Reaction Diagram





STEP_PKASTEP r097 IC HMMIrreversible
STEPSTEP_PKA r096 IC HMMIrreversible
ATPcAMP r010 PM HMMIrreversible
ERK_activeERK_Tyr r093 IC HMMIrreversible
ERK_TyrERK r094 IC HMMIrreversible
PDE1_cAMPPDE1+AMP r027 IC MassAction
R2C2_cAMP4PKA+R2C_cAMP4 r044 IC MassAction
DARPP32_Pi_PP1PP1+DARPP32 r073 IC MassAction
PDE1+MMPXPDE1_inhibited r051 IC MassAction
DARPP32DARPP32_Pi r070 IC HMMIrreversible
DARPP32_Pi+PP1DARPP32_Pi_PP1 r071 IC MassAction
PDE2_active+cGMPPDE2_active_cGMP r019 IC MassAction
PDE2+Bay60PDE2_inhibited r054 IC MassAction
PDE2_active_cAMP+Bay60PDE2_inhibited r058 IC MassAction
Gaby+D1RD1R_Gaby r001 PM MassAction
PDE1_cGMPGMP+PDE1 r029 IC MassAction
PDE2_active_cGMP+Bay60PDE2_inhibited r059 IC MassAction
cGMPGMP r060 IC HMMIrreversible
Four1N+GluA1_845AMPAR r048 PM MassAction
PDE2_cGMPGMP+PDE2 r017 IC MassAction
PDE2_cAMPAMP+PDE2 r016 IC MassAction
PDE2+cAMPPDE2_cAMP r018 IC MassAction
PDE1+cGMPPDE1_cGMP r028 IC MassAction
DA_D1R_GabyGby+Ga_GTP+DA_D1R r005 PM MassAction
PDE1_cGMP+MMPXPDE1_inhibited r053 IC MassAction
DARPP32_PiDARPP32 r072 IC HMMIrreversible
D1R_Gaby+DADA_D1R_Gaby r002 PM MassAction
PDE1+cAMPPDE1_cAMP r026 IC MassAction
PDE1_cAMP+MMPXPDE1_inhibited r052 IC MassAction
PDE2+cGMPPDE2_active r011 IC MassAction
R2C2_cAMP2+cAMPR2C2_cAMP3 r042 IC MassAction
BRafBRaf_PKA r085 IC HMMIrreversible
BRaf_PKABRaf r086 IC HMMIrreversible
MEKMEK_Ser r087 IC HMMIrreversible
MEK_SerMEK_active r088 IC HMMIrreversible
ERKERK_Tyr r091 IC HMMIrreversible
MEK_activeMEK_Ser r089 IC HMMIrreversible
MEK_SerMEK r090 IC HMMIrreversible
ERK_TyrERK_active r092 IC HMMIrreversible
ERK_TyrERK r095 IC HMMIrreversible
ATPcAMP r025 PM HMMIrreversible
D1R+DADA_D1R r000 PM MassAction
GluA1_845GluA1 r047 IC HMMIrreversible
AMPARGluA1_dephos r049 PM HMMIrreversible
GluA1_dephosGluA1+Four1N r050 PM MassAction
PDE4PDE4_PKA r075 IC HMMIrreversible
Ga_GTP+AC5AC5_Ga r007 PM MassAction
Ga_GTPGa_GDP r006 PM MassAction
PDE4_ERKPDE4_ERK_PKA r077 IC HMMIrreversible
PDE4_ERK_PKAPDE4 r078 IC HMMIrreversible
PDE4_PKAPDE4_ERK_PKA r080 IC HMMIrreversible
PDE4_ERKPDE4 r076 IC HMMIrreversible
PDE4_PKAPDE4 r079 IC HMMIrreversible
cAMPAMP r083 IC HMMIrreversible
cAMPAMP r084 IC HMMIrreversible
cAMPAMP r024 IC HMMIrreversible
Bay60+PDE2_cGMPPDE2_inhibited r056 IC MassAction
PDE4PDE4_ERK r074 IC HMMIrreversible
cAMPAMP r081 IC HMMIrreversible
cGMP+PDE2PDE2_cGMP r012 IC MassAction
GluA1GluA1_845 r046 IC HMMIrreversible
cAMPAMP r082 IC HMMIrreversible
PDE2_active+Bay60PDE2_inhibited r057 IC MassAction
Bay60+PDE2_cAMPPDE2_inhibited r055 IC MassAction
PDE2_active_cGMPGMP+PDE2_active r015 IC MassAction
ATPcAMP r009 PM HMMIrreversible
PDE2_active_cAMPAMP+PDE2_active r014 IC MassAction
GTPcGMP r039 IC HMMIrreversible
R2C2_cAMP+cAMPR2C2_cAMP2 r041 IC MassAction
R2C_cAMP4R2_cAMP4+PKA r045 IC MassAction
PDE2_active+cAMPPDE2_active_cAMP r013 IC MassAction
R2C2_cAMP3+cAMPR2C2_cAMP4 r043 IC MassAction
Ga_GDP+GbyGaby r004 PM MassAction
DA_D1R+GabyDA_D1R_Gaby r003 PM MassAction
cAMP+R2C2R2C2_cAMP r040 IC MassAction
sGC_inactive+SNAPsGC_active r098 IC MassAction
GTPcGMP r099 IC HMMIrreversible


PM Membrane IC(+)   EC(-)
IC Compartment (+)   (-)
EC Compartment (+)   (-)



BioNetGen Definition


BNGL Definition
Sequence Type


Properties Math Type
Application0 Specs - Species
Specs - Reaction
Deterministic (ODE) Compartmental

Specifications (Species) - Application0 go to Simulations

Initial Condition
Diffusion Constant
PDE2_cGMP 0.0 [uM] 0.0 [um2/s] IC
PDE2_inhibited 0.0 [uM] 0.0 [um2/s] IC
Bay60 0.0 [uM] 0.0 [um2/s] IC
PDEbg_cGMP 0.1 [uM] 0.0 [um2/s] IC
GMP 0.0 [uM] 0.0 [um2/s] IC
PDE2_cAMP 0.0 [uM] 0.0 [um2/s] IC
GTP 500.0 [uM] 0.0 [um2/s] IC
sGC_basal 0.15 [uM] 0.0 [um2/s] IC
R2C2_cAMP 0.0 [uM] 0.0 [um2/s] IC
R2C2 0.5 [uM] 0.0 [um2/s] IC
R2C2_cAMP2 0.0 [uM] 0.0 [um2/s] IC
PKA 0.0 [uM] 0.0 [um2/s] IC
R2C_cAMP4 0.0 [uM] 0.0 [um2/s] IC
R2_cAMP4 0.0 [uM] 0.0 [um2/s] IC
R2C2_cAMP4 0.0 [uM] 0.0 [um2/s] IC
GluA1_845 0.0 [uM] 0.0 [um2/s] IC
Four1N 0.01 [uM] 0.0 [um2/s] IC
PDE1 0.5 [uM] 0.0 [um2/s] IC
GluA1 0.01 [uM] 0.0 [um2/s] IC
cAMP 0.0 [uM] 0.0 [um2/s] IC
PDE1_cGMP 0.0 [uM] 0.0 [um2/s] IC
R2C2_cAMP3 0.0 [uM] 0.0 [um2/s] IC
PDE2 0.5 [uM] 0.0 [um2/s] IC
cGMP 0.0 [uM] 0.0 [um2/s] IC
PDE2_active_cAMP 0.0 [uM] 0.0 [um2/s] IC
AMP 0.0 [uM] 0.0 [um2/s] IC
PDE2_active_cGMP 0.0 [uM] 0.0 [um2/s] IC
PDEbg_cAMP 0.1 [uM] 0.0 [um2/s] IC
PDE1_cAMP 0.0 [uM] 0.0 [um2/s] IC
DARPP32 0.5 [uM] 0.0 [um2/s] IC
DARPP32_Pi 0.0 [uM] 0.0 [um2/s] IC
DARPP32_Pi_PP1 0.0 [uM] 0.0 [um2/s] IC
PP2A 0.1 [uM] 0.0 [um2/s] IC
MMPX 0.0 [uM] 0.0 [um2/s] IC
PP1 0.11 [uM] 0.0 [um2/s] IC
ERK_active 0.0 [uM] 0.0 [um2/s] IC
PDE4_ERK 0.0 [uM] 0.0 [um2/s] IC
PDE4 0.1 [uM] 0.0 [um2/s] IC
PDE4_PKA 0.0 [uM] 0.0 [um2/s] IC
PDE4_ERK_PKA 0.0 [uM] 0.0 [um2/s] IC
PDE1_inhibited 0.0 [uM] 0.0 [um2/s] IC
ATP 5000.0 [uM] 0.0 [um2/s] IC
BRaf 0.18 [uM] 0.0 [um2/s] IC
BRaf_PKA 0.0 [uM] 0.0 [um2/s] IC
MEK_active 0.0 [uM] 0.0 [um2/s] IC
MEK_Ser 0.0 [uM] 0.0 [um2/s] IC
MEK 0.18 [uM] 0.0 [um2/s] IC
ERK_Tyr 0.0 [uM] 0.0 [um2/s] IC
ERK 0.36 [uM] 0.0 [um2/s] IC
STEP 0.2 [uM] 0.0 [um2/s] IC
STEP_PKA 0.0 [uM] 0.0 [um2/s] IC
PDE2_active 0.0 [uM] 0.0 [um2/s] IC
SNAP 0.0 [uM] 0.0 [um2/s] IC
sGC_inactive 0.15 [uM] 0.0 [um2/s] IC
sGC_active 0.0 [uM] 0.0 [um2/s] IC
DA 0.0 [uM] 0.0 [um2/s] EC
AMPAR 0.0 [uM] 0.0 [um2/s] PM
GluA1_dephos 0.0 [uM] 0.0 [um2/s] PM
Ga_GTP 0.0 [uM] 0.0 [um2/s] PM
D1R 20.0 [uM] 0.0 [um2/s] PM
Gaby 20.0 [uM] 0.0 [um2/s] PM
DA_D1R_Gaby 0.0 [uM] 0.0 [um2/s] PM
Gby 0.0 [uM] 0.0 [um2/s] PM
Ga_GDP 0.0 [uM] 0.0 [um2/s] PM
D1R_Gaby 0.0 [uM] 0.0 [um2/s] PM
DA_D1R 0.0 [uM] 0.0 [um2/s] PM
ACbg 15.0 [uM] 0.0 [um2/s] PM
AC5 55.0 [uM] 0.0 [um2/s] PM
AC5_Ga 0.0 [uM] 0.0 [um2/s] PM

Specifications (Reaction) - Application0 go to Simulations

r097 included
r096 included
r010 included
r093 included
r094 included
r027 included
r044 included
r073 included
r051 included
r070 included
r071 included
r019 included
r054 included
r058 included
r001 included
r029 included
r059 included
r060 included
r048 included
r017 included
r016 included
r018 included
r028 included
r005 included
r053 included
r072 included
r002 included
r026 included
r052 included
r011 included
r042 included
r085 included
r086 included
r087 included
r088 included
r091 included
r089 included
r090 included
r092 included
r095 included
r025 included
r000 included
r047 included
r049 included
r050 included
r075 included
r007 included
r006 included
r077 included
r078 included
r080 included
r076 included
r079 included
r083 included
r084 included
r024 included
r056 included
r074 included
r081 included
r012 included
r046 included
r082 included
r057 included
r055 included
r015 included
r009 included
r014 included
r039 included
r041 included
r045 included
r013 included
r043 included
r004 included
r003 included
r040 included
r098 included
r099 included

Simulations - Application0 go to Specifications

End Time
Output Options
DA1.0 63000.0

OutputTimeStep 60.0

DA0.1 63000.0

OutputTimeStep 60.0

DA0.1 + MMPX 63000.0

OutputTimeStep 60.0

DA0.1 + BAY607550 63000.0

OutputTimeStep 60.0

DA0.1 + SNAP 63000.0

OutputTimeStep 60.0


Name Variable Assignment Function Expression


Name Trigger Type Variable Assignment
dopamine on condition: 61200.0 DA --> 0.1
drug on condition: 61800.0 MMPX --> 0.0, Bay60 --> 0.0, SNAP --> 0.0

Geometry non-spatial1459406324

(Origin: 0.0, 0.0, 0.0; Extent: 10.0, 10.0, 10.0 [um])

Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Compartmental Compartment PM


Name Variable Rate Expression

Global Parameters



Model Format
Model Downloads
Virtual Cell Markup Language VCML File
PDF Report Report
File Format
Application Downloads
BNGL Application0.bngl
SBML Application0.sbml
Matlab Application0.m
NFSim XML Application0.xml