# The following model is an intracellular model of the light-sensing and light-producing pathways as described upon our website, coupled to the Elowitz repressilator.
# In order to run it, rename the file as RepressilatingLights.ka and import it to Kappa RuleStudio (http://www.kappalanguage.org/tools) or an alternate Kappa simulator.
#
# 2010 University of Edinburgh iGEM Team
# John Wilson-Kanamori


# Signal transduction pathway for red light.

'Cph8 auto-activation{80001}' Cph8(active~off) -> Cph8(active~on) @ 0.01
'Cph8 auto-deactivation{80002}' Cph8(active~on) -> Cph8(active~off) @ 0.001
'Cph8 deactivation by RED light{80003}' Cph8(active~on), RED() -> Cph8(active~off), RED() @ 0.1

'OmpR auto-phosphorylation{80004}' OmpR(site~u) -> OmpR(site~p) @ 0.001
'OmpR auto-dephosphorylation{80005}' OmpR(dna,site~p) -> OmpR(dna,site~u) @ 0.03
'OmpR binding to Cph8{80006}' OmpR(dna,cph8,site~u), Cph8(active~on,ompr) -> OmpR(dna,cph8!1,site~u), Cph8(active~on,ompr!1) @ 0.01
'OmpR dissociation from Cph8{80007}' OmpR(cph8!1), Cph8(ompr!1) -> OmpR(cph8), Cph8(ompr) @ 0.01
'OmpR phosphorylation by Cph8{80008}' OmpR(cph8!1,site~u), Cph8(active~on,ompr!1) -> OmpR(cph8!1,site~p), Cph8(active~on,ompr!1) @ 0.1


# Signal transduction pathway for blue light.

'LOVTAP auto-activation{81001}' LOVTAP(active~dark) -> LOVTAP(active~light) @ 0.0001
'LOVTAP auto-deactivation{81002}' LOVTAP(dna,active~light) -> LOVTAP(dna,active~dark) @ 0.01
'LOVTAP activation by BLUE light(81003}' LOVTAP(active~dark), BLUE() -> LOVTAP(active~light), BLUE() @ 0.1


# Signal transduction pathway for green light.

'CcaS-PhoR auto-activation{82001}' CcaS(active~off) -> CcaS(active~on) @ 0.001
'CcaS-PhoR auto-deactivation{82002}' CcaS(active~on) -> CcaS(active~off) @ 0.01
'CcaS-PhoR activation by GREEN light{82003}' CcaS(active~off), GREEN() -> CcaS(active~on), GREEN() @ 0.1

'PhoB auto-phosphorylation{82004}' PhoB(site~u) -> PhoB(site~p) @ 0.001
'PhoB auto-dephosphorylation{82005}' PhoB(dna,site~p) -> PhoB(dna,site~u) @ 0.03
'PhoB binding to CcaS{82006}' PhoB(dna,ccas,site~u), CcaS(active~on,phob) -> PhoB(dna,ccas!1,site~u), CcaS(active~on,phob!1) @ 0.01
'PhoB dissociation from CcaS{82007}' PhoB(ccas!1), CcaS(phob!1) -> PhoB(ccas), CcaS(phob) @ 0.01
'PhoB phosphorylation by CcaS{82008}' PhoB(ccas!1,site~u), CcaS(active~on,phob!1) -> PhoB(ccas!1,site~p), CcaS(active~on,phob!1) @ 0.1


# Transcription factor binding to promoter region.

'Repressor binding (with RNAP){76996}' DNA(downstream!1,binding,type~BBaR0000p2), DNA(upstream!1,binding!2,type~BBaR0000p3), Repressor(dna), RNAP(dna!2) <-> DNA(downstream!1,binding!2,type~BBaR0000p2), DNA(upstream!1,binding!3,type~BBaR0000p3), Repressor(dna!2), RNAP(dna!3) @ 1.66e-05,1.0
'Repressor binding (no RNAP){76995}' DNA(downstream!1,binding,type~BBaR0000p2), DNA(upstream!1,binding,type~BBaR0000p3), Repressor(dna) <-> DNA(downstream!1,binding!2,type~BBaR0000p2), DNA(upstream!1,binding,type~BBaR0000p3), Repressor(dna!2) @ 0.0166,1.0
'LacI binding to R0010p2 (no LacI){77308}' DNA(binding,type~BBaR0010p3,upstream!2), LacI(dna,lactose), DNA(downstream!2,binding,type~BBaR0010p2) <-> DNA(binding,type~BBaR0010p3,upstream!3), LacI(dna!1,lactose), DNA(downstream!3,binding!1,type~BBaR0010p2) @ 0.01,2.24
'LacI binding to R0010p2 (LacI bound){77310}' DNA(binding!1,type~BBaR0010p3,upstream!2), LacI(dna!1), DNA(downstream!2,binding,type~BBaR0010p2), LacI(dna,lactose) <-> DNA(binding!2,type~BBaR0010p3,upstream!3), LacI(dna!2), DNA(downstream!3,binding!1,type~BBaR0010p2), LacI(dna!1,lactose) @ 0.01,0.09
'LacI binding to R0010p3 (no LacI){77309}' DNA(binding,type~BBaR0010p3,upstream!2), LacI(dna,lactose), DNA(downstream!2,binding,type~BBaR0010p2) <-> DNA(binding!1,type~BBaR0010p3,upstream!3), LacI(dna!1,lactose), DNA(downstream!3,binding,type~BBaR0010p2) @ 0.01,2.24
'LacI binding to R0010p3 (LacI bound){77311}' DNA(binding,type~BBaR0010p3,upstream!2), LacI(dna!1), DNA(downstream!2,binding!1,type~BBaR0010p2), LacI(dna,lactose) <-> DNA(binding!1,type~BBaR0010p3,upstream!3), LacI(dna!2), DNA(downstream!3,binding!2,type~BBaR0010p2), LacI(dna!1,lactose) @ 0.01,0.09
'TetR binding to R0040p2 (no TetR){77296}' DNA(binding,type~BBaR0040p3,upstream!2), TetR(dna,atc), DNA(downstream!2,binding,type~BBaR0040p2) <-> DNA(binding,type~BBaR0040p3,upstream!3), TetR(dna!1,atc), DNA(downstream!3,binding!1,type~BBaR0040p2) @ 0.01,2.24
'TetR binding to R0040p2 (TetR bound){77299}' DNA(binding!1,type~BBaR0040p3,upstream!2), TetR(dna!1), TetR(dna,atc), DNA(downstream!2,binding,type~BBaR0040p2) <-> DNA(binding!2,type~BBaR0040p3,upstream!3), TetR(dna!2), TetR(dna!1,atc), DNA(downstream!3,binding!1,type~BBaR0040p2) @ 0.01,0.09
'TetR binding to R0040p3 (no TetR){77297}' DNA(binding,type~BBaR0040p3,upstream!2), TetR(dna,atc), DNA(downstream!2,binding,type~BBaR0040p2) <-> DNA(binding!1,type~BBaR0040p3,upstream!3), TetR(dna!1,atc), DNA(downstream!3,binding,type~BBaR0040p2) @ 0.01,2.24
'TetR binding to R0040p3 (TetR bound){77300}' DNA(binding,type~BBaR0040p3,upstream!2), TetR(dna,atc), TetR(dna!1), DNA(downstream!2,binding!1,type~BBaR0040p2) <-> DNA(binding!2,type~BBaR0040p3,upstream!3), TetR(dna!2,atc), TetR(dna!1), DNA(downstream!3,binding!1,type~BBaR0040p2) @ 0.01,0.09
'cI binding to R0051p2 (no cI){77258}' DNA(binding,type~BBaR0051p3,upstream!2), cI(dna), DNA(downstream!2,binding,type~BBaR0051p2) <-> DNA(binding,type~BBaR0051p3,upstream!3), cI(dna!1), DNA(downstream!3,binding!1,type~BBaR0051p2) @ 0.01,2.24
'cI binding to R0051p2 (cI bound){77260}' DNA(binding!1,type~BBaR0051p3,upstream!2), cI(dna), cI(dna!1), DNA(downstream!2,binding,type~BBaR0051p2) <-> DNA(binding!2,type~BBaR0051p3,upstream!3), cI(dna!1), cI(dna!2), DNA(downstream!3,binding!1,type~BBaR0051p2) @ 0.01,0.09
'cI binding to R0051p3 (no cI){77259}' DNA(binding,type~BBaR0051p3,upstream!2), cI(dna), DNA(downstream!2,binding,type~BBaR0051p2) <-> DNA(binding!1,type~BBaR0051p3,upstream!3), cI(dna!1), DNA(downstream!3,binding,type~BBaR0051p2) @ 0.01,2.24
'cI binding to R0051p3 (cI bound){77261}' DNA(binding,type~BBaR0051p3,upstream!2), cI(dna!1), cI(dna), DNA(downstream!2,binding!1,type~BBaR0051p2) <-> DNA(binding!1,type~BBaR0051p3,upstream!3), cI(dna!2), cI(dna!1), DNA(downstream!3,binding!2,type~BBaR0051p2) @ 0.01,0.09
'OmpR binding to R0082p2{80100}' DNA(binding,type~BBaR0082p2,downstream!2), DNA(upstream!2,type~BBaR0082p3,downstream!3), DNA(upstream!3,type~BBaR0082p4), OmpR(cph8,site~p,dna) <-> DNA(binding!1,type~BBaR0082p2,downstream!2), DNA(upstream!2,type~BBaR0082p3,downstream!3), DNA(upstream!3,type~BBaR0082p4), OmpR(cph8,site~p,dna!1) @ 0.01,0.03
'OmpR binding to R0082p3{80101}' DNA(type~BBaR0082p2,downstream!2), DNA(upstream!2,binding,type~BBaR0082p3,downstream!3), DNA(upstream!3,type~BBaR0082p4), OmpR(cph8,site~p,dna) <-> DNA(type~BBaR0082p2,downstream!2), DNA(upstream!2,binding!1,type~BBaR0082p3,downstream!3), DNA(upstream!3,type~BBaR0082p4), OmpR(cph8,site~p,dna!1) @ 0.01,0.03
'OmpR binding to R0082p4{80102}' DNA(type~BBaR0082p2,downstream!2), DNA(upstream!2,type~BBaR0082p3,downstream!3), DNA(upstream!3,binding,type~BBaR0082p4), OmpR(cph8,site~p,dna) <-> DNA(type~BBaR0082p2,downstream!2), DNA(upstream!2,type~BBaR0082p3,downstream!3), DNA(upstream!3,binding!1,type~BBaR0082p4), OmpR(cph8,site~p,dna!1) @ 0.01,0.03
'OmpR binding to R0084p2{80103}' DNA(binding,type~BBaR0084p2,downstream!2), DNA(upstream!2,type~BBaR0084p3,downstream!3), DNA(upstream!3,type~BBaR0084p4), OmpR(cph8,site~u,dna) <-> DNA(binding!1,type~BBaR0084p2,downstream!2), DNA(upstream!2,type~BBaR0084p3,downstream!3), DNA(upstream!3,type~BBaR0084p4), OmpR(cph8,site~u,dna!1) @ 0.01,0.03
'OmpR binding to R0084p3{80104}' DNA(type~BBaR0084p2,downstream!2), DNA(upstream!2,binding,type~BBaR0084p3,downstream!3), DNA(upstream!3,type~BBaR0084p4), OmpR(cph8,site~u,dna) <-> DNA(type~BBaR0084p2,downstream!2), DNA(upstream!2,binding!1,type~BBaR0084p3,downstream!3), DNA(upstream!3,type~BBaR0084p4), OmpR(cph8,site~u,dna!1) @ 0.01,0.03
'OmpR binding to R0084p4{80105}' DNA(type~BBaR0084p2,downstream!2), DNA(upstream!2,type~BBaR0084p3,downstream!3), DNA(upstream!3,binding,type~BBaR0084p4), OmpR(cph8,site~u,dna) <-> DNA(type~BBaR0084p2,downstream!2), DNA(upstream!2,type~BBaR0084p3,downstream!3), DNA(upstream!3,binding!1,type~BBaR0084p4), OmpR(cph8,site~u,dna!1) @ 0.01,0.03
'LOVTAP binding to K191007{80106}' DNA(binding,type~BBaK191007p2,downstream!2), DNA(upstream!2,binding,type~BBaK191007p3), LOVTAP(active~light,dna) <-> DNA(binding!1,type~BBaK191007p2,downstream!2), DNA(upstream!2,binding,type~BBaK191007p3), LOVTAP(active~light,dna!1) @ 0.01,0.03
'PhoB binding to R0PHO{80107}' DNA(binding,type~BBaR0PHOp2,downstream!2), DNA(upstream!2,binding,type~BBaR0PHOp3), PhoB(ccas,site~p,dna) <-> DNA(binding!1,type~BBaR0PHOp2,downstream!2), DNA(upstream!2,binding,type~BBaR0PHOp3), PhoB(ccas,site~p,dna!1) @ 0.01,0.03


# RNAP binding to promoter regions.

'RNAP binding (no repressor){76998}' DNA(downstream!1,binding,type~BBaR0000p2), DNA(upstream!1,binding,type~BBaR0000p3), RNAP(dna,rna) -> DNA(downstream!1,binding,type~BBaR0000p2), DNA(upstream!1,binding!3,type~BBaR0000p3), RNAP(dna!3,rna) @ 0.000830269391581363
'RNAP binding (with repressor){76997}' DNA(downstream!1,binding!3,type~BBaR0000p2), DNA(upstream!1,binding,type~BBaR0000p3), Repressor(dna!3), RNAP(dna,rna) -> DNA(downstream!1,binding!2,type~BBaR0000p2), DNA(upstream!1,binding!3,type~BBaR0000p3), Repressor(dna!2), RNAP(dna!3,rna) @ 8.30269391581363e-07
'RNAP binding to R0010 (no LacI){77312}' DNA(binding,type~BBaR0010p3,upstream!2,downstream!1), DNA(upstream!1,binding,type~BBaR0010p4), RNAP(dna,rna), DNA(downstream!2,binding,type~BBaR0010p2) -> DNA(binding,type~BBaR0010p3,upstream!3,downstream!1), DNA(upstream!1,binding!2,type~BBaR0010p4), RNAP(dna!2,rna), DNA(downstream!3,binding,type~BBaR0010p2) @ 0.0007
'RNAP binding to R0010 (LacI on p2){77313}' DNA(binding,type~BBaR0010p3,upstream!2,downstream!1), DNA(upstream!1,binding,type~BBaR0010p4), RNAP(dna,rna), DNA(downstream!2,binding!3,type~BBaR0010p2), LacI(dna!3) -> DNA(binding,type~BBaR0010p3,upstream!3,downstream!1), DNA(upstream!1,binding!2,type~BBaR0010p4), RNAP(dna!2,rna), DNA(downstream!3,binding!4,type~BBaR0010p2), LacI(dna!4) @ 7e-07
'RNAP binding to R0010 (LacI on p3){77314}' DNA(binding!3,type~BBaR0010p3,upstream!2,downstream!1), DNA(upstream!1,binding,type~BBaR0010p4), RNAP(dna,rna), DNA(downstream!2,binding,type~BBaR0010p2), LacI(dna!3) -> DNA(binding!4,type~BBaR0010p3,upstream!3,downstream!1), DNA(upstream!1,binding!2,type~BBaR0010p4), RNAP(dna!2,rna), DNA(downstream!3,binding,type~BBaR0010p2), LacI(dna!4) @ 7e-07
'RNAP binding to R0010 (LacI on p2 and p3){77315}' DNA(binding!3,type~BBaR0010p3,upstream!2,downstream!1), DNA(upstream!1,binding,type~BBaR0010p4), RNAP(dna,rna), DNA(downstream!2,binding!4,type~BBaR0010p2), LacI(dna!3), LacI(dna!4) -> DNA(binding!4,type~BBaR0010p3,upstream!3,downstream!1), DNA(upstream!1,binding!2,type~BBaR0010p4), RNAP(dna!2,rna), DNA(downstream!3,binding!5,type~BBaR0010p2), LacI(dna!4), LacI(dna!5) @ 7e-07
'RNAP binding to R0040 (no TetR){77301}' DNA(binding,type~BBaR0040p3,upstream!2,downstream!1), DNA(upstream!1,binding,type~BBaR0040p4), RNAP(dna,rna), DNA(downstream!2,binding,type~BBaR0040p2) -> DNA(binding,type~BBaR0040p3,upstream!3,downstream!1), DNA(upstream!1,binding!2,type~BBaR0040p4), RNAP(dna!2,rna), DNA(downstream!3,binding,type~BBaR0040p2) @ 0.0007
'RNAP binding to R0040 (TetR on p2){77302}' DNA(binding,type~BBaR0040p3,upstream!2,downstream!1), DNA(upstream!1,binding,type~BBaR0040p4), RNAP(dna,rna), DNA(downstream!2,binding!3,type~BBaR0040p2), TetR(dna!3) -> DNA(binding,type~BBaR0040p3,upstream!3,downstream!1), DNA(upstream!1,binding!2,type~BBaR0040p4), RNAP(dna!2,rna), DNA(downstream!3,binding!4,type~BBaR0040p2), TetR(dna!4) @ 7e-07
'RNAP binding to R0040 (TetR on p3){77303}' DNA(binding!3,type~BBaR0040p3,upstream!2,downstream!1), DNA(upstream!1,binding,type~BBaR0040p4), RNAP(dna,rna), DNA(downstream!2,binding,type~BBaR0040p2), TetR(dna!3) -> DNA(binding!4,type~BBaR0040p3,upstream!3,downstream!1), DNA(upstream!1,binding!2,type~BBaR0040p4), RNAP(dna!2,rna), DNA(downstream!3,binding,type~BBaR0040p2), TetR(dna!4) @ 7e-07
'RNAP binding to R0040 (TetR on p2 and p3){77304}' DNA(binding!3,type~BBaR0040p3,upstream!2,downstream!1), DNA(upstream!1,binding,type~BBaR0040p4), RNAP(dna,rna), DNA(downstream!2,binding!4,type~BBaR0040p2), TetR(dna!3), TetR(dna!4) -> DNA(binding!4,type~BBaR0040p3,upstream!3,downstream!1), DNA(upstream!1,binding!2,type~BBaR0040p4), RNAP(dna!2,rna), DNA(downstream!3,binding!5,type~BBaR0040p2), TetR(dna!4), TetR(dna!5) @ 7e-07
'RNAP binding to R0051 (no cI){77266}' DNA(binding,type~BBaR0051p3,upstream!2,downstream!1), DNA(upstream!1,binding,type~BBaR0051p4), RNAP(dna,rna), DNA(downstream!2,binding,type~BBaR0051p2) -> DNA(binding,type~BBaR0051p3,upstream!3,downstream!1), DNA(upstream!1,binding!2,type~BBaR0051p4), RNAP(dna!2,rna), DNA(downstream!3,binding,type~BBaR0051p2) @ 0.0007
'RNAP binding to R0051 (cI on p2){77267}' DNA(binding,type~BBaR0051p3,upstream!2,downstream!1), DNA(upstream!1,binding,type~BBaR0051p4), RNAP(dna,rna), DNA(downstream!2,binding!3,type~BBaR0051p2), cI(dna!3) -> DNA(binding,type~BBaR0051p3,upstream!3,downstream!1), DNA(upstream!1,binding!2,type~BBaR0051p4), RNAP(dna!2,rna), DNA(downstream!3,binding!4,type~BBaR0051p2), cI(dna!4) @ 7e-07
'RNAP binding to R0051 (cI on p3){77268}' DNA(binding!3,type~BBaR0051p3,upstream!2,downstream!1), DNA(upstream!1,binding,type~BBaR0051p4), RNAP(dna,rna), DNA(downstream!2,binding,type~BBaR0051p2), cI(dna!3) -> DNA(binding!4,type~BBaR0051p3,upstream!3,downstream!1), DNA(upstream!1,binding!2,type~BBaR0051p4), RNAP(dna!2,rna), DNA(downstream!3,binding,type~BBaR0051p2), cI(dna!4) @ 7e-07
'RNAP binding to R0051 (cI on p2 and p3){77269}' DNA(binding!3,type~BBaR0051p3,upstream!2,downstream!1), DNA(upstream!1,binding,type~BBaR0051p4), RNAP(dna,rna), DNA(downstream!2,binding!4,type~BBaR0051p2), cI(dna!3), cI(dna!4) -> DNA(binding!4,type~BBaR0051p3,upstream!3,downstream!1), DNA(upstream!1,binding!2,type~BBaR0051p4), RNAP(dna!2,rna), DNA(downstream!3,binding!5,type~BBaR0051p2), cI(dna!4), cI(dna!5) @ 7e-07
'RNAP binding to R0082 (no OmpR){80200}' DNA(binding,type~BBaR0082p2,downstream!1), DNA(upstream!1,binding,type~BBaR0082p3,downstream!2), DNA(upstream!2,binding,type~BBaR0082p4,downstream!3), DNA(upstream!3,binding,type~BBaR0082p5), RNAP(dna,rna) -> DNA(binding,type~BBaR0082p2,downstream!1), DNA(upstream!1,binding,type~BBaR0082p3,downstream!2), DNA(upstream!2,binding,type~BBaR0082p4,downstream!3), DNA(upstream!3,binding!4,type~BBaR0082p5), RNAP(dna!4,rna) @ 7e-07
'RNAP binding to R0082 (OmpR on p2){80201}' DNA(binding!5,type~BBaR0082p2,downstream!1), DNA(upstream!1,binding,type~BBaR0082p3,downstream!2), DNA(upstream!2,binding,type~BBaR0082p4,downstream!3), DNA(upstream!3,binding,type~BBaR0082p5), RNAP(dna,rna), OmpR(dna!5) -> DNA(binding!5,type~BBaR0082p2,downstream!1), DNA(upstream!1,binding,type~BBaR0082p3,downstream!2), DNA(upstream!2,binding,type~BBaR0082p4,downstream!3), DNA(upstream!3,binding!4,type~BBaR0082p5), RNAP(dna!4,rna), OmpR(dna!5) @ 7e-07
'RNAP binding to R0082 (OmpR on p3){80202}' DNA(binding,type~BBaR0082p2,downstream!1), DNA(upstream!1,binding!5,type~BBaR0082p3,downstream!2), DNA(upstream!2,binding,type~BBaR0082p4,downstream!3), DNA(upstream!3,binding,type~BBaR0082p5), RNAP(dna,rna), OmpR(dna!5) -> DNA(binding,type~BBaR0082p2,downstream!1), DNA(upstream!1,binding!5,type~BBaR0082p3,downstream!2), DNA(upstream!2,binding,type~BBaR0082p4,downstream!3), DNA(upstream!3,binding!4,type~BBaR0082p5), RNAP(dna!4,rna), OmpR(dna!5) @ 7e-07
'RNAP binding to R0082 (OmpR on p4){80203}' DNA(binding,type~BBaR0082p2,downstream!1), DNA(upstream!1,binding,type~BBaR0082p3,downstream!2), DNA(upstream!2,binding!5,type~BBaR0082p4,downstream!3), DNA(upstream!3,binding,type~BBaR0082p5), RNAP(dna,rna), OmpR(dna!5) -> DNA(binding,type~BBaR0082p2,downstream!1), DNA(upstream!1,binding,type~BBaR0082p3,downstream!2), DNA(upstream!2,binding!5,type~BBaR0082p4,downstream!3), DNA(upstream!3,binding!4,type~BBaR0082p5), RNAP(dna!4,rna), OmpR(dna!5) @ 7e-07
'RNAP binding to R0082 (OmpR on p2 and p3){80204}' DNA(binding!5,type~BBaR0082p2,downstream!1), DNA(upstream!1,binding!6,type~BBaR0082p3,downstream!2), DNA(upstream!2,binding,type~BBaR0082p4,downstream!3), DNA(upstream!3,binding,type~BBaR0082p5), RNAP(dna,rna), OmpR(dna!5), OmpR(dna!6) -> DNA(binding!5,type~BBaR0082p2,downstream!1), DNA(upstream!1,binding!6,type~BBaR0082p3,downstream!2), DNA(upstream!2,binding,type~BBaR0082p4,downstream!3), DNA(upstream!3,binding!4,type~BBaR0082p5), RNAP(dna!4,rna), OmpR(dna!5), OmpR(dna!6) @ 0.0007
'RNAP binding to R0082 (OmpR on p2 and p4){80205}' DNA(binding!5,type~BBaR0082p2,downstream!1), DNA(upstream!1,binding,type~BBaR0082p3,downstream!2), DNA(upstream!2,binding!6,type~BBaR0082p4,downstream!3), DNA(upstream!3,binding,type~BBaR0082p5), RNAP(dna,rna), OmpR(dna!5), OmpR(dna!6) -> DNA(binding!5,type~BBaR0082p2,downstream!1), DNA(upstream!1,binding,type~BBaR0082p3,downstream!2), DNA(upstream!2,binding!6,type~BBaR0082p4,downstream!3), DNA(upstream!3,binding!4,type~BBaR0082p5), RNAP(dna!4,rna), OmpR(dna!5), OmpR(dna!6) @ 0.0007
'RNAP binding to R0082 (OmpR on p3 and p4){80206}' DNA(binding,type~BBaR0082p2,downstream!1), DNA(upstream!1,binding!5,type~BBaR0082p3,downstream!2), DNA(upstream!2,binding!6,type~BBaR0082p4,downstream!3), DNA(upstream!3,binding,type~BBaR0082p5), RNAP(dna,rna), OmpR(dna!5), OmpR(dna!6) -> DNA(binding,type~BBaR0082p2,downstream!1), DNA(upstream!1,binding!5,type~BBaR0082p3,downstream!2), DNA(upstream!2,binding!6,type~BBaR0082p4,downstream!3), DNA(upstream!3,binding!4,type~BBaR0082p5), RNAP(dna!4,rna), OmpR(dna!5), OmpR(dna!6) @ 0.0007
'RNAP binding to R0082 (OmpR on p2 and p3 and p4){80207}' DNA(binding!5,type~BBaR0082p2,downstream!1), DNA(upstream!1,binding!6,type~BBaR0082p3,downstream!2), DNA(upstream!2,binding!7,type~BBaR0082p4,downstream!3), DNA(upstream!3,binding,type~BBaR0082p5), RNAP(dna,rna), OmpR(dna!5), OmpR(dna!6), OmpR(dna!7) -> DNA(binding!5,type~BBaR0082p2,downstream!1), DNA(upstream!1,binding!6,type~BBaR0082p3,downstream!2), DNA(upstream!2,binding!7,type~BBaR0082p4,downstream!3), DNA(upstream!3,binding!4,type~BBaR0082p5), RNAP(dna!4,rna), OmpR(dna!5), OmpR(dna!6), OmpR(dna!7) @ 0.0007
'RNAP binding to R0084 (no OmpR){80208}' DNA(binding,type~BBaR0084p2,downstream!1), DNA(upstream!1,binding,type~BBaR0084p3,downstream!2), DNA(upstream!2,binding,type~BBaR0084p4,downstream!3), DNA(upstream!3,binding,type~BBaR0084p5), RNAP(dna,rna) -> DNA(binding,type~BBaR0084p2,downstream!1), DNA(upstream!1,binding,type~BBaR0084p3,downstream!2), DNA(upstream!2,binding,type~BBaR0084p4,downstream!3), DNA(upstream!3,binding!4,type~BBaR0084p5), RNAP(dna!4,rna) @ 0.0007
'RNAP binding to R0084 (OmpR on p2){80209}' DNA(binding!5,type~BBaR0084p2,downstream!1), DNA(upstream!1,binding,type~BBaR0084p3,downstream!2), DNA(upstream!2,binding,type~BBaR0084p4,downstream!3), DNA(upstream!3,binding,type~BBaR0084p5), RNAP(dna,rna), OmpR(dna!5) -> DNA(binding!5,type~BBaR0084p2,downstream!1), DNA(upstream!1,binding,type~BBaR0084p3,downstream!2), DNA(upstream!2,binding,type~BBaR0084p4,downstream!3), DNA(upstream!3,binding!4,type~BBaR0084p5), RNAP(dna!4,rna), OmpR(dna!5) @ 0.0007
'RNAP binding to R0084 (OmpR on p3){80210}' DNA(binding,type~BBaR0084p2,downstream!1), DNA(upstream!1,binding!5,type~BBaR0084p3,downstream!2), DNA(upstream!2,binding,type~BBaR0084p4,downstream!3), DNA(upstream!3,binding,type~BBaR0084p5), RNAP(dna,rna), OmpR(dna!5) -> DNA(binding,type~BBaR0084p2,downstream!1), DNA(upstream!1,binding!5,type~BBaR0084p3,downstream!2), DNA(upstream!2,binding,type~BBaR0084p4,downstream!3), DNA(upstream!3,binding!4,type~BBaR0084p5), RNAP(dna!4,rna), OmpR(dna!5) @ 0.0007
'RNAP binding to R0084 (OmpR on p4){80211}' DNA(binding,type~BBaR0084p2,downstream!1), DNA(upstream!1,binding,type~BBaR0084p3,downstream!2), DNA(upstream!2,binding!5,type~BBaR0084p4,downstream!3), DNA(upstream!3,binding,type~BBaR0084p5), RNAP(dna,rna), OmpR(dna!5) -> DNA(binding,type~BBaR0084p2,downstream!1), DNA(upstream!1,binding,type~BBaR0084p3,downstream!2), DNA(upstream!2,binding!5,type~BBaR0084p4,downstream!3), DNA(upstream!3,binding!4,type~BBaR0084p5), RNAP(dna!4,rna), OmpR(dna!5) @ 0.0007
'RNAP binding to R0084 (OmpR on p2 and p3){80212}' DNA(binding!5,type~BBaR0084p2,downstream!1), DNA(upstream!1,binding!6,type~BBaR0084p3,downstream!2), DNA(upstream!2,binding,type~BBaR0084p4,downstream!3), DNA(upstream!3,binding,type~BBaR0084p5), RNAP(dna,rna), OmpR(dna!5), OmpR(dna!6) -> DNA(binding!5,type~BBaR0084p2,downstream!1), DNA(upstream!1,binding!6,type~BBaR0084p3,downstream!2), DNA(upstream!2,binding,type~BBaR0084p4,downstream!3), DNA(upstream!3,binding!4,type~BBaR0084p5), RNAP(dna!4,rna), OmpR(dna!5), OmpR(dna!6) @ 7e-07
'RNAP binding to R0084 (OmpR on p2 and p4){80213}' DNA(binding!5,type~BBaR0084p2,downstream!1), DNA(upstream!1,binding,type~BBaR0084p3,downstream!2), DNA(upstream!2,binding!6,type~BBaR0084p4,downstream!3), DNA(upstream!3,binding,type~BBaR0084p5), RNAP(dna,rna), OmpR(dna!5), OmpR(dna!6) -> DNA(binding!5,type~BBaR0084p2,downstream!1), DNA(upstream!1,binding,type~BBaR0084p3,downstream!2), DNA(upstream!2,binding!6,type~BBaR0084p4,downstream!3), DNA(upstream!3,binding!4,type~BBaR0084p5), RNAP(dna!4,rna), OmpR(dna!5), OmpR(dna!6) @ 7e-07
'RNAP binding to R0084 (OmpR on p3 and p4){80214}' DNA(binding,type~BBaR0084p2,downstream!1), DNA(upstream!1,binding!5,type~BBaR0084p3,downstream!2), DNA(upstream!2,binding!6,type~BBaR0084p4,downstream!3), DNA(upstream!3,binding,type~BBaR0084p5), RNAP(dna,rna), OmpR(dna!5), OmpR(dna!6) -> DNA(binding,type~BBaR0084p2,downstream!1), DNA(upstream!1,binding!5,type~BBaR0084p3,downstream!2), DNA(upstream!2,binding!6,type~BBaR0084p4,downstream!3), DNA(upstream!3,binding!4,type~BBaR0084p5), RNAP(dna!4,rna), OmpR(dna!5), OmpR(dna!6) @ 7e-07
'RNAP binding to R0084 (OmpR on p2 and p3 and p4){80215}' DNA(binding!5,type~BBaR0084p2,downstream!1), DNA(upstream!1,binding!6,type~BBaR0084p3,downstream!2), DNA(upstream!2,binding!7,type~BBaR0084p4,downstream!3), DNA(upstream!3,binding,type~BBaR0084p5), RNAP(dna,rna), OmpR(dna!5), OmpR(dna!6), OmpR(dna!7) -> DNA(binding!5,type~BBaR0084p2,downstream!1), DNA(upstream!1,binding!6,type~BBaR0084p3,downstream!2), DNA(upstream!2,binding!7,type~BBaR0084p4,downstream!3), DNA(upstream!3,binding!4,type~BBaR0084p5), RNAP(dna!4,rna), OmpR(dna!5), OmpR(dna!6), OmpR(dna!7) @ 7e-07
'RNAP binding to K191007 (no LOVTAP) {80216}' DNA(binding,type~BBaK191007p2,downstream!1), DNA(upstream!1,binding,type~BBaK191007p3), RNAP(dna,rna) -> DNA(binding,type~BBaK191007p2,downstream!1), DNA(upstream!1,binding!2,type~BBaK191007p3), RNAP(dna!2,rna) @ 0.0007
'RNAP binding to K191007 (LOVTAP on p2) {80217}' DNA(binding!1,type~BBaK191007p2,downstream!2), DNA(upstream!2,binding,type~BBaK191007p3), LOVTAP(dna!1), RNAP(dna,rna) -> DNA(binding!1,type~BBaK191007p2,downstream!2), DNA(upstream!2,binding!3,type~BBaK191007p3), LOVTAP(dna!1), RNAP(dna!3,rna) @ 7e-07
'RNAP binding to R0PHO (no PhoB) {80218}' DNA(binding,type~BBaR0PHOp2,downstream!1), DNA(upstream!1,binding,type~BBaR0PHOp3), RNAP(dna,rna) -> DNA(binding,type~BBaR0PHOp2,downstream!1), DNA(upstream!1,binding!2,type~BBaR0PHOp3), RNAP(dna!2,rna) @ 0.0007
'RNAP binding to R0PHO (PhoB on p2) {80219}' DNA(binding!1,type~BBaR0PHOp2,downstream!2), DNA(upstream!2,binding,type~BBaR0PHOp3), PhoB(dna!1), RNAP(dna,rna) -> DNA(binding!1,type~BBaR0PHOp2,downstream!2), DNA(upstream!2,binding!3,type~BBaR0PHOp3), PhoB(dna!1), RNAP(dna!3,rna) @ 7e-07



# Transcription.

'Transcription initiation{58498}' DNA(binding!1,type~BBaR0000p3,downstream!2), RNAP(dna!1,rna), DNA(upstream!2,binding) -> DNA(binding,type~BBaR0000p3,downstream!3), RNAP(dna!1,rna!2), DNA(upstream!3,binding!1), RNA(binding,upstream,downstream!2,type~BBaR0000) @ 10.0
'Transcription initiation of R0051{77270}' DNA(binding!1,type~BBaR0051p4,downstream!2), RNAP(dna!1,rna), DNA(upstream!2,binding) -> DNA(binding,type~BBaR0051p4,downstream!3), RNAP(dna!1,rna!2), DNA(upstream!3,binding!1), RNA(binding,upstream,downstream!2,type~BBaR0051) @ 10.0
'Transcription initiation of R0010{77316}' DNA(binding!1,type~BBaR0010p4,downstream!2), RNAP(dna!1,rna), DNA(upstream!2,binding) -> DNA(binding,type~BBaR0010p4,downstream!3), RNAP(dna!1,rna!2), DNA(upstream!3,binding!1), RNA(binding,upstream,downstream!2,type~BBaR0010) @ 10.0
'Transcription initiation of R0040{77305}' DNA(binding!1,type~BBaR0040p4,downstream!2), RNAP(dna!1,rna), DNA(upstream!2,binding) -> DNA(binding,type~BBaR0040p4,downstream!3), RNAP(dna!1,rna!2), DNA(upstream!3,binding!1), RNA(binding,upstream,downstream!2,type~BBaR0040) @ 10.0
'Transcription initiation of R0082{80220}' DNA(binding!1,type~BBaR0082p5,downstream!2), RNAP(dna!1,rna), DNA(upstream!2,binding) -> DNA(binding,type~BBaR0082p5,downstream!3), RNAP(dna!1,rna!2), DNA(upstream!3,binding!1), RNA(binding,upstream,downstream!2,type~BBaR0082) @ 10.0
'Transcription initiation of R0084{80221}' DNA(binding!1,type~BBaR0084p5,downstream!2), RNAP(dna!1,rna), DNA(upstream!2,binding) -> DNA(binding,type~BBaR0084p5,downstream!3), RNAP(dna!1,rna!2), DNA(upstream!3,binding!1), RNA(binding,upstream,downstream!2,type~BBaR0084) @ 10.0
'Transcription initiation of K191007{80222}' DNA(binding!1,type~BBaK191007p3,downstream!2), RNAP(dna!1,rna), DNA(upstream!2,binding) -> DNA(binding,type~BBaK191007p3,downstream!3), RNAP(dna!1,rna!2), DNA(upstream!3,binding!1), RNA(binding,upstream,downstream!2,type~BBaK191007) @ 10.0
'Transcription initiation of R0PHO{80223}' DNA(binding!1,type~BBaR0PHOp3,downstream!2), RNAP(dna!1,rna), DNA(upstream!2,binding) -> DNA(binding,type~BBaR0PHOp3,downstream!3), RNAP(dna!1,rna!2), DNA(upstream!3,binding!1), RNA(binding,upstream,downstream!2,type~BBaR0PHO) @ 10.0

'RBS transcription{58497}' DNA(binding!1,downstream!2,type~BBaB0000), RNAP(dna!1,rna!3), DNA(upstream!2,binding), RNA(downstream!3) -> DNA(binding,downstream!2,type~BBaB0000), RNAP(dna!1,rna!3), DNA(upstream!2,binding!1), RNA(downstream!4), RNA(binding,upstream!4,downstream!3,type~BBaB0000) @ 10.0
'RBS BBa_B0034 transcription{77253}' DNA(binding!1,downstream!2,type~BBaB0034), RNAP(dna!1,rna!3), DNA(upstream!2,binding), RNA(downstream!3) -> DNA(binding,downstream!2,type~BBaB0034), RNAP(dna!1,rna!3), DNA(upstream!2,binding!1), RNA(downstream!4), RNA(binding,upstream!4,downstream!3,type~BBaB0034) @ 10.0

'Coding sequence transcription{77009}' DNA(binding!1,downstream!2,type~BBaC0000), RNAP(dna!1,rna!3), DNA(upstream!2,binding), RNA(downstream!3) -> DNA(binding,downstream!2,type~BBaC0000), RNAP(dna!1,rna!3), DNA(upstream!2,binding!1), RNA(downstream!4), RNA(binding,upstream!4,downstream!3,type~BBaC0000) @ 10.0
'C0012 transcription{77279}' DNA(binding!1,downstream!2,type~BBaC0012), RNAP(dna!1,rna!3), DNA(upstream!2,binding), RNA(downstream!3) -> DNA(binding,downstream!2,type~BBaC0012), RNAP(dna!1,rna!3), DNA(upstream!2,binding!1), RNA(downstream!4), RNA(binding,upstream!4,downstream!3,type~BBaC0012) @ 10.0
'C0051 transcription{77272}' DNA(binding!1,downstream!2,type~BBaC0051), RNAP(dna!1,rna!3), DNA(upstream!2,binding), RNA(downstream!3) -> DNA(binding,downstream!2,type~BBaC0051), RNAP(dna!1,rna!3), DNA(upstream!2,binding!1), RNA(downstream!4), RNA(binding,upstream!4,downstream!3,type~BBaC0051) @ 10.0
'C0040 transcription{77278}' DNA(binding!1,downstream!2,type~BBaC0040), RNAP(dna!1,rna!3), DNA(upstream!2,binding), RNA(downstream!3) -> DNA(binding,downstream!2,type~BBaC0040), RNAP(dna!1,rna!3), DNA(upstream!2,binding!1), RNA(downstream!4), RNA(binding,upstream!4,downstream!3,type~BBaC0040) @ 10.0
'C0RED transcription{77500}' DNA(binding!1,downstream!2,type~BBaC0RED), RNAP(dna!1,rna!3), DNA(upstream!2,binding), RNA(downstream!3) -> DNA(binding,downstream!2,type~BBaC0RED), RNAP(dna!1,rna!3), DNA(upstream!2,binding!1), RNA(downstream!4), RNA(binding,upstream!4,downstream!3,type~BBaC0RED) @ 10.0
'C0BLUE transcription{77501}' DNA(binding!1,downstream!2,type~BBaC0BLUE), RNAP(dna!1,rna!3), DNA(upstream!2,binding), RNA(downstream!3) -> DNA(binding,downstream!2,type~BBaC0BLUE), RNAP(dna!1,rna!3), DNA(upstream!2,binding!1), RNA(downstream!4), RNA(binding,upstream!4,downstream!3,type~BBaC0BLUE) @ 10.0
'C0GREEN transcription{77502}' DNA(binding!1,downstream!2,type~BBaC0GREEN), RNAP(dna!1,rna!3), DNA(upstream!2,binding), RNA(downstream!3) -> DNA(binding,downstream!2,type~BBaC0GREEN), RNAP(dna!1,rna!3), DNA(upstream!2,binding!1), RNA(downstream!4), RNA(binding,upstream!4,downstream!3,type~BBaC0GREEN) @ 10.0

'Termination{77013}' DNA(binding!1,type~BBaK0000), RNAP(dna!1,rna!2), RNA(downstream!2) -> DNA(binding,type~BBaK0000), RNAP(dna,rna), RNA(downstream) @ 10.0
'Termination - B0011{77290}' DNA(binding!1,type~BBaB0011), RNAP(dna!1,rna!2), RNA(downstream!2) -> DNA(binding,type~BBaB0011), RNAP(dna,rna), RNA(downstream) @ 10.0

'RNAP falloff{76542}' DNA(binding!1,downstream!3), RNAP(dna!1,rna!2), RNA(downstream!2), DNA(upstream!3,binding!_) -> DNA(binding,downstream!1), RNAP(dna,rna), RNA(downstream), DNA(upstream!1,binding!_) @ 1.0

'Terminator transcription (readthrough){77015}' DNA(binding!1,downstream!2,type~BBaK0000), RNAP(dna!1,rna!3), DNA(upstream!2,binding), RNA(downstream!3) -> DNA(binding,downstream!2,type~BBaK0000), RNAP(dna!1,rna!3), DNA(upstream!2,binding!1), RNA(downstream!4), RNA(binding,upstream!4,downstream!3,type~BBaK0000) @ 1.0
'B0011 terminator transcription (readthrough){77291}' DNA(binding!1,downstream!2,type~BBaB0011), RNAP(dna!1,rna!3), DNA(upstream!2,binding), RNA(downstream!3) -> DNA(binding,downstream!2,type~BBaR0011), RNAP(dna!1,rna!3), DNA(upstream!2,binding!1), RNA(downstream!4), RNA(binding,upstream!4,downstream!3,type~BBaR0011) @ 0.5

'Promoter transcription (readthrough){77000}' DNA(binding,type~BBaR0000p3,downstream!2,upstream!3), RNAP(dna!1,rna!5), DNA(upstream!2,binding), DNA(upstream!4,downstream!3,binding,type~BBaR0000p2), DNA(downstream!4,binding!1,type~BBaR0000p1), RNA(downstream!5) -> DNA(binding,type~BBaR0000p3,downstream!3,upstream!5), RNAP(dna!1,rna!6), DNA(upstream!3,binding!1), DNA(upstream!4,downstream!5,binding,type~BBaR0000p2), DNA(downstream!4,binding,type~BBaR0000p1), RNA(downstream!2), RNA(binding,upstream!2,downstream!6,type~BBaR0000) @ 10.0
'Transcription of R0051 (readthrough){77271}' DNA(binding,type~BBaR0051p3,downstream!2,upstream!3), RNAP(dna!1,rna!5), DNA(upstream!6,binding), DNA(upstream!4,downstream!3,binding,type~BBaR0051p2), DNA(downstream!4,binding!1,type~BBaR0051p1), RNA(downstream!5), DNA(upstream!2,downstream!6,binding,type~BBaR0051p4) -> DNA(binding,type~BBaR0051p3,downstream!3,upstream!5), RNAP(dna!1,rna!6), DNA(upstream!7,binding!1), DNA(upstream!4,downstream!5,binding,type~BBaR0051p2), DNA(downstream!4,binding,type~BBaR0051p1), RNA(downstream!2), DNA(upstream!3,downstream!7,binding,type~BBaR0051p4), RNA(binding,upstream!2,downstream!6,type~BBaR0051) @ 10.0
'Transcription of R0010 (readthrough){77317}' DNA(binding,type~BBaR0010p3,downstream!2,upstream!3), RNAP(dna!1,rna!5), DNA(upstream!6,binding), DNA(upstream!4,downstream!3,binding,type~BBaR0010p2), DNA(downstream!4,binding!1,type~BBaR0010p1), RNA(downstream!5), DNA(upstream!2,downstream!6,binding,type~BBaR0010p4) -> DNA(binding,type~BBaR0010p3,downstream!3,upstream!5), RNAP(dna!1,rna!6), DNA(upstream!7,binding!1), DNA(upstream!4,downstream!5,binding,type~BBaR0010p2), DNA(downstream!4,binding,type~BBaR0010p1), RNA(downstream!2), DNA(upstream!3,downstream!7,binding,type~BBaR0010p4), RNA(binding,upstream!2,downstream!6,type~BBaR0010) @ 10.0
'Transcription of R0040 (readthrough){77306}' DNA(binding,type~BBaR0040p3,downstream!2,upstream!3), RNAP(dna!1,rna!5), DNA(upstream!6,binding), DNA(upstream!4,downstream!3,binding,type~BBaR0040p2), DNA(downstream!4,binding!1,type~BBaR0040p1), RNA(downstream!5), DNA(upstream!2,downstream!6,binding,type~BBaR0040p4) -> DNA(binding,type~BBaR0040p3,downstream!3,upstream!5), RNAP(dna!1,rna!6), DNA(upstream!7,binding!1), DNA(upstream!4,downstream!5,binding,type~BBaR0040p2), DNA(downstream!4,binding,type~BBaR0040p1), RNA(downstream!2), DNA(upstream!3,downstream!7,binding,type~BBaR0040p4), RNA(binding,upstream!2,downstream!6,type~BBaR0040) @ 10.0
'Transcription of R0082 (readthrough){80222}' DNA(binding!1,type~BBaR0082p1,downstream!2), DNA(upstream!2,binding,type~BBaR0082p2,downstream!3), DNA(upstream!3,binding,type~BBaR0082p3,downstream!4), DNA(upstream!4,binding,type~BBaR0082p4,downstream!5), DNA(upstream!5,binding,type~BBaR0082p5,downstream!6), DNA(upstream!6,binding), RNAP(dna!1,rna!7), RNA(downstream!7) -> DNA(binding,type~BBaR0082p1,downstream!2), DNA(upstream!2,binding,type~BBaR0082p2,downstream!3), DNA(upstream!3,binding,type~BBaR0082p3,downstream!4), DNA(upstream!4,binding,type~BBaR0082p4,downstream!5), DNA(upstream!5,binding,type~BBaR0082p5,downstream!6), DNA(upstream!6,binding!1), RNAP(dna!1,rna!7),RNA(downstream!8),RNA(binding,upstream!8,downstream!7,type~BBaR0082) @ 10.0 
'Transcription of R0084 (readthrough){80223}' DNA(binding!1,type~BBaR0084p1,downstream!2), DNA(upstream!2,binding,type~BBaR0084p2,downstream!3), DNA(upstream!3,binding,type~BBaR0084p3,downstream!4), DNA(upstream!4,binding,type~BBaR0084p4,downstream!5), DNA(upstream!5,binding,type~BBaR0084p5,downstream!6), DNA(upstream!6,binding), RNAP(dna!1,rna!7), RNA(downstream!7) -> DNA(binding,type~BBaR0084p1,downstream!2), DNA(upstream!2,binding,type~BBaR0084p2,downstream!3), DNA(upstream!3,binding,type~BBaR0084p3,downstream!4), DNA(upstream!4,binding,type~BBaR0084p4,downstream!5), DNA(upstream!5,binding,type~BBaR0084p5,downstream!6), DNA(upstream!6,binding!1), RNAP(dna!1,rna!7),RNA(downstream!8),RNA(binding,upstream!8,downstream!7,type~BBaR0084) @ 10.0 
'Transcription of K191007 (readthrough){80224}' DNA(binding!1,type~BBaK191007p1,downstream!2), DNA(upstream!2,binding,type~BBaK191007p2,downstream!3), DNA(upstream!3,binding,type~BBaK191007p3,downstream!4), DNA(upstream!4,binding), RNAP(dna!1,rna!5), RNA(downstream!5) -> DNA(binding,type~BBaK191007p1,downstream!2), DNA(upstream!2,binding,type~BBaK191007p2,downstream!3), DNA(upstream!3,binding,type~BBaK191007p3,downstream!4), DNA(upstream!4,binding!1), RNAP(dna!1,rna!5),RNA(downstream!6),RNA(binding,upstream!6,downstream!5,type~BBaK191007) @ 10.0 
'Transcription of R0PHO (readthrough){80223}' DNA(binding!1,type~BBaR0PHOp1,downstream!2), DNA(upstream!2,binding,type~BBaR0PHOp2,downstream!3), DNA(upstream!3,binding,type~BBaR0PHOp3,downstream!4), DNA(upstream!4,binding), RNAP(dna!1,rna!5), RNA(downstream!5) -> DNA(binding,type~BBaR0PHOp1,downstream!2), DNA(upstream!2,binding,type~BBaR0PHOp2,downstream!3), DNA(upstream!3,binding,type~BBaR0PHOp3,downstream!4), DNA(upstream!4,binding!1), RNAP(dna!1,rna!5),RNA(downstream!6),RNA(binding,upstream!6,downstream!5,type~BBaR0PHO) @ 10.0 


# Translation.

'Ribosome binding{77002}' RNA(binding,type~BBaB0000), Ribosome(rna) -> RNA(binding!1,type~BBaB0000), Ribosome(rna!1) @ 0.000166
'RBS BBa_B0034 Ribosome binding{77254}' RNA(binding,type~BBaB0034), Ribosome(rna) -> RNA(binding!1,type~BBaB0034), Ribosome(rna!1) @ 0.000166

'Translation initiation{77010}' RNA(binding!2,downstream!1), RNA(binding,upstream!1,type~BBaC0000), Ribosome(rna!2) -> RNA(binding,downstream!1), RNA(binding!2,upstream!1,type~BBaC0000), Ribosome(rna!2) @ 0.167
'LacI translation initiation{77282}' RNA(binding!2,downstream!1), RNA(binding,upstream!1,type~BBaC0012), Ribosome(rna!2) -> RNA(binding,downstream!1), RNA(binding!2,upstream!1,type~BBaC0012), Ribosome(rna!2) @ 0.167
'TetR translation initiation{77281}' RNA(binding!2,downstream!1), RNA(binding,upstream!1,type~BBaC0040), Ribosome(rna!2) -> RNA(binding,downstream!1), RNA(binding!2,upstream!1,type~BBaC0040), Ribosome(rna!2) @ 0.167
'cI translation initiation{77280}' RNA(binding!2,downstream!1), RNA(binding,upstream!1,type~BBaC0051), Ribosome(rna!2) -> RNA(binding,downstream!1), RNA(binding!2,upstream!1,type~BBaC0051), Ribosome(rna!2) @ 0.167
'REDLuc translation initiation{77501}' RNA(binding!2,downstream!1), RNA(binding,upstream!1,type~BBaC0RED), Ribosome(rna!2) -> RNA(binding,downstream!1), RNA(binding!2,upstream!1,type~BBaC0RED), Ribosome(rna!2) @ 0.167
'BLUELuc translation initiation{77502}' RNA(binding!2,downstream!1), RNA(binding,upstream!1,type~BBaC0BLUE), Ribosome(rna!2) -> RNA(binding,downstream!1), RNA(binding!2,upstream!1,type~BBaC0BLUE), Ribosome(rna!2) @ 0.167
'GREENLuc translation initiation{77503}' RNA(binding!2,downstream!1), RNA(binding,upstream!1,type~BBaC0GREEN), Ribosome(rna!2) -> RNA(binding,downstream!1), RNA(binding!2,upstream!1,type~BBaC0GREEN), Ribosome(rna!2) @ 0.167

'Coding sequence translation{77005}' RNA(binding!1,type~BBaC0000), Ribosome(rna!1) -> RNA(binding,type~BBaC0000), Ribosome(rna), Repressor(dna) @ 10.0
'LacI translation{77285}' RNA(binding!1,type~BBaC0012), Ribosome(rna!1) -> RNA(binding,type~BBaC0012), Ribosome(rna), LacI(dna,lactose) @ 10.0
'TetR translation{77284}' RNA(binding!1,type~BBaC0040), Ribosome(rna!1) -> RNA(binding,type~BBaC0040), Ribosome(rna), TetR(dna,atc) @ 10.0
'cI translation{77283}' RNA(binding!1,type~BBaC0051), Ribosome(rna!1) -> RNA(binding,type~BBaC0051), Ribosome(rna), cI(dna) @ 10.0
'REDLuc translation{77504}' RNA(binding!1,type~BBaC0RED), Ribosome(rna!1) -> RNA(binding,type~BBaC0RED), Ribosome(rna), REDLuc() @ 10.0
'BLUELuc translation{77505}' RNA(binding!1,type~BBaC0BLUE), Ribosome(rna!1) -> RNA(binding,type~BBaC0BLUE), Ribosome(rna), BLUELuc() @ 10.0
'GREENLuc translation{77506}' RNA(binding!1,type~BBaC0GREEN), Ribosome(rna!1) -> RNA(binding,type~BBaC0GREEN), Ribosome(rna), GREENLuc() @ 10.0

'Ribosome falloff{76777}' Ribosome(rna!1), RNA(binding!1) -> Ribosome(rna), RNA(binding) @ 0.01


# Creation and communication of light.

'Creation of RED light{77700}' REDLuc() -> REDLuc(), RED() @ 0.003
#'Communication of RED light{77701}'  -> RED() @ 0.0

'Creation of BLUE light{77710}' BLUELuc() -> BLUELuc(), BLUE() @ 0.003
#'Communication of BLUE light{77711}'  -> BLUE() @ 0.0

'Creation of GREEN light{77720}' GREENLuc() -> GREENLuc(), GREEN() @ 0.003
#'Communication of GREEN light{77721}'  -> GREEN() @ 0.0


# Degradation of various agents.

'RNA degradation{76543}' RNA(binding) ->  @ 0.0058

'Repressor degradation{77212}' Repressor(dna) ->  @ 0.00115
'LacI degradation{77288}' LacI(dna) ->  @ 0.00115
'TetR degradation{77287}' TetR(dna) ->  @ 0.00115
'cI degradation{77286}' cI(dna) ->  @ 0.00115

'REDLuc degradation{77503}' REDLuc() ->  @ 0.00115
'BLUELuc degradation{77513}' BLUELuc() ->  @ 0.00115
'GREENLuc degradation{77523}' GREENLuc() ->  @ 0.00115

'RED light dissipation{77702}' RED() ->  @ 0.05
'BLUE light dissipation{77712}' BLUE() ->  @ 0.05
'GREEN light dissipation{77722}' GREEN() -> @ 0.05

#'REDo light dissipation{77732}' REDo() ->  @ 0.05
#'BLUEo light dissipation{77742}' BLUEo() ->  @ 0.05
#'GREENo light dissipation{77752}' GREENo() -> @ 0.05


# Perturbatory effects of IPTG and ATC.

#'ATC addition{77334}'  -> ATC(tetr) @ 0.0
'ATC washout{77333}' ATC(tetr) ->  @ 0.0
#'IPTG addition{77331}'  -> IPTG(laci) @ 0.0
'IPTG washout{77329}' IPTG(laci) ->  @ 0.0

'Binding of IPTG to LacI{77327}' IPTG(laci), LacI(dna,lactose) <-> IPTG(laci!1), LacI(dna,lactose!1) @ 0.00166,0.02
'Binding of ATC to TetR{77325}' TetR(dna,atc), ATC(tetr) <-> TetR(dna,atc!1), ATC(tetr!1) @ 1.66,0.001

# Initial conditions, observables, and perturbations.

%init: 700 * (RNAP(dna,rna))
%init: 18000 * (Ribosome(rna))
%init: 50 * (Cph8(ompr,active~on))
%init: 50 * (OmpR(dna,cph8,site~p))
%init: 50 * (CcaS(phob,active~on))
%init: 50 * (PhoR(dna,ccas,site~p))
%init: 50 * (LOVTAP(dna,active~dark))
#%init: 1 * (DNA(upstream,downstream!1,binding,type~BBaR0051p1), DNA(upstream!1,downstream!2,binding,type~BBaR0051p2), DNA(upstream!2,downstream!3,binding,type~BBaR0051p3), DNA(upstream!3,downstream!4,binding,type~BBaR0051p4), DNA(upstream!4,downstream!5,binding,type~BBaB0034), DNA(upstream!5,downstream!6,binding,type~BBaC0012), DNA(upstream!6,downstream,binding,type~BBaB0011))
%init: 1 * (DNA(upstream,downstream!1,binding,type~BBaR0PHOp1), DNA(upstream!1,downstream!2,binding,type~BBaR0PHOp2), DNA(upstream!2,downstream!3,binding,type~BBaR0PHOp3), DNA(upstream!3,downstream!4,binding,type~BBaR0051p1), DNA(upstream!4,downstream!5,binding,type~BBaR0051p2), DNA(upstream!5,downstream!6,binding,type~BBaR0051p3), DNA(upstream!6,downstream!7,binding,type~BBaR0051p4), DNA(upstream!7,downstream!8,binding,type~BBaB0034), DNA(upstream!8,downstream!9,binding,type~BBaC0012), DNA(upstream!9,downstream,binding,type~BBaB0011))
#%init: 1 * (DNA(upstream,downstream!1,binding,type~BBaR0010p1), DNA(upstream!1,downstream!2,binding,type~BBaR0010p2), DNA(upstream!2,downstream!3,binding,type~BBaR0010p3), DNA(upstream!3,downstream!4,binding,type~BBaR0010p4), DNA(upstream!4,downstream!5,binding,type~BBaB0034), DNA(upstream!5,downstream!6,binding,type~BBaC0040), DNA(upstream!6,downstream,binding,type~BBaB0011))
%init: 1 * (DNA(upstream,downstream!1,binding,type~BBaR0082p1), DNA(upstream!1,downstream!2,binding,type~BBaR0082p2), DNA(upstream!2,downstream!3,binding,type~BBaR0082p3), DNA(upstream!3,downstream!4,binding,type~BBaR0082p4), DNA(upstream!4,downstream!5,binding,type~BBaR0082p5), DNA(upstream!5,downstream!6,binding,type~BBaR0010p1), DNA(upstream!6,downstream!7,binding,type~BBaR0010p2), DNA(upstream!7,downstream!8,binding,type~BBaR0010p3), DNA(upstream!8,downstream!9,binding,type~BBaR0010p4), DNA(upstream!9,downstream!10,binding,type~BBaB0034), DNA(upstream!10,downstream!11,binding,type~BBaC0040), DNA(upstream!11,downstream,binding,type~BBaB0011))
#%init: 1 * (DNA(upstream,downstream!1,binding,type~BBaR0040p1), DNA(upstream!1,downstream!2,binding,type~BBaR0040p2), DNA(upstream!2,downstream!3,binding,type~BBaR0040p3), DNA(upstream!3,downstream!4,binding,type~BBaR0040p4), DNA(upstream!4,downstream!5,binding,type~BBaB0034), DNA(upstream!5,downstream!6,binding,type~BBaC0051), DNA(upstream!6,downstream,binding,type~BBaB0011))
%init: 1 * (DNA(upstream,downstream!1,binding,type~BBaK191007p1), DNA(upstream!1,downstream!2,binding,type~BBaK191007p2), DNA(upstream!2,downstream!3,binding,type~BBaK191007p3), DNA(upstream!3,downstream!4,binding,type~BBaR0040p1), DNA(upstream!4,downstream!5,binding,type~BBaR0040p2), DNA(upstream!5,downstream!6,binding,type~BBaR0040p3), DNA(upstream!6,downstream!7,binding,type~BBaR0040p4), DNA(upstream!7,downstream!8,binding,type~BBaB0034), DNA(upstream!8,downstream!9,binding,type~BBaC0051), DNA(upstream!9,downstream,binding,type~BBaB0011))
%init: 1 * (DNA(upstream,downstream!1,binding,type~BBaR0010p1), DNA(upstream!1,downstream!2,binding,type~BBaR0010p2), DNA(upstream!2,downstream!3,binding,type~BBaR0010p3), DNA(upstream!3,downstream!4,binding,type~BBaR0010p4), DNA(upstream!4,downstream!5,binding,type~BBaB0034), DNA(upstream!5,downstream!6,binding,type~BBaC0RED), DNA(upstream!6,downstream,binding,type~BBaB0011))
%init: 1 * (DNA(upstream,downstream!1,binding,type~BBaR0040p1), DNA(upstream!1,downstream!2,binding,type~BBaR0040p2), DNA(upstream!2,downstream!3,binding,type~BBaR0040p3), DNA(upstream!3,downstream!4,binding,type~BBaR0040p4), DNA(upstream!4,downstream!5,binding,type~BBaB0034), DNA(upstream!5,downstream!6,binding,type~BBaC0BLUE), DNA(upstream!6,downstream,binding,type~BBaB0011))
%init: 1 * (DNA(upstream,downstream!1,binding,type~BBaR0051p1), DNA(upstream!1,downstream!2,binding,type~BBaR0051p2), DNA(upstream!2,downstream!3,binding,type~BBaR0051p3), DNA(upstream!3,downstream!4,binding,type~BBaR0051p4), DNA(upstream!4,downstream!5,binding,type~BBaB0034), DNA(upstream!5,downstream!6,binding,type~BBaC0GREEN), DNA(upstream!6,downstream,binding,type~BBaB0011))
#%init: 1 * (DNA(upstream,downstream!1,binding,type~BBaR0084p1), DNA(upstream!1,downstream!2,binding,type~BBaR0084p2), DNA(upstream!2,downstream!3,binding,type~BBaR0084p3), DNA(upstream!3,downstream!4,binding,type~BBaR0084p4), DNA(upstream!4,downstream!5,binding,type~BBaR0084p5), DNA(upstream!5,downstream!6,binding,type~BBaB0034), DNA(upstream!6,downstream!7,binding,type~BBaC0012), DNA(upstream!7,downstream,binding,type~BBaB0011))
#%init: 1 * (DNA(upstream,downstream!1,binding,type~BBaR0082p1), DNA(upstream!1,downstream!2,binding,type~BBaR0082p2), DNA(upstream!2,downstream!3,binding,type~BBaR0082p3), DNA(upstream!3,downstream!4,binding,type~BBaR0082p4), DNA(upstream!4,downstream!5,binding,type~BBaR0082p5), DNA(upstream!5,downstream!6,binding,type~BBaB0034), DNA(upstream!6,downstream!7,binding,type~BBaC0040), DNA(upstream!7,downstream,binding,type~BBaB0011))

#%mod: $T>10000 do 'Communication of GREEN light{77721}' := 1000
#%mod: $T>10500 do 'Communication of GREEN light{77721}' := 0

#%mod: $T>15000 do 'Communication of RED light{77701}' := 1000
#%mod: $T>15500 do 'Communication of RED light{77701}' := 0

%obs: 'RED' RED()
%obs: 'GREEN' GREEN()
%obs: 'BLUE' BLUE()
#%obs: 'Sensed RED' RED()
#%obs: 'Sensed BLUE' BLUE()
#%obs: 'Sensed GREEN' GREEN()