@model:2.3.1=Urease Production "iGEM 2010 Urease Production model"
@units
 volume=litre:s=-15
 substance=mole:s=-9
@compartments
 Cell=1.0

@species
 Cell:AhrC_mRNA=0 s
 Cell:SR1_antisenseRNA=0 s "SR1 antisense RNA"
 Cell:AhrC_mRNA_SR1_antisenseRNA=0 s "ahrC mRNA SR1 antisense RNA complex"
 Cell:AhrC=0 s
 Cell:RocR_mRNA=0 s
 Cell:RocR=0 s
 Cell:RocF_mRNA=0 s
 Cell:Arginase=0 s
 Cell:ArgC_mRNA=0 s
 Cell:Arginine=0 s
 Cell:Urea=0 s
 Cell:UreABC_mRNA=0 s
 Cell:Urease=0 s
 Cell:Carbonate=0 s
 Cell:LacI=0 s
 Cell:LacI_mRNA=0 s
 Cell:IPTG=1000 c
 Cell:IPTG_LacI=0 s

@parameters
 kf=0.001
 kb=0.5
 k_generic_protein_decayrate=0.0012
 k_generic_decay_mRNA=0.0058
 k_Arginine_decayrate=0.0012
 k_Urea_decayrate=0.0012
 k_generic_transcription_rate=0.1
 k_generic_translation_rate=0.1
 k_antisense_pairing_rate=0.001
 k_antisense_dissociation_rate=0.5
 Km_A_To_B=300

@reactions

@r=AhrC_Transcription
 -> AhrC_mRNA
 k_generic_transcription_rate

@r=SR1_antisenseRNA_Transcription
 -> SR1_antisenseRNA : LacI
 k_generic_transcription_rate  * (Km_A_To_B/(Km_A_To_B + LacI))

@r=SR1_antisense_AhrC_mRNA_Pairing
 AhrC_mRNA + SR1_antisenseRNA -> AhrC_mRNA_SR1_antisenseRNA
 k_antisense_pairing_rate * AhrC_mRNA * SR1_antisenseRNA 

@r=SR1_antisense_AhrC_mRNA_Dissociation
 AhrC_mRNA_SR1_antisenseRNA -> AhrC_mRNA + SR1_antisenseRNA
 k_antisense_dissociation_rate * AhrC_mRNA_SR1_antisenseRNA
 
@r=AhrC_Translation
 AhrC_mRNA -> AhrC_mRNA + AhrC
 k_generic_translation_rate * AhrC_mRNA

@r=AhrC_mRNA_Degradation
 AhrC_mRNA ->
 k_generic_decay_mRNA * AhrC_mRNA

@r=AhrC_Degradation
 AhrC ->
 k_generic_protein_decayrate * AhrC

@r=SR1_antisenseRNA_Degradation
 SR1_antisenseRNA ->
 k_generic_decay_mRNA * SR1_antisenseRNA

@r=RocR_Transcription
 -> RocR_mRNA : AhrC,RocR
 k_generic_transcription_rate * (AhrC/(Km_A_To_B + AhrC)) * (Km_A_To_B/(Km_A_To_B + RocR))

@r=RocR_Translation
 RocR_mRNA -> RocR_mRNA + RocR
 k_generic_translation_rate * RocR_mRNA

@r=RocF_Transcription
 -> RocF_mRNA : RocR
 k_generic_transcription_rate * (RocR/(Km_A_To_B + RocR))

@r=RocF_Transcription_From_BioBrick
 -> RocF_mRNA : LacI
 k_generic_transcription_rate * (Km_A_To_B/(Km_A_To_B + LacI))

@r=Arginase_Translation
 RocF_mRNA -> RocF_mRNA + Arginase
 k_generic_translation_rate * RocF_mRNA

@r=ArgC_Transcription
 -> ArgC_mRNA : AhrC
 k_generic_transcription_rate * (Km_A_To_B/(Km_A_To_B + AhrC))

@r=ArgC_mRNA_Degradation
 ArgC_mRNA ->
 k_generic_decay_mRNA * ArgC_mRNA

@r=Arginine_Translation
 ArgC_mRNA -> ArgC_mRNA + Arginine
 k_generic_translation_rate * ArgC_mRNA

@r=UreaABC_Transcription
 -> UreABC_mRNA : Urea
 k_generic_transcription_rate * (Urea/(Km_A_To_B + Urea))

@r=Urease_Translation
 UreABC_mRNA -> UreABC_mRNA + Urease
 k_generic_translation_rate * UreABC_mRNA

@r=LacI_Transcription
 -> LacI_mRNA
 k_generic_transcription_rate

@r=LacI_Translation
 LacI_mRNA -> LacI_mRNA + LacI
 k_generic_translation_rate * LacI_mRNA

@r=LacI_Degradation
 LacI->
 k_generic_protein_decayrate * LacI

@r=LacI_mRNA_Degradation
 LacI_mRNA ->
 k_generic_decay_mRNA * LacI_mRNA

@r=RocR_mRNA_Degradation
 RocR_mRNA ->
 k_generic_decay_mRNA * RocR_mRNA

@r=RocF_mRNA_Degradation
 RocF_mRNA ->
 k_generic_decay_mRNA * RocF_mRNA

@r=UreABC_mRNA_Degradation
 UreABC_mRNA ->
 k_generic_decay_mRNA * UreABC_mRNA

@r=RocR_Degradation
 RocR ->
 k_generic_protein_decayrate * RocR

@r=Arginase_Degradation
 Arginase ->
 k_generic_protein_decayrate * Arginase

@r=Arginine_Degradation
 Arginine ->
 k_Arginine_decayrate * Arginine

@r=Urea_Degradation
 Urea ->
 k_Urea_decayrate * Urea

@r=Urease_Degradation
 Urease ->
 k_generic_protein_decayrate * Urease

@r=Arginine_Breakdown
 Arginine + Arginase -> Arginase + Urea
 kf * Arginine * Arginase

@r=Urea_Breakdown
 Urea + Urease -> Urease + Carbonate
 kf * Urea * Urease

@rr=IPTG_LacIFormation
 LacI -> IPTG_LacI : IPTG
 kf * IPTG * LacI - kb * IPTG_LacI

@r=IPTG_LacI_Degradation
 IPTG_LacI ->
 k_generic_protein_decayrate * IPTG_LacI