//genesis
// kkit Version 11 flat dumpfile
// Saved on Wed Feb 15 14:40:56 2006
include kkit {argv 1}
FASTDT = 5e-05
SIMDT = 0.01
CONTROLDT = 0.1
PLOTDT = 20
MAXTIME = 30000
TRANSIENT_TIME = 2
VARIABLE_DT_FLAG = 1
DEFAULT_VOL = 3e-18
VERSION = 11.0
setfield /file/modpath value /home2/bhalla/scripts/modules
kparms
//genesis
initdump -version 3 -ignoreorphans 1
simobjdump doqcsinfo filename accessname accesstype transcriber developer \
citation species tissue cellcompartment methodology sources \
model_implementation model_validation x y z
simobjdump table input output alloced step_mode stepsize x y z
simobjdump xtree path script namemode sizescale
simobjdump xcoredraw xmin xmax ymin ymax
simobjdump xtext editable
simobjdump xgraph xmin xmax ymin ymax overlay
simobjdump xplot pixflags script fg ysquish do_slope wy
simobjdump group xtree_fg_req xtree_textfg_req plotfield expanded movealone \
link savename file version md5sum mod_save_flag x y z
simobjdump geometry size dim shape outside xtree_fg_req xtree_textfg_req x y \
z
simobjdump kpool DiffConst CoInit Co n nInit mwt nMin vol slave_enable \
geomname xtree_fg_req xtree_textfg_req x y z
simobjdump kreac kf kb notes xtree_fg_req xtree_textfg_req x y z
simobjdump kenz CoComplexInit CoComplex nComplexInit nComplex vol k1 k2 k3 \
keepconc usecomplex notes xtree_fg_req xtree_textfg_req link x y z
simobjdump stim level1 width1 delay1 level2 width2 delay2 baselevel trig_time \
trig_mode notes xtree_fg_req xtree_textfg_req is_running x y z
simobjdump xtab input output alloced step_mode stepsize notes editfunc \
xtree_fg_req xtree_textfg_req baselevel last_x last_y is_running x y z
simobjdump kchan perm gmax Vm is_active use_nernst notes xtree_fg_req \
xtree_textfg_req x y z
simobjdump transport input output alloced step_mode stepsize dt delay clock \
kf xtree_fg_req xtree_textfg_req x y z
simobjdump proto x y z
simundump geometry /kinetics/geometry 0 3e-18 3 sphere "" white black 492 4 0
simundump kpool /kinetics/AI-extracellular 0 0 0 0 0 0 0 0 1800 0 \
/kinetics/geometry brown yellow 575 -18 0
simundump kpool /kinetics/Degraded_AI 0 0 0 0 0 0 0 0 1800 4 \
/kinetics/geometry 2 yellow 397 -18 0
simundump kreac /kinetics/AI_degradation 0 3 0 "" white yellow 479 -20 0
simundump doqcsinfo /kinetics/doqcsinfo 0 \
/home/harsha/DOQCS_DB_files/Upload_model_Dec2006/Quorum_repressilator/Quorum_repressilator.g \
Quorum_repressilator network " Sharat J. Vayttaden and Pragati Jain, NCBS" \
"Jordia Garcia-Ojalvo, Elowitz and Strogatz" \
"Modelling a synthetic multicellular clock: Repressilators coupled by quorum sensing" \
"E. Coli" "E.coli Expression, Transposon Tn10, Lambda phage Expression" \
"Cytosol, Extracellular" Qualitative \
" Garcia-Ojalvo J, Elowitz MB, Strogatz SH. Proc Natl Acad Sci U S A. 2004 Jul 27;101(30):10955-60. ( Peer-reviewed publication )" \
"Exact GENESIS implementation" "Approximates original data " 435 4 0
simundump group /kinetics/TetR 0 61 yellow x 0 0 "" TetR \
/home2/bhalla/scripts/modules/TetR_gene_0.g 0 0 0 311 1 0
simundump kreac /kinetics/TetR/TetR_degradation 0 0.005676 0 "" white 61 303 \
-13 0
simundump kpool /kinetics/TetR/TetR_operator 0 0 0.022222 0.022222 40 40 0 0 \
1800 0 /kinetics/geometry 36 61 334 -8 0
simundump kenz /kinetics/TetR/TetR_operator/TetR_basal_transcription 0 0 0 0 \
0 1800 1079.9 864 216 0 1 "" red 36 "" 334 -7 0
simundump kpool /kinetics/TetR/Nucleotides 0 0 0.00055555 0.00055555 0.99999 \
0.99999 0 0 1800 4 /kinetics/geometry blue 61 323 -4 0
simundump kpool /kinetics/TetR/TetR-1 0 0 0 0 0 0 0 0 1800 0 \
/kinetics/geometry 0 61 303 -11 0
simundump kpool /kinetics/TetR/TetR_operator_1st_bound 0 0 0 0 0 0 0 0 1800 0 \
/kinetics/geometry 2 61 308 -8 0
simundump kenz /kinetics/TetR/TetR_operator_1st_bound/TetR_transcription 0 0 \
0 0 0 1800 0.0024998 0.002 0.0005 0 1 "" red 2 "" 308 -6 0
simundump kpool /kinetics/TetR/TetR_operator_2nd_bound 0 0 0 0 0 0 0 0 1800 0 \
/kinetics/geometry 46 61 282 -8 0
simundump kenz /kinetics/TetR/TetR_operator_2nd_bound/TetR_transcription1 0 0 \
0 0 0 1800 0.0024998 0.002 0.0005 0 1 "" red 46 "" 282 -7 0
simundump kpool /kinetics/TetR/Amino_Acids 0 0 0.00055555 0.00055555 0.99999 \
0.99999 0 0 1800 4 /kinetics/geometry blue 61 303 -4 0
simundump kreac /kinetics/TetR/tetR_mRNA_degradation 0 0.00577 0 "" white 61 \
313 -3 0
simundump kpool /kinetics/TetR/Degraded_tetR_mRNA 0 0 0 0 0 0 0 0 1800 4 \
/kinetics/geometry 1 61 316 -4 0
simundump kpool /kinetics/TetR/Degraded_TetR 0 0 0 0 0 0 0 0 1800 4 \
/kinetics/geometry 2 61 303 -15 0
simundump kreac /kinetics/TetR/TetR_operator_inhibition_reaction 0 0.55556 \
224 "" white 61 319 -9 0
simundump kreac /kinetics/TetR/TetR_operator_inhibition_reaction[1] 0 0.55556 \
9 "" white 61 313 -9 0
simundump kpool /kinetics/TetR/tetR_mRNA1 0 0 0 0 0 0 0 0 1800 0 \
/kinetics/geometry 12 61 309 -4 0
simundump kenz /kinetics/TetR/tetR_mRNA1/tetR_translation 0 0 0 0 0 1800 \
0.83494 0.668 0.167 0 1 "" red 12 "" 303 -6 0
simundump group /kinetics/LacI 0 yellow yellow x 0 0 "" LacI \
/home2/bhalla/scripts/modules/lac_gene_0.g 0 0 0 345 1 0
simundump kpool /kinetics/LacI/Nucleotides 0 0 0.00055555 0.00055555 0.99999 \
0.99999 0 0 1800 4 /kinetics/geometry 6 yellow 358 -4 0
simundump kreac /kinetics/LacI/lac_mRNA_degradation 0 0.00577 0 "" white \
yellow 347 -3 0
simundump kpool /kinetics/LacI/Degraded_lac_mRNA 0 0 0 0 0 0 0 0 1800 4 \
/kinetics/geometry 1 yellow 351 -4 0
simundump kpool /kinetics/LacI/Lac_operator 0 0 0.022222 0.022222 40 40 0 0 \
1800 0 /kinetics/geometry 36 yellow 358 -8 0
simundump kenz /kinetics/LacI/Lac_operator/Lac_basal_transcription 0 0 0 0 0 \
1800 1079.9 864 216 0 1 "" red 36 "" 362 -7 0
simundump kpool /kinetics/LacI/Lac_operator_1st_bound 0 0 0 0 0 0 0 0 1800 0 \
/kinetics/geometry 2 yellow 351 -8 0
simundump kenz /kinetics/LacI/Lac_operator_1st_bound/Lac_transcription 0 0 0 \
0 0 1800 0.0024998 0.002 0.0005 0 1 "" red 2 "" 351 -6 0
simundump kpool /kinetics/LacI/Lac_operator_2nd_bound 0 0 0 0 0 0 0 0 1800 0 \
/kinetics/geometry 52 yellow 344 -8 0
simundump kenz /kinetics/LacI/Lac_operator_2nd_bound/Lac_transcription1 0 0 0 \
0 0 1800 0.0024998 0.002 0.0005 0 1 "" red 52 "" 344 -7 0
simundump kpool /kinetics/LacI/Lac-1 0 0 0 0 0 0 0 0 1800 0 \
/kinetics/geometry 4 yellow 338 -11 0
simundump kreac /kinetics/LacI/Lac_degradation 0 0.005676 0 "" white yellow \
338 -13 0
simundump kpool /kinetics/LacI/Degraded_lac 0 0 0 0 0 0 0 0 1800 4 \
/kinetics/geometry 2 yellow 338 -15 0
simundump kpool /kinetics/LacI/Amino_Acids 0 0 0.00055555 0.00055555 0.99999 \
0.99999 0 0 1800 4 /kinetics/geometry 52 yellow 338 -4 0
simundump kreac /kinetics/LacI/Lac_operator_inhibition_reaction 0 0.55556 224 \
"" white yellow 354 -9 0
simundump kreac /kinetics/LacI/Lac_operator_inhibition_reaction[1] 0 0.55556 \
9 "" white yellow 348 -9 0
simundump kpool /kinetics/LacI/lac_mRNA1 0 0 0 0 0 0 0 0 1800 0 \
/kinetics/geometry 12 yellow 344 -4 0
simundump kenz /kinetics/LacI/lac_mRNA1/lac_translation 0 0 0 0 0 1800 \
0.83494 0.668 0.167 0 1 "" red 12 "" 338 -6 0
simundump group /kinetics/Lambda-cl 0 15 yellow x 0 0 "" Lambda-cl \
/home2/bhalla/scripts/modules/yellow_0.g 0 0 0 386 1 0
simundump kpool /kinetics/Lambda-cl/Nucleotides 0 0 0.00055555 0.00055555 \
0.99999 0.99999 0 0 1800 4 /kinetics/geometry 6 15 400 -4 0
simundump kpool /kinetics/Lambda-cl/Amino_Acids 0 0 0.00055555 0.00055555 \
0.99999 0.99999 0 0 1800 4 /kinetics/geometry 52 15 379 -4 0
simundump kpool /kinetics/Lambda-cl/Lambda-cl-1 0 0 0 0 0 0 0 0 1800 0 \
/kinetics/geometry 0 15 379 -11 0
simundump kpool /kinetics/Lambda-cl/Degraded_lambda-cl_mRNA 0 0 0 0 0 0 0 0 \
1800 4 /kinetics/geometry 1 15 393 -4 0
simundump kpool /kinetics/Lambda-cl/Lambda-cl_operator 0 0 0.022222 0.022222 \
40 40 0 0 1800 0 /kinetics/geometry 36 15 400 -8 0
simundump kenz /kinetics/Lambda-cl/Lambda-cl_operator/Lambda-cl_basal_transcription 0 \
0 0 0 0 1800 1079.9 864 216 0 1 "" red 36 "" 400 -7 0
simundump kreac /kinetics/Lambda-cl/Lambda-cl_operator_inhibition_reaction 0 \
0.55556 224 "" white 15 396 -9 0
simundump kreac /kinetics/Lambda-cl/Lambda-cl_operator_inhibition_reaction[1] 0 \
0.55556 9 "" white 15 390 -9 0
simundump kpool /kinetics/Lambda-cl/Lambda-cl_operator_1st_bound 0 0 0 0 0 0 \
0 0 1800 0 /kinetics/geometry 2 15 393 -8 0
simundump kenz /kinetics/Lambda-cl/Lambda-cl_operator_1st_bound/Lambda-cl_transcription 0 \
0 0 0 0 1800 0.0024998 0.002 0.0005 0 1 "" red 2 "" 393 -6 0
simundump kpool /kinetics/Lambda-cl/Degraded_Lambda-cl 0 0 0 0 0 0 0 0 1800 4 \
/kinetics/geometry 2 15 379 -15 0
simundump kreac /kinetics/Lambda-cl/lambda-cl_mRNA_degradation 0 0.00577 0 "" \
white 15 389 -3 0
simundump kreac /kinetics/Lambda-cl/Lambda-cl_degradation 0 0.005676 0 "" \
white 15 379 -13 0
simundump kpool /kinetics/Lambda-cl/Lambda-cl_operator_2nd_bound 0 0 0 0 0 0 \
0 0 1800 0 /kinetics/geometry 52 15 386 -8 0
simundump kenz /kinetics/Lambda-cl/Lambda-cl_operator_2nd_bound/Lambda-cl_transcription1 0 \
0 0 0 0 1800 0.0024998 0.002 0.0005 0 1 "" red 52 "" 386 -7 0
simundump kpool /kinetics/Lambda-cl/lambda-cl_mRNA1 0 0 0 0 0 0 0 0 1800 0 \
/kinetics/geometry 5 15 386 -4 0
simundump kenz /kinetics/Lambda-cl/lambda-cl_mRNA1/lambda-cl_translation 0 0 \
0 0 0 1800 0.83494 0.668 0.167 0 1 "" red 5 "" 379 -6 0
simundump group /kinetics/LacI_2nd_copy 0 yellow yellow x 0 0 "" \
LacI_2nd_copy /home2/bhalla/scripts/modules/lac_gene_0.g 0 0 0 423 1 0
simundump kpool /kinetics/LacI_2nd_copy/lac_mRNA 0 0 0 0 0 0 0 0 1800 0 \
/kinetics/geometry 12 yellow 417 -4 0
simundump kenz /kinetics/LacI_2nd_copy/lac_mRNA/lac_translation 0 0 0 0 0 \
1800 0.83494 0.668 0.167 0 1 "" red 12 "" 411 -6 0
simundump kpool /kinetics/LacI_2nd_copy/Nucleotides 0 0 0.00055555 0.00055555 \
0.99999 0.99999 0 0 1800 4 /kinetics/geometry 6 yellow 444 -4 0
simundump kreac /kinetics/LacI_2nd_copy/lac_mRNA_degradation 0 0.00577 0 "" \
white yellow 425 -3 0
simundump kpool /kinetics/LacI_2nd_copy/Degraded_lac_mRNA 0 0 0 0 0 0 0 0 \
1800 4 /kinetics/geometry 1 yellow 429 -4 0
simundump kpool /kinetics/LacI_2nd_copy/Lac_operator 0 0 0.022222 0.022222 40 \
40 0 0 1800 0 /kinetics/geometry 36 yellow 435 -8 0
simundump kenz /kinetics/LacI_2nd_copy/Lac_operator/Lac_basal_transcription 0 \
0 0 0 0 1800 1079.9 864 216 0 1 "" red 36 "" 436 -7 0
simundump kpool /kinetics/LacI_2nd_copy/Lac_operator_1st_bound 0 0 0 0 0 0 0 \
0 1800 0 /kinetics/geometry 2 yellow 428 -8 0
simundump kenz /kinetics/LacI_2nd_copy/Lac_operator_1st_bound/Lac_transcription 0 \
0 0 0 0 1800 0.0024998 0.002 0.0005 0 1 "" red 2 "" 428 -6 0
simundump kpool /kinetics/LacI_2nd_copy/Lac_operator_2nd_bound 0 0 0 0 0 0 0 \
0 1800 0 /kinetics/geometry 52 yellow 422 -8 0
simundump kenz /kinetics/LacI_2nd_copy/Lac_operator_2nd_bound/Lac_transcription1 0 \
0 0 0 0 1800 0.0024998 0.002 0.0005 0 1 "" red 52 "" 422 -7 0
simundump kpool /kinetics/LacI_2nd_copy/Amino_Acids 0 0 0.00055555 0.00055555 \
0.99999 0.99999 0 0 1800 4 /kinetics/geometry 52 yellow 411 -4 0
simundump kreac /kinetics/LacI_2nd_copy/Lac_operator_inhibition_reaction 0 \
0.55556 224 "" white yellow 432 -9 0
simundump kreac /kinetics/LacI_2nd_copy/Lac_operator_inhibition_reaction[1] 0 \
0.55556 9 "" white yellow 426 -9 0
simundump kreac /kinetics/LacI_2nd_copy/Lac_operator_activation_reaction 0 \
1000 224 "" white yellow 406 -11 0
simundump kpool /kinetics/LacI_2nd_copy/Lac_operator_activator_bound 0 0 0 0 \
0 0 0 0 1800 0 /kinetics/geometry 24 yellow 445 -8 0
simundump kenz /kinetics/LacI_2nd_copy/Lac_operator_activator_bound/Lac_active_transcription 0 \
0 0 0 0 1800 99.992 80 20 0 1 "" red 24 "" 441 -6 0
simundump group /kinetics/LuxI 0 1 yellow x 0 0 "" LuxI \
/home2/bhalla/scripts/modules/yellow_0.g 0 0 0 470 1 0
simundump kpool /kinetics/LuxI/Nucleotides 0 0 0.00055555 0.00055555 0.99999 \
0.99999 0 0 1800 4 /kinetics/geometry 6 1 483 -4 0
simundump kpool /kinetics/LuxI/luxI_mRNA 0 0 0 0 0 0 0 0 1800 0 \
/kinetics/geometry 5 1 469 -4 0
simundump kenz /kinetics/LuxI/luxI_mRNA/luxI_translation 0 0 0 0 0 1800 \
0.83494 0.668 0.167 0 1 "" red 5 "" 460 -6 0
simundump kreac /kinetics/LuxI/luxI_mRNA_degradation 0 0.00577 0 "" white 1 \
472 -3 0
simundump kreac /kinetics/LuxI/AI_degradation 0 0.2 0 "" white 1 462 -13 0
simundump kpool /kinetics/LuxI/LuxR 0 0 0.055555 0.055555 99.999 99.999 0 0 \
1800 4 /kinetics/geometry 12 1 454 -7 0
simundump kreac /kinetics/LuxI/LuxR_binding_autoinducer 0 0.0027778 0.1 "" \
white 1 454 -10 0
simundump kpool /kinetics/LuxI/LuxR-AI 0 0 0 0 0 0 0 0 1800 0 \
/kinetics/geometry 51 1 446 -11 0
simundump kpool /kinetics/LuxI/AI-1 0 0 0 0 0 0 0 0 1800 0 /kinetics/geometry \
4 1 462 -11 0
simundump kreac /kinetics/LuxI/AI_diffusion 0 2 2 "" white 1 478 -11 0
simundump kpool /kinetics/LuxI/Degraded_luxI_mRNA 0 0 0 0 0 0 0 0 1800 4 \
/kinetics/geometry 1 1 476 -4 0
simundump kreac /kinetics/LuxI/LuxR-AI_complex_dimerization 0 0.001 0.1 "" \
white 1 431 -10 0
simundump kpool /kinetics/LuxI/Amino_Acids 0 0 0.00055555 0.00055555 0.99999 \
0.99999 0 0 1800 4 /kinetics/geometry 52 1 462 -4 0
simundump kpool /kinetics/LuxI/LuxI_operator_1st_bound 0 0 0 0 0 0 0 0 1800 0 \
/kinetics/geometry 2 1 476 -8 0
simundump kenz /kinetics/LuxI/LuxI_operator_1st_bound/LuxI_transcription 0 0 \
0 0 0 1800 0.0024998 0.002 0.0005 0 1 "" red 2 "" 476 -6 0
simundump kpool /kinetics/LuxI/LuxI_operator_2nd_bound 0 0 0 0 0 0 0 0 1800 0 \
/kinetics/geometry 52 1 469 -8 0
simundump kenz /kinetics/LuxI/LuxI_operator_2nd_bound/LuxI_transcription1 0 0 \
0 0 0 1800 0.0024998 0.002 0.0005 0 1 "" red 52 "" 469 -7 0
simundump kpool /kinetics/LuxI/LuxI_operator 0 0 0.022222 0.022222 40 40 0 0 \
1800 0 /kinetics/geometry 36 1 483 -8 0
simundump kenz /kinetics/LuxI/LuxI_operator/LuxI_basal_transcription 0 0 0 0 \
0 1800 1079.9 864 216 0 1 "" red 36 "" 483 -7 0
simundump kreac /kinetics/LuxI/LuxR-AI_degradation 0 0.2 0 "" white 1 446 -13 \
0
simundump kpool /kinetics/LuxI/Degraded_AI 0 0 0 0 0 0 0 0 1800 4 \
/kinetics/geometry 2 1 462 -15 0
simundump kpool /kinetics/LuxI/Degraded_LuxR-AI 0 0 0 0 0 0 0 0 1800 4 \
/kinetics/geometry 2 1 446 -15 0
simundump kreac /kinetics/LuxI/LuxI_operator_inhibitor_reaction[1] 0 0.55556 \
9 "" white 1 473 -9 0
simundump kreac /kinetics/LuxI/LuxI_operator_inhibitor_reaction 0 0.55556 224 \
"" white 1 480 -9 0
simundump kpool /kinetics/LuxI/LuxI 0 0 0 0 0 0 0 0 1800 0 /kinetics/geometry \
blue 1 491 -11 0
simundump kreac /kinetics/LuxI/LuxI_degradation 0 25 0 "" white 1 486 -13 0
simundump kpool /kinetics/LuxI/degraded_LuxI 0 0 0 0 0 0 0 0 1800 4 \
/kinetics/geometry blue 1 488 -15 0
simundump kreac /kinetics/LuxI/AI_form 0 0.01 0 "" 1 1 484 -10 0
simundump kpool /kinetics/LuxI/2_LuxR-AI 0 0 0 0 0 0 0 0 1800 0 \
/kinetics/geometry 62 1 428 -11 0
simundump kpool /kinetics/LuxI/Degraded_2_LuxR-AI 0 0 0 0 0 0 0 0 1800 4 \
/kinetics/geometry 2 1 425 -15 0
simundump kreac /kinetics/LuxI/2_LuxR-AI_degradation 0 0.2 0 "" white 1 428 \
-13 0
simundump xgraph /graphs/conc1 0 0 30000 0.00011999 111.74 0
simundump xgraph /graphs/conc2 0 0 30000 0 1 0
simundump xplot /graphs/conc1/lambda-cl_mRNA1.Co 3 524288 \
"delete_plot.w ; edit_plot.D " 5 0 0 1
simundump xgraph /moregraphs/conc3 0 0 30000 0 1 0
simundump xgraph /moregraphs/conc4 0 0 30000 0 1 0
simundump xcoredraw /edit/draw 0 280 577 -22 7
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 \
"Cleaned up version of a single cell." \
"Repressilator coupled to quorum sensing mechanism:" \
"A synthetic oscillatory network of transcriptional regulators " \
"coupled to quorum sensing module." \
"" \
"Garcia-Ojalvo, J. et al. (2004)" \
"PNAS USA 101(30):10955-10960"
addmsg /kinetics/LuxI/AI_diffusion /kinetics/AI-extracellular REAC B A
addmsg /kinetics/AI_degradation /kinetics/AI-extracellular REAC A B
addmsg /kinetics/AI_degradation /kinetics/Degraded_AI REAC B A
addmsg /kinetics/AI-extracellular /kinetics/AI_degradation SUBSTRATE n
addmsg /kinetics/Degraded_AI /kinetics/AI_degradation PRODUCT n
addmsg /kinetics/TetR/TetR-1 /kinetics/TetR/TetR_degradation SUBSTRATE n
addmsg /kinetics/TetR/Degraded_TetR /kinetics/TetR/TetR_degradation PRODUCT n
addmsg /kinetics/TetR/TetR_operator_inhibition_reaction /kinetics/TetR/TetR_operator REAC A B
addmsg /kinetics/TetR/TetR_operator /kinetics/TetR/TetR_operator/TetR_basal_transcription ENZYME n
addmsg /kinetics/TetR/Nucleotides /kinetics/TetR/TetR_operator/TetR_basal_transcription SUBSTRATE n
addmsg /kinetics/TetR/TetR_operator/TetR_basal_transcription /kinetics/TetR/Nucleotides REAC sA B
addmsg /kinetics/TetR/TetR_operator_1st_bound/TetR_transcription /kinetics/TetR/Nucleotides REAC sA B
addmsg /kinetics/TetR/TetR_operator_2nd_bound/TetR_transcription1 /kinetics/TetR/Nucleotides REAC sA B
addmsg /kinetics/TetR/tetR_mRNA1/tetR_translation /kinetics/TetR/TetR-1 MM_PRD pA
addmsg /kinetics/TetR/TetR_degradation /kinetics/TetR/TetR-1 REAC A B
addmsg /kinetics/Lambda-cl/Lambda-cl_operator_inhibition_reaction[1] /kinetics/TetR/TetR-1 REAC A B
addmsg /kinetics/Lambda-cl/Lambda-cl_operator_inhibition_reaction /kinetics/TetR/TetR-1 REAC A B
addmsg /kinetics/TetR/TetR_operator_inhibition_reaction[1] /kinetics/TetR/TetR_operator_1st_bound REAC A B
addmsg /kinetics/TetR/TetR_operator_inhibition_reaction /kinetics/TetR/TetR_operator_1st_bound REAC B A
addmsg /kinetics/TetR/TetR_operator_1st_bound /kinetics/TetR/TetR_operator_1st_bound/TetR_transcription ENZYME n
addmsg /kinetics/TetR/Nucleotides /kinetics/TetR/TetR_operator_1st_bound/TetR_transcription SUBSTRATE n
addmsg /kinetics/TetR/TetR_operator_inhibition_reaction[1] /kinetics/TetR/TetR_operator_2nd_bound REAC B A
addmsg /kinetics/TetR/TetR_operator_2nd_bound /kinetics/TetR/TetR_operator_2nd_bound/TetR_transcription1 ENZYME n
addmsg /kinetics/TetR/Nucleotides /kinetics/TetR/TetR_operator_2nd_bound/TetR_transcription1 SUBSTRATE n
addmsg /kinetics/TetR/tetR_mRNA1/tetR_translation /kinetics/TetR/Amino_Acids REAC sA B
addmsg /kinetics/TetR/tetR_mRNA1 /kinetics/TetR/tetR_mRNA_degradation SUBSTRATE n
addmsg /kinetics/TetR/Degraded_tetR_mRNA /kinetics/TetR/tetR_mRNA_degradation PRODUCT n
addmsg /kinetics/TetR/tetR_mRNA_degradation /kinetics/TetR/Degraded_tetR_mRNA REAC B A
addmsg /kinetics/TetR/TetR_degradation /kinetics/TetR/Degraded_TetR REAC B A
addmsg /kinetics/TetR/TetR_operator_1st_bound /kinetics/TetR/TetR_operator_inhibition_reaction PRODUCT n
addmsg /kinetics/TetR/TetR_operator /kinetics/TetR/TetR_operator_inhibition_reaction SUBSTRATE n
addmsg /kinetics/LacI/Lac-1 /kinetics/TetR/TetR_operator_inhibition_reaction SUBSTRATE n
addmsg /kinetics/TetR/TetR_operator_2nd_bound /kinetics/TetR/TetR_operator_inhibition_reaction[1] PRODUCT n
addmsg /kinetics/TetR/TetR_operator_1st_bound /kinetics/TetR/TetR_operator_inhibition_reaction[1] SUBSTRATE n
addmsg /kinetics/LacI/Lac-1 /kinetics/TetR/TetR_operator_inhibition_reaction[1] SUBSTRATE n
addmsg /kinetics/TetR/TetR_operator_2nd_bound/TetR_transcription1 /kinetics/TetR/tetR_mRNA1 MM_PRD pA
addmsg /kinetics/TetR/TetR_operator_1st_bound/TetR_transcription /kinetics/TetR/tetR_mRNA1 MM_PRD pA
addmsg /kinetics/TetR/TetR_operator/TetR_basal_transcription /kinetics/TetR/tetR_mRNA1 MM_PRD pA
addmsg /kinetics/TetR/tetR_mRNA_degradation /kinetics/TetR/tetR_mRNA1 REAC A B
addmsg /kinetics/TetR/tetR_mRNA1 /kinetics/TetR/tetR_mRNA1/tetR_translation ENZYME n
addmsg /kinetics/TetR/Amino_Acids /kinetics/TetR/tetR_mRNA1/tetR_translation SUBSTRATE n
addmsg /kinetics/LacI/Lac_operator/Lac_basal_transcription /kinetics/LacI/Nucleotides REAC sA B
addmsg /kinetics/LacI/Lac_operator_2nd_bound/Lac_transcription1 /kinetics/LacI/Nucleotides REAC sA B
addmsg /kinetics/LacI/Lac_operator_1st_bound/Lac_transcription /kinetics/LacI/Nucleotides REAC sA B
addmsg /kinetics/LacI/lac_mRNA1 /kinetics/LacI/lac_mRNA_degradation SUBSTRATE n
addmsg /kinetics/LacI/Degraded_lac_mRNA /kinetics/LacI/lac_mRNA_degradation PRODUCT n
addmsg /kinetics/Lambda-cl/Nucleotides /kinetics/LacI/lac_mRNA_degradation PRODUCT n
addmsg /kinetics/LacI/lac_mRNA_degradation /kinetics/LacI/Degraded_lac_mRNA REAC B A
addmsg /kinetics/LacI/Lac_operator_inhibition_reaction /kinetics/LacI/Lac_operator REAC A B
addmsg /kinetics/LacI/Lac_operator /kinetics/LacI/Lac_operator/Lac_basal_transcription ENZYME n
addmsg /kinetics/LacI/Nucleotides /kinetics/LacI/Lac_operator/Lac_basal_transcription SUBSTRATE n
addmsg /kinetics/LacI/Lac_operator_inhibition_reaction /kinetics/LacI/Lac_operator_1st_bound REAC B A
addmsg /kinetics/LacI/Lac_operator_inhibition_reaction[1] /kinetics/LacI/Lac_operator_1st_bound REAC A B
addmsg /kinetics/LacI/Lac_operator_1st_bound /kinetics/LacI/Lac_operator_1st_bound/Lac_transcription ENZYME n
addmsg /kinetics/LacI/Nucleotides /kinetics/LacI/Lac_operator_1st_bound/Lac_transcription SUBSTRATE n
addmsg /kinetics/LacI/Lac_operator_inhibition_reaction[1] /kinetics/LacI/Lac_operator_2nd_bound REAC B A
addmsg /kinetics/LacI/Lac_operator_2nd_bound /kinetics/LacI/Lac_operator_2nd_bound/Lac_transcription1 ENZYME n
addmsg /kinetics/LacI/Nucleotides /kinetics/LacI/Lac_operator_2nd_bound/Lac_transcription1 SUBSTRATE n
addmsg /kinetics/LacI/Lac_degradation /kinetics/LacI/Lac-1 REAC A B
addmsg /kinetics/LacI/lac_mRNA1/lac_translation /kinetics/LacI/Lac-1 MM_PRD pA
addmsg /kinetics/TetR/TetR_operator_inhibition_reaction /kinetics/LacI/Lac-1 REAC A B
addmsg /kinetics/TetR/TetR_operator_inhibition_reaction[1] /kinetics/LacI/Lac-1 REAC A B
addmsg /kinetics/LuxI/LuxI_operator_inhibitor_reaction[1] /kinetics/LacI/Lac-1 REAC A B
addmsg /kinetics/LuxI/LuxI_operator_inhibitor_reaction /kinetics/LacI/Lac-1 REAC A B
addmsg /kinetics/LacI_2nd_copy/lac_mRNA/lac_translation /kinetics/LacI/Lac-1 MM_PRD pA
addmsg /kinetics/LacI/Degraded_lac /kinetics/LacI/Lac_degradation PRODUCT n
addmsg /kinetics/LacI/Lac-1 /kinetics/LacI/Lac_degradation SUBSTRATE n
addmsg /kinetics/LacI/Lac_degradation /kinetics/LacI/Degraded_lac REAC B A
addmsg /kinetics/LacI/lac_mRNA1/lac_translation /kinetics/LacI/Amino_Acids REAC sA B
addmsg /kinetics/LacI/Lac_operator /kinetics/LacI/Lac_operator_inhibition_reaction SUBSTRATE n
addmsg /kinetics/LacI/Lac_operator_1st_bound /kinetics/LacI/Lac_operator_inhibition_reaction PRODUCT n
addmsg /kinetics/Lambda-cl/Lambda-cl-1 /kinetics/LacI/Lac_operator_inhibition_reaction SUBSTRATE n
addmsg /kinetics/LacI/Lac_operator_1st_bound /kinetics/LacI/Lac_operator_inhibition_reaction[1] SUBSTRATE n
addmsg /kinetics/LacI/Lac_operator_2nd_bound /kinetics/LacI/Lac_operator_inhibition_reaction[1] PRODUCT n
addmsg /kinetics/Lambda-cl/Lambda-cl-1 /kinetics/LacI/Lac_operator_inhibition_reaction[1] SUBSTRATE n
addmsg /kinetics/LacI/Lac_operator/Lac_basal_transcription /kinetics/LacI/lac_mRNA1 MM_PRD pA
addmsg /kinetics/LacI/Lac_operator_2nd_bound/Lac_transcription1 /kinetics/LacI/lac_mRNA1 MM_PRD pA
addmsg /kinetics/LacI/Lac_operator_1st_bound/Lac_transcription /kinetics/LacI/lac_mRNA1 MM_PRD pA
addmsg /kinetics/LacI/lac_mRNA_degradation /kinetics/LacI/lac_mRNA1 REAC A B
addmsg /kinetics/LacI/lac_mRNA1 /kinetics/LacI/lac_mRNA1/lac_translation ENZYME n
addmsg /kinetics/LacI/Amino_Acids /kinetics/LacI/lac_mRNA1/lac_translation SUBSTRATE n
addmsg /kinetics/Lambda-cl/Lambda-cl_operator_2nd_bound/Lambda-cl_transcription1 /kinetics/Lambda-cl/Nucleotides REAC sA B
addmsg /kinetics/Lambda-cl/Lambda-cl_operator_1st_bound/Lambda-cl_transcription /kinetics/Lambda-cl/Nucleotides REAC sA B
addmsg /kinetics/Lambda-cl/Lambda-cl_operator/Lambda-cl_basal_transcription /kinetics/Lambda-cl/Nucleotides REAC sA B
addmsg /kinetics/LacI/lac_mRNA_degradation /kinetics/Lambda-cl/Nucleotides REAC B A
addmsg /kinetics/Lambda-cl/lambda-cl_mRNA1/lambda-cl_translation /kinetics/Lambda-cl/Amino_Acids REAC sA B
addmsg /kinetics/Lambda-cl/lambda-cl_mRNA1/lambda-cl_translation /kinetics/Lambda-cl/Lambda-cl-1 MM_PRD pA
addmsg /kinetics/LacI/Lac_operator_inhibition_reaction /kinetics/Lambda-cl/Lambda-cl-1 REAC A B
addmsg /kinetics/LacI/Lac_operator_inhibition_reaction[1] /kinetics/Lambda-cl/Lambda-cl-1 REAC A B
addmsg /kinetics/Lambda-cl/Lambda-cl_degradation /kinetics/Lambda-cl/Lambda-cl-1 REAC A B
addmsg /kinetics/LacI_2nd_copy/Lac_operator_inhibition_reaction[1] /kinetics/Lambda-cl/Lambda-cl-1 REAC A B
addmsg /kinetics/LacI_2nd_copy/Lac_operator_inhibition_reaction /kinetics/Lambda-cl/Lambda-cl-1 REAC A B
addmsg /kinetics/Lambda-cl/lambda-cl_mRNA_degradation /kinetics/Lambda-cl/Degraded_lambda-cl_mRNA REAC B A
addmsg /kinetics/Lambda-cl/Lambda-cl_operator_inhibition_reaction /kinetics/Lambda-cl/Lambda-cl_operator REAC A B
addmsg /kinetics/Lambda-cl/Lambda-cl_operator /kinetics/Lambda-cl/Lambda-cl_operator/Lambda-cl_basal_transcription ENZYME n
addmsg /kinetics/Lambda-cl/Nucleotides /kinetics/Lambda-cl/Lambda-cl_operator/Lambda-cl_basal_transcription SUBSTRATE n
addmsg /kinetics/Lambda-cl/Lambda-cl_operator_1st_bound /kinetics/Lambda-cl/Lambda-cl_operator_inhibition_reaction PRODUCT n
addmsg /kinetics/Lambda-cl/Lambda-cl_operator /kinetics/Lambda-cl/Lambda-cl_operator_inhibition_reaction SUBSTRATE n
addmsg /kinetics/TetR/TetR-1 /kinetics/Lambda-cl/Lambda-cl_operator_inhibition_reaction SUBSTRATE n
addmsg /kinetics/Lambda-cl/Lambda-cl_operator_2nd_bound /kinetics/Lambda-cl/Lambda-cl_operator_inhibition_reaction[1] PRODUCT n
addmsg /kinetics/Lambda-cl/Lambda-cl_operator_1st_bound /kinetics/Lambda-cl/Lambda-cl_operator_inhibition_reaction[1] SUBSTRATE n
addmsg /kinetics/TetR/TetR-1 /kinetics/Lambda-cl/Lambda-cl_operator_inhibition_reaction[1] SUBSTRATE n
addmsg /kinetics/Lambda-cl/Lambda-cl_operator_inhibition_reaction[1] /kinetics/Lambda-cl/Lambda-cl_operator_1st_bound REAC A B
addmsg /kinetics/Lambda-cl/Lambda-cl_operator_inhibition_reaction /kinetics/Lambda-cl/Lambda-cl_operator_1st_bound REAC B A
addmsg /kinetics/Lambda-cl/Lambda-cl_operator_1st_bound /kinetics/Lambda-cl/Lambda-cl_operator_1st_bound/Lambda-cl_transcription ENZYME n
addmsg /kinetics/Lambda-cl/Nucleotides /kinetics/Lambda-cl/Lambda-cl_operator_1st_bound/Lambda-cl_transcription SUBSTRATE n
addmsg /kinetics/Lambda-cl/Lambda-cl_degradation /kinetics/Lambda-cl/Degraded_Lambda-cl REAC B A
addmsg /kinetics/Lambda-cl/lambda-cl_mRNA1 /kinetics/Lambda-cl/lambda-cl_mRNA_degradation SUBSTRATE n
addmsg /kinetics/Lambda-cl/Degraded_lambda-cl_mRNA /kinetics/Lambda-cl/lambda-cl_mRNA_degradation PRODUCT n
addmsg /kinetics/Lambda-cl/Lambda-cl-1 /kinetics/Lambda-cl/Lambda-cl_degradation SUBSTRATE n
addmsg /kinetics/Lambda-cl/Degraded_Lambda-cl /kinetics/Lambda-cl/Lambda-cl_degradation PRODUCT n
addmsg /kinetics/Lambda-cl/Lambda-cl_operator_inhibition_reaction[1] /kinetics/Lambda-cl/Lambda-cl_operator_2nd_bound REAC B A
addmsg /kinetics/Lambda-cl/Lambda-cl_operator_2nd_bound /kinetics/Lambda-cl/Lambda-cl_operator_2nd_bound/Lambda-cl_transcription1 ENZYME n
addmsg /kinetics/Lambda-cl/Nucleotides /kinetics/Lambda-cl/Lambda-cl_operator_2nd_bound/Lambda-cl_transcription1 SUBSTRATE n
addmsg /kinetics/Lambda-cl/Lambda-cl_operator_2nd_bound/Lambda-cl_transcription1 /kinetics/Lambda-cl/lambda-cl_mRNA1 MM_PRD pA
addmsg /kinetics/Lambda-cl/Lambda-cl_operator_1st_bound/Lambda-cl_transcription /kinetics/Lambda-cl/lambda-cl_mRNA1 MM_PRD pA
addmsg /kinetics/Lambda-cl/Lambda-cl_operator/Lambda-cl_basal_transcription /kinetics/Lambda-cl/lambda-cl_mRNA1 MM_PRD pA
addmsg /kinetics/Lambda-cl/lambda-cl_mRNA_degradation /kinetics/Lambda-cl/lambda-cl_mRNA1 REAC A B
addmsg /kinetics/Lambda-cl/lambda-cl_mRNA1 /kinetics/Lambda-cl/lambda-cl_mRNA1/lambda-cl_translation ENZYME n
addmsg /kinetics/Lambda-cl/Amino_Acids /kinetics/Lambda-cl/lambda-cl_mRNA1/lambda-cl_translation SUBSTRATE n
addmsg /kinetics/LacI_2nd_copy/lac_mRNA_degradation /kinetics/LacI_2nd_copy/lac_mRNA REAC A B
addmsg /kinetics/LacI_2nd_copy/Lac_operator/Lac_basal_transcription /kinetics/LacI_2nd_copy/lac_mRNA MM_PRD pA
addmsg /kinetics/LacI_2nd_copy/Lac_operator_1st_bound/Lac_transcription /kinetics/LacI_2nd_copy/lac_mRNA MM_PRD pA
addmsg /kinetics/LacI_2nd_copy/Lac_operator_2nd_bound/Lac_transcription1 /kinetics/LacI_2nd_copy/lac_mRNA MM_PRD pA
addmsg /kinetics/LacI_2nd_copy/Lac_operator_activator_bound/Lac_active_transcription /kinetics/LacI_2nd_copy/lac_mRNA MM_PRD pA
addmsg /kinetics/LacI_2nd_copy/lac_mRNA /kinetics/LacI_2nd_copy/lac_mRNA/lac_translation ENZYME n
addmsg /kinetics/LacI_2nd_copy/Amino_Acids /kinetics/LacI_2nd_copy/lac_mRNA/lac_translation SUBSTRATE n
addmsg /kinetics/LacI_2nd_copy/Lac_operator/Lac_basal_transcription /kinetics/LacI_2nd_copy/Nucleotides REAC sA B
addmsg /kinetics/LacI_2nd_copy/Lac_operator_1st_bound/Lac_transcription /kinetics/LacI_2nd_copy/Nucleotides REAC sA B
addmsg /kinetics/LacI_2nd_copy/Lac_operator_2nd_bound/Lac_transcription1 /kinetics/LacI_2nd_copy/Nucleotides REAC sA B
addmsg /kinetics/LacI_2nd_copy/Lac_operator_activator_bound/Lac_active_transcription /kinetics/LacI_2nd_copy/Nucleotides REAC sA B
addmsg /kinetics/LacI_2nd_copy/lac_mRNA /kinetics/LacI_2nd_copy/lac_mRNA_degradation SUBSTRATE n
addmsg /kinetics/LacI_2nd_copy/Degraded_lac_mRNA /kinetics/LacI_2nd_copy/lac_mRNA_degradation PRODUCT n
addmsg /kinetics/LacI_2nd_copy/lac_mRNA_degradation /kinetics/LacI_2nd_copy/Degraded_lac_mRNA REAC B A
addmsg /kinetics/LacI_2nd_copy/Lac_operator_inhibition_reaction /kinetics/LacI_2nd_copy/Lac_operator REAC A B
addmsg /kinetics/LacI_2nd_copy/Nucleotides /kinetics/LacI_2nd_copy/Lac_operator/Lac_basal_transcription SUBSTRATE n
addmsg /kinetics/LacI_2nd_copy/Lac_operator /kinetics/LacI_2nd_copy/Lac_operator/Lac_basal_transcription ENZYME n
addmsg /kinetics/LacI_2nd_copy/Lac_operator_inhibition_reaction /kinetics/LacI_2nd_copy/Lac_operator_1st_bound REAC B A
addmsg /kinetics/LacI_2nd_copy/Lac_operator_inhibition_reaction[1] /kinetics/LacI_2nd_copy/Lac_operator_1st_bound REAC A B
addmsg /kinetics/LacI_2nd_copy/Nucleotides /kinetics/LacI_2nd_copy/Lac_operator_1st_bound/Lac_transcription SUBSTRATE n
addmsg /kinetics/LacI_2nd_copy/Lac_operator_1st_bound /kinetics/LacI_2nd_copy/Lac_operator_1st_bound/Lac_transcription ENZYME n
addmsg /kinetics/LacI_2nd_copy/Lac_operator_inhibition_reaction[1] /kinetics/LacI_2nd_copy/Lac_operator_2nd_bound REAC B A
addmsg /kinetics/LacI_2nd_copy/Nucleotides /kinetics/LacI_2nd_copy/Lac_operator_2nd_bound/Lac_transcription1 SUBSTRATE n
addmsg /kinetics/LacI_2nd_copy/Lac_operator_2nd_bound /kinetics/LacI_2nd_copy/Lac_operator_2nd_bound/Lac_transcription1 ENZYME n
addmsg /kinetics/LacI_2nd_copy/lac_mRNA/lac_translation /kinetics/LacI_2nd_copy/Amino_Acids REAC sA B
addmsg /kinetics/LacI_2nd_copy/Lac_operator /kinetics/LacI_2nd_copy/Lac_operator_inhibition_reaction SUBSTRATE n
addmsg /kinetics/LacI_2nd_copy/Lac_operator_1st_bound /kinetics/LacI_2nd_copy/Lac_operator_inhibition_reaction PRODUCT n
addmsg /kinetics/Lambda-cl/Lambda-cl-1 /kinetics/LacI_2nd_copy/Lac_operator_inhibition_reaction SUBSTRATE n
addmsg /kinetics/LacI_2nd_copy/Lac_operator_1st_bound /kinetics/LacI_2nd_copy/Lac_operator_inhibition_reaction[1] SUBSTRATE n
addmsg /kinetics/LacI_2nd_copy/Lac_operator_2nd_bound /kinetics/LacI_2nd_copy/Lac_operator_inhibition_reaction[1] PRODUCT n
addmsg /kinetics/Lambda-cl/Lambda-cl-1 /kinetics/LacI_2nd_copy/Lac_operator_inhibition_reaction[1] SUBSTRATE n
addmsg /kinetics/LacI_2nd_copy/Lac_operator_activator_bound /kinetics/LacI_2nd_copy/Lac_operator_activation_reaction PRODUCT n
addmsg /kinetics/LuxI/2_LuxR-AI /kinetics/LacI_2nd_copy/Lac_operator_activation_reaction SUBSTRATE n
addmsg /kinetics/LacI_2nd_copy/Lac_operator_activation_reaction /kinetics/LacI_2nd_copy/Lac_operator_activator_bound REAC B A
addmsg /kinetics/LacI_2nd_copy/Lac_operator_activator_bound /kinetics/LacI_2nd_copy/Lac_operator_activator_bound/Lac_active_transcription ENZYME n
addmsg /kinetics/LacI_2nd_copy/Nucleotides /kinetics/LacI_2nd_copy/Lac_operator_activator_bound/Lac_active_transcription SUBSTRATE n
addmsg /kinetics/LuxI/LuxI_operator_2nd_bound/LuxI_transcription1 /kinetics/LuxI/Nucleotides REAC sA B
addmsg /kinetics/LuxI/LuxI_operator_1st_bound/LuxI_transcription /kinetics/LuxI/Nucleotides REAC sA B
addmsg /kinetics/LuxI/LuxI_operator/LuxI_basal_transcription /kinetics/LuxI/Nucleotides REAC sA B
addmsg /kinetics/LuxI/LuxI_operator_2nd_bound/LuxI_transcription1 /kinetics/LuxI/luxI_mRNA MM_PRD pA
addmsg /kinetics/LuxI/LuxI_operator_1st_bound/LuxI_transcription /kinetics/LuxI/luxI_mRNA MM_PRD pA
addmsg /kinetics/LuxI/luxI_mRNA_degradation /kinetics/LuxI/luxI_mRNA REAC A B
addmsg /kinetics/LuxI/LuxI_operator/LuxI_basal_transcription /kinetics/LuxI/luxI_mRNA MM_PRD pA
addmsg /kinetics/LuxI/Amino_Acids /kinetics/LuxI/luxI_mRNA/luxI_translation SUBSTRATE n
addmsg /kinetics/LuxI/luxI_mRNA /kinetics/LuxI/luxI_mRNA/luxI_translation ENZYME n
addmsg /kinetics/LuxI/luxI_mRNA /kinetics/LuxI/luxI_mRNA_degradation SUBSTRATE n
addmsg /kinetics/LuxI/Degraded_luxI_mRNA /kinetics/LuxI/luxI_mRNA_degradation PRODUCT n
addmsg /kinetics/LuxI/AI-1 /kinetics/LuxI/AI_degradation SUBSTRATE n
addmsg /kinetics/LuxI/Degraded_AI /kinetics/LuxI/AI_degradation PRODUCT n
addmsg /kinetics/LuxI/LuxR_binding_autoinducer /kinetics/LuxI/LuxR REAC A B
addmsg /kinetics/LuxI/AI-1 /kinetics/LuxI/LuxR_binding_autoinducer SUBSTRATE n
addmsg /kinetics/LuxI/LuxR-AI /kinetics/LuxI/LuxR_binding_autoinducer PRODUCT n
addmsg /kinetics/LuxI/LuxR /kinetics/LuxI/LuxR_binding_autoinducer SUBSTRATE n
addmsg /kinetics/LuxI/LuxR_binding_autoinducer /kinetics/LuxI/LuxR-AI REAC B A
addmsg /kinetics/LuxI/LuxR-AI_complex_dimerization /kinetics/LuxI/LuxR-AI REAC A B
addmsg /kinetics/LuxI/LuxR-AI_complex_dimerization /kinetics/LuxI/LuxR-AI REAC A B
addmsg /kinetics/LuxI/LuxR-AI_degradation /kinetics/LuxI/LuxR-AI REAC A B
addmsg /kinetics/LuxI/AI_diffusion /kinetics/LuxI/AI-1 REAC A B
addmsg /kinetics/LuxI/AI_degradation /kinetics/LuxI/AI-1 REAC A B
addmsg /kinetics/LuxI/LuxR_binding_autoinducer /kinetics/LuxI/AI-1 REAC A B
addmsg /kinetics/LuxI/AI_form /kinetics/LuxI/AI-1 REAC B A
addmsg /kinetics/LuxI/AI-1 /kinetics/LuxI/AI_diffusion SUBSTRATE n
addmsg /kinetics/AI-extracellular /kinetics/LuxI/AI_diffusion PRODUCT n
addmsg /kinetics/LuxI/luxI_mRNA_degradation /kinetics/LuxI/Degraded_luxI_mRNA REAC B A
addmsg /kinetics/LuxI/LuxR-AI /kinetics/LuxI/LuxR-AI_complex_dimerization SUBSTRATE n
addmsg /kinetics/LuxI/2_LuxR-AI /kinetics/LuxI/LuxR-AI_complex_dimerization PRODUCT n
addmsg /kinetics/LuxI/LuxR-AI /kinetics/LuxI/LuxR-AI_complex_dimerization SUBSTRATE n
addmsg /kinetics/LuxI/luxI_mRNA/luxI_translation /kinetics/LuxI/Amino_Acids REAC sA B
addmsg /kinetics/LuxI/LuxI_operator_inhibitor_reaction[1] /kinetics/LuxI/LuxI_operator_1st_bound REAC A B
addmsg /kinetics/LuxI/LuxI_operator_inhibitor_reaction /kinetics/LuxI/LuxI_operator_1st_bound REAC B A
addmsg /kinetics/LuxI/LuxI_operator_1st_bound /kinetics/LuxI/LuxI_operator_1st_bound/LuxI_transcription ENZYME n
addmsg /kinetics/LuxI/Nucleotides /kinetics/LuxI/LuxI_operator_1st_bound/LuxI_transcription SUBSTRATE n
addmsg /kinetics/LuxI/LuxI_operator_inhibitor_reaction[1] /kinetics/LuxI/LuxI_operator_2nd_bound REAC B A
addmsg /kinetics/LuxI/LuxI_operator_2nd_bound /kinetics/LuxI/LuxI_operator_2nd_bound/LuxI_transcription1 ENZYME n
addmsg /kinetics/LuxI/Nucleotides /kinetics/LuxI/LuxI_operator_2nd_bound/LuxI_transcription1 SUBSTRATE n
addmsg /kinetics/LuxI/LuxI_operator_inhibitor_reaction /kinetics/LuxI/LuxI_operator REAC A B
addmsg /kinetics/LuxI/Nucleotides /kinetics/LuxI/LuxI_operator/LuxI_basal_transcription SUBSTRATE n
addmsg /kinetics/LuxI/LuxI_operator /kinetics/LuxI/LuxI_operator/LuxI_basal_transcription ENZYME n
addmsg /kinetics/LuxI/LuxR-AI /kinetics/LuxI/LuxR-AI_degradation SUBSTRATE n
addmsg /kinetics/LuxI/Degraded_LuxR-AI /kinetics/LuxI/LuxR-AI_degradation PRODUCT n
addmsg /kinetics/LuxI/AI_degradation /kinetics/LuxI/Degraded_AI REAC B A
addmsg /kinetics/LuxI/LuxR-AI_degradation /kinetics/LuxI/Degraded_LuxR-AI REAC B A
addmsg /kinetics/LuxI/LuxI_operator_2nd_bound /kinetics/LuxI/LuxI_operator_inhibitor_reaction[1] PRODUCT n
addmsg /kinetics/LuxI/LuxI_operator_1st_bound /kinetics/LuxI/LuxI_operator_inhibitor_reaction[1] SUBSTRATE n
addmsg /kinetics/LacI/Lac-1 /kinetics/LuxI/LuxI_operator_inhibitor_reaction[1] SUBSTRATE n
addmsg /kinetics/LuxI/LuxI_operator /kinetics/LuxI/LuxI_operator_inhibitor_reaction SUBSTRATE n
addmsg /kinetics/LuxI/LuxI_operator_1st_bound /kinetics/LuxI/LuxI_operator_inhibitor_reaction PRODUCT n
addmsg /kinetics/LacI/Lac-1 /kinetics/LuxI/LuxI_operator_inhibitor_reaction SUBSTRATE n
addmsg /kinetics/LuxI/luxI_mRNA/luxI_translation /kinetics/LuxI/LuxI MM_PRD pA
addmsg /kinetics/LuxI/AI_form /kinetics/LuxI/LuxI REAC A B
addmsg /kinetics/LuxI/LuxI_degradation /kinetics/LuxI/LuxI REAC A B
addmsg /kinetics/LuxI/LuxI /kinetics/LuxI/LuxI_degradation SUBSTRATE n
addmsg /kinetics/LuxI/degraded_LuxI /kinetics/LuxI/LuxI_degradation PRODUCT n
addmsg /kinetics/LuxI/LuxI_degradation /kinetics/LuxI/degraded_LuxI REAC B A
addmsg /kinetics/LuxI/LuxI /kinetics/LuxI/AI_form SUBSTRATE n
addmsg /kinetics/LuxI/AI-1 /kinetics/LuxI/AI_form PRODUCT n
addmsg /kinetics/LuxI/LuxR-AI_complex_dimerization /kinetics/LuxI/2_LuxR-AI REAC B A
addmsg /kinetics/LacI_2nd_copy/Lac_operator_activation_reaction /kinetics/LuxI/2_LuxR-AI REAC A B
addmsg /kinetics/LuxI/2_LuxR-AI_degradation /kinetics/LuxI/2_LuxR-AI REAC A B
addmsg /kinetics/LuxI/2_LuxR-AI_degradation /kinetics/LuxI/Degraded_2_LuxR-AI REAC B A
addmsg /kinetics/LuxI/2_LuxR-AI /kinetics/LuxI/2_LuxR-AI_degradation SUBSTRATE n
addmsg /kinetics/LuxI/Degraded_2_LuxR-AI /kinetics/LuxI/2_LuxR-AI_degradation PRODUCT n
addmsg /kinetics/Lambda-cl/lambda-cl_mRNA1 /graphs/conc1/lambda-cl_mRNA1.Co PLOT Co *lambda-cl_mRNA1.Co *5
enddump
// End of dump
call /kinetics/AI-extracellular/notes LOAD \
"Extracellular AI"
call /kinetics/Degraded_AI/notes LOAD \
"Degradation product of autoinducer"
call /kinetics/AI_degradation/notes LOAD \
"Degradation of autoinducer" \
"Garcia-Ojalvo, J et al. (2004)" \
"PNAS USA 101(30):10955-10960"
call /kinetics/doqcsinfo/notes LOAD \
"This model represents a single cell with the repressilator circuit, which is part of a" \
"population of similar cells. The repressilator circuit is a network of three proteins," \
"i.e. LacI, TetR, Lambda-cI. " \
"The single repressilator model is at accession number 68 in the" \
"DOQCS database. " \
"In the current model, the LacI is coupled with LuxI which forms an" \
"Autoinducer(AI) protein, which couples to LuxR which activates LacI. The AI protein" \
"difffuses across the cell membrane so that the population of cells can interact." \
"" \
"The lifetime ratio is the ratio between the mRNA and protein lifetimes. This" \
"ratio in different cells is chosen from a random gaussian distribution of mean" \
"1 and standard deviation 0.05. The lifetime ratio of this example cell is 0.9837"
call /kinetics/TetR/notes LOAD \
"This is a group of reactions resulting in the production" \
"of Tet R" \
"" \
"Elowitz, M. et al. (2000)" \
"Nature 403:335-338"
call /kinetics/TetR/TetR_degradation/notes LOAD \
"This reaction denotes the degradation of TetR, " \
"" \
"kf is chosen from a random gaussian distribution. " \
"Ref: Fig 2" \
"Garcia and Elowitz et al. (2004)" \
"PNAS 101(30) 10955 - 60" \
""
call /kinetics/TetR/TetR_operator/notes LOAD \
"The TetR operator under normal conditions" \
"drives transcription of TetR" \
"" \
"Elowitz, M. et al. (2000)" \
"Nature 403:335-338"
call /kinetics/TetR/TetR_operator/TetR_basal_transcription/notes LOAD \
"Basal transcription of the Tet R gene." \
"" \
"Rates from Fig 2" \
"Garcia & Elowitz et al. (2004)" \
"PNAS Vol.101"
call /kinetics/TetR/TetR-1/notes LOAD \
"TetR translated from tetR m-RNA" \
"Derived from Figure 1(c) stochastic version" \
"" \
"Elowitz, M. et al. (2000)" \
"Nature 403:335-338"
call /kinetics/TetR/TetR_operator_1st_bound/notes LOAD \
"This represents the promoter " \
"with one of its sites bound by the inhibitor" \
"" \
"Elowitz, M. et al. (2000)" \
"Nature 403:335-338"
call /kinetics/TetR/TetR_operator_1st_bound/TetR_transcription/notes LOAD \
"Transcription of the TetR gene " \
"with only one of its promoter sites activated." \
"" \
"Rates from Box 1 " \
"Elowitz, M. et al (2000)" \
"Nature 403:335-338"
call /kinetics/TetR/TetR_operator_2nd_bound/notes LOAD \
"This represents the promoter " \
"with both of its sites bound by the inhibitor." \
"" \
"Elowitz, M. et al. (2000)" \
"Nature 403:335-338"
call /kinetics/TetR/TetR_operator_2nd_bound/TetR_transcription1/notes LOAD \
"Transcription of the TetR gene " \
"with both its promoter sites activated." \
"" \
"Rates from Box 1 " \
"Elowitz, M. et al. (2000)" \
"Nature 403:335-338"
call /kinetics/TetR/tetR_mRNA_degradation/notes LOAD \
"This reaction denotes the degradation of the tetR m-RNA," \
"the half life of which is two minutes." \
"t1/2 = 0.693/k where k denotes kf" \
"" \
"Elowitz, M. et al. (2000)" \
"Nature 403:335-338"
call /kinetics/TetR/Degraded_tetR_mRNA/notes LOAD \
"Degradation product of tetR m-RNA"
call /kinetics/TetR/Degraded_TetR/notes LOAD \
"Degradation product of TetR protein"
call /kinetics/TetR/TetR_operator_inhibition_reaction/notes LOAD \
"It signifies the first binding of the repressor " \
"with the operator" \
"" \
"Kf = 1 /nM/sec" \
"Kb = 224 /sec" \
"" \
"Box 1 " \
"Elowitz, M. et al. (2000) " \
"Nature 403:335-338"
call /kinetics/TetR/TetR_operator_inhibition_reaction[1]/notes LOAD \
"It signifies the second binding of the repressor" \
"with the operator" \
"" \
"Kf = 1 /nM/sec" \
"Kb = 9 /sec" \
"" \
"Box 1 " \
"Elowitz, M. et al. (2000) " \
"Nature 403:335-338"
call /kinetics/TetR/tetR_mRNA1/notes LOAD \
"The mRNA transcribed by the TetR operator" \
"" \
"Elowitz, M, et al. (2000) " \
"Nature 403:335-338"
call /kinetics/TetR/tetR_mRNA1/tetR_translation/notes LOAD \
"Translation of the tetR mRNA." \
"" \
"Rates from Box 1 " \
"Elowitz, M. et al. (2000)" \
"Nature 403:335-338"
call /kinetics/LacI/notes LOAD \
"This is a group of reactions resulting in the production" \
"of Lac." \
"" \
"Elowitz, M. et al. (2000)" \
"Nature 403:335-338"
call /kinetics/LacI/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 = 0.693/k where k denotes kf" \
"" \
"Elowitz, M. et al. (2000)" \
"Nature 403:335-338"
call /kinetics/LacI/Degraded_lac_mRNA/notes LOAD \
"Degradation product of lac m-RNA"
call /kinetics/LacI/Lac_operator/notes LOAD \
"The Lac operator under normal conditions" \
"drives transcription of Lac" \
"" \
"Elowitz, M. et al. (2000) " \
"Nature 403:335-338"
call /kinetics/LacI/Lac_operator/Lac_basal_transcription/notes LOAD \
"Basal transcription of the Lac gene." \
"" \
"Rates from Fig2" \
"Garcia & Elowitz et al. (2004)" \
"PNAS 101:10955-60" \
""
call /kinetics/LacI/Lac_operator_1st_bound/notes LOAD \
"This represents the promoter " \
"with one of its sites bound by the inhibitor." \
"" \
"Elowitz, M. et al. (2000)" \
"Nature 403:335-338"
call /kinetics/LacI/Lac_operator_1st_bound/Lac_transcription/notes LOAD \
"Transcription of the lac gene " \
"with only one of its promoter sites activated." \
"" \
"Rates from Box 1 " \
"Elowitz, M. et al. (2000) N" \
"Nature 403: 335-338"
call /kinetics/LacI/Lac_operator_2nd_bound/notes LOAD \
"This represents the promoter " \
"with both of its sites bound by the inhibitor." \
"" \
"Elowitz, M. et al. (2000)" \
"Nature 403:335-338"
call /kinetics/LacI/Lac_operator_2nd_bound/Lac_transcription1/notes LOAD \
"Transcription of the Lac gene " \
"with both its promoter sites activated." \
"" \
"Rates from Box 1 " \
"Elowitz, M. et al. (2000) " \
"Nature 403: 335-338"
call /kinetics/LacI/Lac-1/notes LOAD \
"Lac translated from lac m-RNA" \
"Derived from Figure 1(c) stochastic version" \
"" \
"Elowitz, M. et al. (2000) " \
"Nature 403:335-338"
call /kinetics/LacI/Lac_degradation/notes LOAD \
"This reaction denotes the degradation of Lac, " \
"" \
"Kf is chosen from a random gaussian distribution. " \
"Ref: Fig 2" \
"Garcia & Elowitz et al (2004)" \
"PNAS 101(30) 10955-60" \
" "
call /kinetics/LacI/Degraded_lac/notes LOAD \
"Degradation product of Lac protein"
call /kinetics/LacI/Lac_operator_inhibition_reaction/notes LOAD \
"It signifies the first binding of the repressor" \
"with the operator" \
"" \
"Kf = 1 /nM/sec" \
"Kb = 224 /sec" \
"" \
"Box 1 " \
"Elowitz, M. et al. (2000) " \
"Nature 403:335-338"
call /kinetics/LacI/Lac_operator_inhibition_reaction[1]/notes LOAD \
"It signifies the second binding of the repressor" \
"with the operator" \
"" \
"Kf = 1 /nM/sec" \
"Kb = 9 /sec" \
"" \
"Box 1 " \
"Elowitz, M. et al (2000)" \
"Nature 403:335-338"
call /kinetics/LacI/lac_mRNA1/notes LOAD \
"The m-RNA transcribed by the lac operator" \
"" \
"Elowitz, M. et al. (2000) " \
"Nature 403:335-338"
call /kinetics/LacI/lac_mRNA1/lac_translation/notes LOAD \
"Translation of the lac mRNA." \
"" \
"Rates from Box 1 " \
"Elowitz, M. et al (2000)" \
"Nature 403: 335-338"
call /kinetics/Lambda-cl/notes LOAD \
"This is a group of reactions resulting in the production" \
"of Lambda cl"
call /kinetics/Lambda-cl/Lambda-cl-1/notes LOAD \
"Lambda-cl translated from lcl m-RNA" \
"Derived from Figure 1(c) stochastic version" \
"" \
"Elowitz, M. et al. (2000) " \
"Nature 403:335-338"
call /kinetics/Lambda-cl/Degraded_lambda-cl_mRNA/notes LOAD \
"Degradation product of lambda cl m-RNA"
call /kinetics/Lambda-cl/Lambda-cl_operator/notes LOAD \
"The lambda cl operator under normal conditions" \
"drives transcription of lambda cl" \
"" \
"Elowitz, M. et al. (2000) " \
"Nature 403:335-338"
call /kinetics/Lambda-cl/Lambda-cl_operator/Lambda-cl_basal_transcription/notes LOAD \
"Basal transcription of the Lambda cl gene." \
"" \
"Rates from Fig 2" \
"Garcia and Elowitz et al. (2004)" \
"PNAS 101:10955-60"
call /kinetics/Lambda-cl/Lambda-cl_operator_inhibition_reaction/notes LOAD \
"It signifies the first binding of the repressor" \
"with the operator" \
"" \
"Kf = 1 /nM/sec" \
"Kb = 224 /sec" \
"" \
"Box 1 " \
"Elowitz, M. et al. (2000) " \
"Nature 403:335-338"
call /kinetics/Lambda-cl/Lambda-cl_operator_inhibition_reaction[1]/notes LOAD \
"It signifies the second binding of the repressor" \
"with the operator" \
"" \
"Kf = 1 /nM/sec" \
"Kb = 9 /sec" \
"" \
"Box 1 " \
"Elowitz, M. et al. (2000) " \
"Nature 403:335-338"
call /kinetics/Lambda-cl/Lambda-cl_operator_1st_bound/notes LOAD \
"This represents the promoter " \
"with one of its sites bound by the inhibitor." \
"" \
"Elowitz, M. et al. (2000)" \
"Nature 403:335-338"
call /kinetics/Lambda-cl/Lambda-cl_operator_1st_bound/Lambda-cl_transcription/notes LOAD \
"Transcription of the Lambda cl gene " \
"with only one of its promoter sites activated." \
"" \
"Rates from Box 1 " \
"Elowitz, M. et al. (2000)" \
"Nature 403:335-338"
call /kinetics/Lambda-cl/Degraded_Lambda-cl/notes LOAD \
"Degradation product of Lambda-cl protein"
call /kinetics/Lambda-cl/lambda-cl_mRNA_degradation/notes LOAD \
"This reaction denotes the degradation of the lambda cl m-RNA," \
"the half life of which is two minutes." \
"" \
"t1/2 = 0.693/k where k denotes kf" \
"Elowitz M et al (2000)" \
"Nature 403 : 335-338" \
""
call /kinetics/Lambda-cl/Lambda-cl_degradation/notes LOAD \
"This reaction denotes the degradation of Lambda cl, " \
"" \
"kf is chosen from a random gaussian distribution. " \
"Ref: Fig 2" \
"Garcia & Elowitz et al. (2004) " \
"PNAS 101(30) 10955 - 60"
call /kinetics/Lambda-cl/Lambda-cl_operator_2nd_bound/notes LOAD \
"This represents the promoter " \
"with both of its sites bound by the inhibitor." \
"" \
"Elowitz, M. et al. (2000)" \
"Nature 403:335-338"
call /kinetics/Lambda-cl/Lambda-cl_operator_2nd_bound/Lambda-cl_transcription1/notes LOAD \
"Transcription of the Lambda cl gene" \
"with both its promoter sites activated." \
"" \
"Rates from Box 1" \
"Elowitz, M. et al. (2000)" \
"Nature 403:335-338"
call /kinetics/Lambda-cl/lambda-cl_mRNA1/notes LOAD \
"The m-RNA transcribed by the Lcl operator" \
"" \
"Elowitz etal Nature 2000 Vol 403:335-338"
call /kinetics/Lambda-cl/lambda-cl_mRNA1/lambda-cl_translation/notes LOAD \
"Translation the lambda cl mRNA." \
"" \
"Rates from Box 1 " \
"Elowitz, M. et al (2000)" \
"Nature 403:335-338"
call /kinetics/LacI_2nd_copy/notes LOAD \
"This is a group of reactions resulting in the production" \
"of Lac." \
"" \
"Elowitz, M. et al. (2000)" \
"Nature 403:335-338" \
"" \
"A second copy of the Lac gene " \
"has been introduced coupled to Lux I gene" \
"" \
"Garcia-Ojalvo, J. et al. (2004)" \
"PNAS USA 101(30):10955-10960"
call /kinetics/LacI_2nd_copy/lac_mRNA/notes LOAD \
"The m-RNA transcribed by the lac operator" \
"" \
"Elowitz, M. et al. (2000) " \
"Nature 403:335-338"
call /kinetics/LacI_2nd_copy/lac_mRNA/lac_translation/notes LOAD \
"Translation of the lac mRNA." \
"" \
"Rates from Box 1 " \
"Elowitz, M. et al (2000)" \
"Nature 403: 335-338"
call /kinetics/LacI_2nd_copy/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 = 0.693/k where k denotes kf" \
"" \
"Elowitz, M. et al. (2000)" \
"Nature 403:335-338"
call /kinetics/LacI_2nd_copy/Degraded_lac_mRNA/notes LOAD \
"Degradation product of lac m-RNA"
call /kinetics/LacI_2nd_copy/Lac_operator/notes LOAD \
"The Lac operator under normal conditions" \
"drives transcription of Lac" \
"" \
"Elowitz, M. et al. (2000) " \
"Nature 403:335-338"
call /kinetics/LacI_2nd_copy/Lac_operator/Lac_basal_transcription/notes LOAD \
"Basal transcription of the Lac gene." \
"" \
"Rates from Fig 2" \
"Garcia and Elowitz et al.(2004)" \
"PNAS 101: 10955-60"
call /kinetics/LacI_2nd_copy/Lac_operator_1st_bound/notes LOAD \
"This represents the promoter " \
"with one of its sites bound by the inhibitor." \
"" \
"Elowitz, M. et al. (2000)" \
"Nature 403:335-338"
call /kinetics/LacI_2nd_copy/Lac_operator_1st_bound/Lac_transcription/notes LOAD \
"Transcription of the Lac gene " \
"with only one of its promoter sites activated." \
"" \
"Rates from Box 1 " \
"Elowitz, M. et al. (2000) N" \
"Nature 403: 335-338"
call /kinetics/LacI_2nd_copy/Lac_operator_2nd_bound/notes LOAD \
"This represents the promoter " \
"with both of its sites bound by the inhibitor." \
"" \
"Elowitz, M. et al. (2000)" \
"Nature 403:335-338"
call /kinetics/LacI_2nd_copy/Lac_operator_2nd_bound/Lac_transcription1/notes LOAD \
"Transcription of the Lac gene " \
"with both its promoter sites activated." \
"" \
"Rates from Box 1 " \
"Elowitz, M. et al. (2000) " \
"Nature 403: 335-338"
call /kinetics/LacI_2nd_copy/Lac_operator_inhibition_reaction/notes LOAD \
"It signifies the first binding of the repressor" \
"with the operator" \
"" \
"Kf = 1 /nM/sec" \
"Kb = 224 /sec" \
"" \
"Box 1 " \
"Elowitz, M. et al. (2000) " \
"Nature 403:335-338"
call /kinetics/LacI_2nd_copy/Lac_operator_inhibition_reaction[1]/notes LOAD \
"It signifies the second binding of the repressor" \
"with the operator" \
"" \
"Kf = 1 /nM/sec" \
"Kb = 9 /sec" \
"" \
"Box 1 " \
"Elowitz, M. et al (2000)" \
"Nature 403:335-338"
call /kinetics/LacI_2nd_copy/Lac_operator_activation_reaction/notes LOAD \
"It signifies the binding of the activator" \
"with the operator" \
"" \
"Kf = 1 /nM/sec" \
"Kb = 224 /sec" \
"" \
"Used first binding rates for repressor from Box 1 " \
"Elowitz, M. et al (2000)" \
"Nature 403:335-338"
call /kinetics/LacI_2nd_copy/Lac_operator_activator_bound/notes LOAD \
"This represents the promoter bound to the activator."
call /kinetics/LacI_2nd_copy/Lac_operator_activator_bound/Lac_active_transcription/notes LOAD \
"Lac transcription from the activator bound Lac gene." \
" " \
"" \
"kcat is taken from Garcia & Elowitz et al. (2004) " \
"PNAS 101: 10955-60"
call /kinetics/LuxI/notes LOAD \
"This is a group of reactions resulting in the production" \
"of autoinducer protein. This has been introduced into" \
"the repressilator as a quorum sensing mechanism." \
"" \
"Garcia-Ojalvo, J. et al. (2004)" \
"PNAS USA 101(30):10955-10960"
call /kinetics/LuxI/luxI_mRNA/notes LOAD \
"The m-RNA transcribed by the luxI operator" \
"" \
"Garcia-Ojalvo, J. et al. (2004)" \
"PNAS USA 101(30):10955-10960" \
"" \
"As described for components of the Repressilator" \
"by Elowitz, M. et al. (2000) " \
"Nature 403:335-338"
call /kinetics/LuxI/luxI_mRNA/luxI_translation/notes LOAD \
"Rates from" \
"Box 1 Elowitz et al (2003)" \
"Nature 403:335-338"
call /kinetics/LuxI/luxI_mRNA_degradation/notes LOAD \
"This reaction denotes the degradation of the luxI m-RNA," \
"the half life of which is two minutes." \
"t1/2 = 0.693/k where k denotes kf" \
"" \
"Garcia-Ojalvo, J. et al. (2004)" \
"PNAS USA 101(30):10955-10960" \
"" \
"As described for components of the Repressilator" \
"by Elowitz, M. et al. (2000)" \
"Nature 403:335-338"
call /kinetics/LuxI/AI_degradation/notes LOAD \
"Degradation of autoinducer." \
"kf = 0.2, McMillen et al (2002) PNAS 99(2): 679-84" \
""
call /kinetics/LuxI/LuxR/notes LOAD \
"Lux R assumed to be constitutively produced." \
""
call /kinetics/LuxI/LuxR_binding_autoinducer/notes LOAD \
"Binding of Lux R to the autoinducer protein" \
"Kf = 5e+06 /M = 5 /uM" \
"" \
"McMillen, M. et al. (2002)" \
"PNAS USA 99(2): 679-84" \
"" \
""
call /kinetics/LuxI/LuxR-AI/notes LOAD \
"Lux R complexed with AI" \
""
call /kinetics/LuxI/AI-1/notes LOAD \
"AI translated from luxI m-RNA" \
"" \
"Garcia-Ojalvo, J. et al. (2004)" \
"PNAS USA 101(30):10955-10960" \
"" \
"As described for components of the Repressilator" \
"by Elowitz, M. et al. (2000)" \
"Nature 403:335-338"
call /kinetics/LuxI/AI_diffusion/notes LOAD \
"Diffusion of the autoinducer from inside the cell to the" \
"outside and vice versa." \
"" \
"Garcia-Ojalvo, J et al. (2004)" \
"PNAS USA 101(30):10955-10960"
call /kinetics/LuxI/Degraded_luxI_mRNA/notes LOAD \
"Degradation product of lux I m-RNA"
call /kinetics/LuxI/LuxR-AI_complex_dimerization/notes LOAD \
"Dimerization of the complex between" \
"Lux R and the autoinducer protein" \
"Kf = 1.8e+18 /sec/M = 1.8 /sec/uM" \
"" \
"McMillen, M. et al. (2002)" \
"PNAS USA 99(2):679-684" \
""
call /kinetics/LuxI/LuxI_operator_1st_bound/notes LOAD \
"This represents the promoter " \
"with one of its sites bound by the inhibitor." \
"" \
"Garcia-Ojalvo, J. et al. (2004)" \
"PNAS USA 101(30):10955-10960" \
"" \
"As described for components of the Repressilator" \
"by Elowitz, M. et al. (2000)" \
"Nature 403:335-338"
call /kinetics/LuxI/LuxI_operator_1st_bound/LuxI_transcription/notes LOAD \
"Transcription of the LuxI gene" \
"with only one of its promoter sites activated." \
"" \
"Garcia-Ojalvo, J. et al (2004)" \
"PNAS USA 101(30):10955-10960" \
"" \
"As described for components of the Repressilator in Box 1 " \
"Elowitz, M. et al. (2000)" \
"Nature 403:335-338"
call /kinetics/LuxI/LuxI_operator_2nd_bound/notes LOAD \
"This represents the promoter" \
"with both of its sites bound by the inhibitor." \
"" \
"Garcia-Ojalvo, J. et al. (2004)" \
"PNAS USA 101(30):10955-10960" \
"" \
"As described for components of the Repressilator" \
"by Elowitz, M. et al. (2000)" \
"Nature 403:335-338"
call /kinetics/LuxI/LuxI_operator/notes LOAD \
"The LuxI operator under normal conditions" \
"drives transcription of LuxI" \
"" \
"Garcia-Ojalvo, J. et al. (2004)" \
"PNAS USA 101(30):10955-10960" \
"" \
"As described for components of the Repressilator" \
"by Elowitz, M. et al. (2000) " \
"Nature 403:335-338"
call /kinetics/LuxI/LuxI_operator/LuxI_basal_transcription/notes LOAD \
"Basal transcription of the Lux I gene." \
"" \
"Garcia-Ojalvo, J. et al. (2004)" \
"PNAS USA 101(30):10955-10960" \
"" \
"As described for components of the Repressilator in Box 1" \
"Elowitz, M. et al. (2000)" \
"Nature 403:335-338"
call /kinetics/LuxI/LuxR-AI_degradation/notes LOAD \
"Degradation of autoinducer complexed to LuxR, " \
"kf = 0.2, " \
"McMillen et al (2002)" \
"PNAS 99(2) 679 - 84" \
""
call /kinetics/LuxI/Degraded_AI/notes LOAD \
"Degradation product of autoinducer."
call /kinetics/LuxI/Degraded_LuxR-AI/notes LOAD \
"Degradation product of the complex of Lux R with AI"
call /kinetics/LuxI/LuxI_operator_inhibitor_reaction[1]/notes LOAD \
"This signifies the second binding of the repressor" \
"with the operator" \
"" \
"Kf = 1 /nM/sec" \
"Kb = 9 /sec" \
"" \
"Garcia-Ojalvo, J. et al. (2004)" \
"PNAS USA 101(30):10955-10960" \
"" \
"As described for components of the Repressilator in Box 1" \
"Elowitz, M. et al. (2000) " \
"Nature 403:335-338"
call /kinetics/LuxI/LuxI_operator_inhibitor_reaction/notes LOAD \
"This signifies the second binding of the repressor" \
"with the operator" \
"" \
"Kf = 1 /nM/sec" \
"Kb = 224 /sec" \
"" \
"Garcia-Ojalvo, J. et al. (2004)" \
"PNAS USA 101(30):10955-10960" \
"" \
"As described for components of the Repressilator in Box 1" \
"Elowitz, M. et al. (2000) " \
"Nature 403:335-338"
call /kinetics/LuxI/LuxI_degradation/notes LOAD \
"This reaction denotes degradation of LuxI, kf = 25, " \
"" \
"McMillen et al (2002)" \
"PNAS 99(2): 679-84" \
""
call /kinetics/LuxI/AI_form/notes LOAD \
"Formation of Autoinducer" \
"The forward rate has taken from " \
"PNAS 101: 10955-60" \
" by Garcia & Elowitz et al (2004)"
call /kinetics/LuxI/2_LuxR-AI/notes LOAD \
"Dimer of Lux R - AI complex" \
""
call /kinetics/LuxI/Degraded_2_LuxR-AI/notes LOAD \
"Degradation product of the dimer " \
"of the complex of Lux R with AI"
call /kinetics/LuxI/2_LuxR-AI_degradation/notes LOAD \
"Degradation of the dimer of the complex between" \
"Lux R and autoinducer. " \
"kf = 0.2, " \
"McMillen et al (2002)" \
"PNAS 99(2) 679-84" \
""
complete_loading