### OR ###

#We assume saturating concentration of HSL wich is required for LasR active form

%agent:  P4_OR(x)

%agent:  lasR_OR(x)

%agent:  GFP-P4_gene(bs)

%agent:  GFP-lasR_gene(bs)

%agent:  GFP_mrna()
%agent:  GFP()

%agent:  RFP_OR()

#AND influx

#we don't know the rate of tf tranference through nanotubes we use only steady concentrations
'P4-nano' -> P4_OR() @ 'nanoRate'

'lasR-nano' -> lasR_OR() @ 'nanoRate'

'RFP-nano' -> RFP_OR() @ 'nanoRate'


'P4-GFP_on'  P4_OR(x),GFP-P4_gene(bs) -> P4_OR(x!11),GFP-P4_gene(bs!11) @ 'TF_onRate'
'P4-GFP_off'  P4_OR(x!11),GFP-P4_gene(bs!11) -> P4_OR(x),GFP-P4_gene(bs) @ 'TF_offRate'

'lasR-GFP_on'  lasR_OR(x),GFP-lasR_gene(bs) -> lasR_OR(x!12),GFP-lasR_gene(bs!12) @ 'TF_onRate'
'lasR-GFP_off'  lasR_OR(x!12),GFP-lasR_gene(bs!12) -> lasR_OR(x),GFP-lasR_gene(bs) @ 'TF_offRate'

'GFP_P4-transc'  GFP-P4_gene(bs) -> GFP-P4_gene(bs),GFP_mrna() @ 'INACTIVEtranscRate'
'A-GFP_P4-transc'  GFP-P4_gene(bs!11),P4_OR(x!11) -> GFP-P4_gene(bs!11),P4_OR(x!11),GFP_mrna() @ 'transcRate'


#A- is for active transcription

'GFP_lasR-transc'  GFP-lasR_gene(bs) -> GFP-lasR_gene(bs),GFP_mrna() @ 'INACTIVEtranscRate'
'A-GFP_lasR-transc'  GFP-lasR_gene(bs!12),lasR_OR(x!12) -> GFP-lasR_gene(bs!12),lasR_OR(x!12),GFP_mrna() @ 'transcRate'

#GFP translate

'GFP-transl' GFP_mrna() -> GFP() @ 'translRate'

### Decay


'P4_OR-dec'  P4_OR()-> @ 'prot-decRate'
'lasR_OR-dec'  lasR_OR()-> @ 'prot-decRate'
'GFP_mrna-dec'  GFP_mrna()-> @ 'mrna-decRate'
'GFP-dec'  GFP()-> @ 'prot-decRate'
'RFP_OR-dec'  RFP_OR()-> @ 'prot-decRate'

## Rates

%var: 'TF_onRate' 0.01
%var: 'TF_offRate' 0.4

%var: 'INACTIVEtranscRate' 0.005 
%var: 'transcRate' 0.1
%var: 'translRate' 0.02
%var: 'dimRate' 1.6e-2


%var: 'mrna-decRate' 0.0041
%var: 'prot-decRate' 0.0002


%var: 'nanoRate' 0.00005

## init

%init: 1 GFP-P4_gene(bs)
%init: 1 GFP-lasR_gene(bs)
%init: 1000 P4_OR()
%init: 1000   lasR_OR()


#observables


%obs: 'P4' P4_OR(x)
%obs: 'GFP' GFP()
%obs: 'lasR' lasR_OR(x)