0 1.0361e-05 1.2433e+08 0 \ 0 0 1.2e+13 0 "" 44 16 22 -13 0 simundump kreac /kinetics/Translation/Rib_mRNA-decay 0 0.0016667 0 "" white \ 16 21 -11 0 simundump kreac /kinetics/Translation/RibosomeDecay 0 0.001667 0 "" white 16 \ 25 -11 0 simundump kpool /kinetics/Translation/decayed_Ribosome 0 0 0 0.0035549 \ 4.2658e+10 0 0 0 1.2e+13 0 "" 53 16 26 -9 0 simundump kreac /kinetics/Translation/B-subunit-bind-to_ribosome 0 1.1667e-14 \ 2.25 "" white 16 19 -15 0 simundump kpool /kinetics/Translation/primed-mRNA 0 0 0 2.3626e-09 28351 0 0 \ 0 1.2e+13 0 "" 50 16 22 -17 0 simundump kpool /kinetics/Translation/decayed_Rib_mRNA 0 0 0 2.048e+09 \ 2.048e+09 0 0 0 1 0 "" 47 16 20 -9 0 simundump kreac /kinetics/Translation/Protein_Decay 0 2.6e-05 0 "" white 16 \ 25 -15 0 simundump kpool /kinetics/Translation/decayed_protein 0 0 0 6.1043e-12 73.252 \ 0 0 0 1.2e+13 0 "" 1 16 26 -17 0 simundump kpool /kinetics/Translation/B-subunit 0 0.00375 0.00375 0.0037488 \ 4.4985e+10 4.5e+10 4.5e+10 0 1.2e+13 0 "" 1 16 20 -17 0 simundump transport /kinetics/Translation/Prot_synthesis 5 1378 1769.6 1 6 0 \ 0.067 120 5 0.053 edit_transport transport_create_func yellow 16 output \ group "kf dt delay" loadtab /kinetics/Translation/Prot_synthesis table 1 1791 0 1791 \ 1704.29 1704.14 1703.98 1703.83 1703.67 1703.52 1703.36 1703.21 1703.05 \ 1702.9 1702.74 1702.59 1702.43 1702.28 1702.12 1701.97 1701.81 1701.66 \ 1701.5 1701.35 1701.19 1701.04 1700.88 1700.73 1700.57 1700.42 1700.26 \ 1700.11 1699.95 1699.8 1699.65 1699.49 1699.34 1699.18 1699.03 1698.87 \ 1698.72 1698.56 1698.41 1698.25 1698.1 1697.95 1697.79 1697.64 1697.48 \ 1697.33 1697.17 1697.02 1696.86 1696.71 1696.55 1696.4 1696.25 1696.09 \ 1695.94 1695.78 1695.63 1695.47 1695.32 1695.17 1695.01 1694.86 1694.7 \ 1694.55 1694.39 1694.24 1694.09 1693.93 1693.78 1693.62 1693.47 1693.32 \ 1693.16 1693.01 1692.85 1692.7 1692.54 1692.39 1692.24 1692.08 1691.93 \ 1691.77 1691.62 1691.47 1691.31 1691.16 1691 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1741.4 \ 1741.25 1741.09 1740.93 1740.77 1740.61 1740.46 1740.3 1740.14 1739.98 \ 1739.82 1739.67 1739.51 1739.35 1739.19 1739.03 1738.88 1738.72 1738.56 \ 1738.4 1738.24 1738.09 1737.93 1737.77 1737.61 1737.45 1737.3 1737.14 \ 1736.98 1736.82 1736.67 1736.51 1736.35 1736.19 1736.03 1735.88 1735.72 \ 1735.56 1735.4 1735.25 1735.09 1734.93 1734.77 1734.62 1734.46 1734.3 loadtab -continue \ 1734.14 1733.99 1733.83 1733.67 1733.51 1733.36 1733.2 1733.04 1732.88 \ 1732.73 1732.57 1732.41 1732.25 1732.1 1731.94 1731.78 1731.62 1731.47 \ 1731.31 1731.15 1730.99 1730.84 1730.68 1730.52 1730.37 1730.21 1730.05 \ 1729.89 1729.74 1729.58 1729.42 1729.27 1729.11 1728.95 1728.79 1728.64 \ 1728.48 1728.32 1728.17 1728.01 1727.85 1727.69 1727.54 1727.38 1727.22 \ 1727.07 1726.91 1726.75 1726.6 1726.44 1726.28 1726.13 1725.97 1725.81 \ 1725.65 1725.5 1725.34 1725.18 1725.03 1724.87 1724.71 1724.56 1724.4 \ 1724.24 1724.09 1723.93 1723.77 1723.62 1723.46 1723.3 1723.15 1722.99 \ 1722.83 1722.68 1722.52 1722.36 1722.21 1722.05 1721.89 1721.74 1721.58 \ 1721.43 1721.27 1721.11 1720.96 1720.8 1720.64 1720.49 1720.33 1720.17 \ 1720.02 1719.86 1719.7 1719.55 1719.39 1719.24 1719.08 1718.92 1718.77 \ 1718.61 1718.45 1718.3 1718.14 1717.99 1717.83 1717.67 1717.52 1717.36 \ 1717.21 1717.05 1716.89 1716.74 1716.58 1716.42 1716.27 1716.11 1715.96 \ 1715.8 1715.64 1715.49 1715.33 1715.18 1715.02 1714.86 1714.71 1714.55 \ 1714.4 1714.24 1714.09 1713.93 1713.77 1713.62 1713.46 1713.31 1713.15 \ 1712.99 1712.84 1712.68 1712.53 1712.37 1712.22 1712.06 1711.9 1711.75 \ 1711.59 1711.44 1711.28 1711.13 1710.97 1710.81 1710.66 1710.5 1710.35 \ 1710.19 1710.04 1709.88 1709.73 1709.57 1709.41 1709.26 1709.1 1708.95 \ 1708.79 1708.64 1708.48 1708.33 1708.17 1708.02 1707.86 1707.71 1707.55 \ 1707.39 1707.24 1707.08 1706.93 1706.77 1706.62 1706.46 1706.31 1706.15 1706 \ 1705.84 1705.69 1705.53 1705.38 1705.22 1705.07 1704.91 1704.76 1704.6 \ 1704.45 0 simundump xgraph /graphs/conc1 0 0 2992 0 2779.2 0 simundump xgraph /graphs/conc2 0 0 3000 0 0.015347 0 simundump xplot /graphs/conc1/PMT_count.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 51 0 1 1 simundump xplot /graphs/conc1/noOligo.output 3 524288 \ "delete_plot.w ; edit_plot.D " white 0 0 1 simundump xplot /graphs/conc2/mRNA.Co 3 524288 \ "delete_plot.w ; edit_plot.D " blue 0 0 1 simundump xplot /graphs/conc2/E.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 54 0 0 1 simundump xgraph /moregraphs/conc3 0 -1 3000 0 9.7826e-06 0 simundump xgraph /moregraphs/conc4 0 0 3000 0 5e-08 0 simundump xcoredraw /edit/draw 0 -2 39 -34 3 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 \ "Input rate at translation is = 0.00016" \ "" \ "Based on B_binding6.g." \ "Fixed dumping of location of transporters." \ "" 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