Dashboard

Name - Song_PNAS_2013

BioModel ID - 84275910

Reaction Diagram

reactionDiagram

Physiology

Universal ID's Text Annotations

Applications

Applications See in Dashboard
Name Math Type Annotation
Application0 Deterministic (ODE) Compartmental

Application - Application0

Specifications(Species) - Application0 See in Dashboard
Species Initial Condition Diffusion Constant
CaM_Ca4 0.0 [uM] 0.0 [um2/s]
PDE2_IBMX 0.0 [uM] 0.0 [um2/s]
Gap 0.01 [uM] 1.0 [um2/s]
R2C2_cAMP3 0.0 [uM] 0.0 [um2/s]
SoS_Pi_Grb2 0.0 [uM] 1.0 [um2/s]
PDE4_ERK_PKA 0.0 [uM] 0.0 [um2/s]
R2C2_cAMP 0.0 [uM] 0.0 [um2/s]
PP1 0.25 [uM] 0.0 [um2/s]
DARPP32_Pi_PP1 0.0 [uM] 0.0 [um2/s]
I1_Pi_PP1 0.0 [uM] 0.0 [um2/s]
PDE4_ERK 0.0 [uM] 0.0 [um2/s]
AMPAR_Bulk 0.011111 [uM] 0.0 [um2/s]
IP3_degraded 0.0 [uM] 0.0 [um2/s]
IP3_14 0.0 [uM] 0.0 [um2/s]
PKC_active 0.05 [uM] 0.0 [um2/s]
PP2A 0.2 [uM] 0.0 [um2/s]
PP1_PDE 0.1 [uM] 0.0 [um2/s]
cAMP 0.0 [uM] 0.0 [um2/s]
U0126 0.0 [uM] 0.0 [um2/s]
DARPP32 0.5 [uM] 0.0 [um2/s]
Rolipram 0.0 [uM] 0.0 [um2/s]
R2C_cAMP4 0.0 [uM] 0.0 [um2/s]
PDE3_IBMX 0.0 [uM] 0.0 [um2/s]
R2_cAMP4 0.0 [uM] 0.0 [um2/s]
STEP_PKA 0.0 [uM] 0.0 [um2/s]
BRaf_Pi 0.0 [uM] 0.0 [um2/s]
PDE1_CaM_Ca4 0.0 [uM] 0.0 [um2/s]
GluR1_845_818 0.0 [uM] 0.0 [um2/s]
Raf 3.0 [uM] 1.0 [um2/s]
IBMX 0.0 [uM] 0.0 [um2/s]
PDEbg 3.0 [uM] 0.0 [um2/s]
PKA_active 0.0 [uM] 0.0 [um2/s]
PDE1_IBMX 0.0 [uM] 0.0 [um2/s]
GluR1_degraded 0.0 [uM] 0.0 [um2/s]
GluR1 0.0 [uM] 0.0 [um2/s]
MEK_Ser 0.0 [uM] 1.0 [um2/s]
ERK_Tyr 0.0 [uM] 1.0 [um2/s]
IP3_5pase1 12.0 [uM] 0.0 [um2/s]
PDE4_PKA 0.0 [uM] 0.0 [um2/s]
MEK 0.18 [uM] 1.0 [um2/s]
CaM 2.0 [uM] 0.0 [um2/s]
Four1N 0.01 [uM] 0.0 [um2/s]
PDE4_IBMX 0.0 [uM] 0.0 [um2/s]
I1_Pi 0.0 [uM] 0.0 [um2/s]
ERK 0.36 [uM] 1.0 [um2/s]
PDE4_Rolipram 0.0 [uM] 0.0 [um2/s]
PKA_Inhibitor 0.25 [uM] 0.0 [um2/s]
CaMKII_286_CaM 0.0 [uM] 0.0 [um2/s]
Ras_GDP 3.0 [uM] 1.0 [um2/s]
MEK_inhibited 0.0 [uM] 0.0 [um2/s]
R2C2_cAMP4 0.0 [uM] 0.0 [um2/s]
Ras_Raf_active 0.0 [uM] 1.0 [um2/s]
SoS_Grb2 0.0 [uM] 1.0 [um2/s]
ATP 2000.0 [uM] 0.0 [um2/s]
GluR1_845 0.0 [uM] 0.0 [um2/s]
IP3_5Pase2 0.463 [uM] 0.0 [um2/s]
Shc 1.0 [uM] 1.0 [um2/s]
Ras_GTP 0.0 [uM] 1.0 [um2/s]
R2C2 0.5 [uM] 0.0 [um2/s]
CaMKII 2.0 [uM] 0.0 [um2/s]
BRaf 0.18 [uM] 0.0 [um2/s]
R2C2_cAMP2 0.0 [uM] 0.0 [um2/s]
PDE1 1.0 [uM] 0.0 [um2/s]
CaM_Ca2 0.0 [uM] 0.0 [um2/s]
PDE2 1.0 [uM] 0.0 [um2/s]
BDNF_TrkB2_Pi 0.0 [uM] 0.0 [um2/s]
ERK_active 0.0 [uM] 1.0 [um2/s]
Shc_Pi 0.0 [uM] 1.0 [um2/s]
IP3_145 0.0 [uM] 0.0 [um2/s]
MEK_active 0.0 [uM] 1.0 [um2/s]
AMP 0.0 [uM] 0.0 [um2/s]
Grb2 1.0 [uM] 1.0 [um2/s]
STEP 0.2 [uM] 0.0 [um2/s]
PDE3 0.005 [uM] 0.0 [um2/s]
Calcium 0.08 [uM] 0.0 [um2/s]
CaMKII_CaM 0.0 [uM] 0.0 [um2/s]
SoS 1.0 [uM] 1.0 [um2/s]
PDE4 0.4 [uM] 0.0 [um2/s]
CaMKII_286 0.0 [uM] 0.0 [um2/s]
SoS_Pi 0.0 [uM] 1.0 [um2/s]
PKA_inhibited 0.0 [uM] 0.0 [um2/s]
CaM_Ca3 0.0 [uM] 0.0 [um2/s]
I1 0.68 [uM] 0.0 [um2/s]
DARPP32_Pi 0.0 [uM] 0.0 [um2/s]
Shc_Pi_SoS_Grb2 0.0 [uM] 1.0 [um2/s]
PP2A_DI 0.11111 [uM] 0.0 [um2/s]
BDNF 0.0 [uM] 1.0 [um2/s]
Da 0.0 [uM] 0.0 [um2/s]
Fsk 0.0 [uM] 0.0 [um2/s]
Calcium_ER 900.0 [uM] 0.0 [um2/s]
Gby 0.0 [uM] 0.0 [um2/s]
AC5_Ga 0.0 [uM] 0.0 [um2/s]
D1LR_Gqby 0.0 [uM] 0.0 [um2/s]
GluR1_Membrane 0.0 [uM] 0.0 [um2/s]
Gqby 20.0 [uM] 0.0 [um2/s]
PLC 20.0 [uM] 0.0 [um2/s]
PLC_Ca 0.0 [uM] 0.0 [um2/s]
PLC_Ca_Gq 0.0 [uM] 0.0 [um2/s]
AC_basal 11.8 [uM] 0.0 [um2/s]
G_by 0.0 [uM] 0.0 [um2/s]
Gq_GDP 0.0 [uM] 0.0 [um2/s]
Da_D5R 0.0 [uM] 0.0 [um2/s]
Gaby 100.0 [uM] 0.0 [um2/s]
Da_D5R_Gaby 0.0 [uM] 0.0 [um2/s]
AC5 45.0 [uM] 0.0 [um2/s]
BDNF_TrkB 0.0 [uM] 0.0 [um2/s]
AC5_Fsk 0.0 [uM] 0.0 [um2/s]
D1R_Gaby 0.0 [uM] 0.0 [um2/s]
Gq_GTP 0.0 [uM] 0.0 [um2/s]
TrkB 200.0 [uM] 0.0 [um2/s]
D1LR 20.0 [uM] 0.0 [um2/s]
PLC_Gq 0.0 [uM] 0.0 [um2/s]
Ga_GDP 0.0 [uM] 0.0 [um2/s]
D5R_Gaby 0.0 [uM] 0.0 [um2/s]
BDNF_TrkB2 0.0 [uM] 0.0 [um2/s]
Ga_GTP 0.0 [uM] 0.0 [um2/s]
Da_D1R_Gaby 0.0 [uM] 0.0 [um2/s]
D1R 100.0 [uM] 0.0 [um2/s]
PIP2 100.0 [uM] 0.0 [um2/s]
Da_D1LR_Gqby 0.0 [uM] 0.0 [um2/s]
Int_TrkB2 0.0 [uM] 0.0 [um2/s]
DAG 0.0 [uM] 0.0 [um2/s]
Da_D1R 0.0 [uM] 0.0 [um2/s]
D5R 10.0 [uM] 0.0 [um2/s]
GluR1_Membrane_dephosphorylated1 0.0 [uM] 0.0 [um2/s]
Da_D1LR 0.0 [uM] 0.0 [um2/s]
IP3R 100.0 [uM] 0.0 [um2/s]
IP3R_open 0.0 [uM] 0.0 [um2/s]
SERCA 250.0 [uM] 0.0 [um2/s]
SERCA_active 0.0 [uM] 0.0 [um2/s]
Specifications(Reaction) - Application0 See in Dashboard
Name Reaction Mapping
091 included
005 included
r44 included
r19 included
r20 included
r40 included
057 included
r28 included
087 included
r10 included
r7 included
r21 included
096 included
056 included
036 included
064 included
r52 included
078 included
103 included
073 included
r38 included
r12 included
r6 included
100 included
r0 included
r11 included
r3 included
r55 included
011 included
012 included
097 included
071 included
002 included
r35 included
023 included
001 included
r36 included
084 included
098 included
r26 included
081 included
104 included
077 included
032 included
008 included
006 included
r27 included
046 included
060 included
018 included
r48 included
045 included
075 included
009 included
r50 included
004 included
r56 included
r37 included
r32 included
007 included
106 included
r29 included
067 included
088 included
r24 included
r31 included
r22 included
r34 included
010 included
r18 included
r1 included
r49 included
105 included
034 included
063 included
r47 included
095 included
065 included
r51 included
029 included
089 included
r43 included
r53 included
r33 included
082 included
040 included
r9 included
052 included
070 included
r30 included
069 included
079 included
r4 included
037 included
016 included
074 included
093 included
r54 included
080 included
072 included
049 included
r16 included
r39 included
068 included
047 included
r5 included
044 included
083 included
090 included
r45 included
028 included
094 included
003 included
035 included
033 included
r14 included
r15 included
108 included
r57 included
r8 included
r23 included
r13 included
061 included
066 included
014 included
r17 included
062 included
r42 included
099 included
r25 included
086 included
r41 included
048 included
043 included
085 included
092 included
041 included
Simulations - Application0 See in Dashboard
Name End Time Output Options
DA0.1 6000.0 [s]

OutputTimeStep 60.0

DA0.1+U0126 5400.0 [s]

OutputTimeStep 60.0

DA0.1+Rolipram 5400.0 [s]

OutputTimeStep 60.0

DA0.1+BDNF 5400.0 [s]

OutputTimeStep 60.0

DA1.0 6000.0 [s]

OutputTimeStep 60.0

DA1.0+U0126 5400.0 [s]

OutputTimeStep 60.0

DA1.0+Rolipram 5400.0 [s]

OutputTimeStep 60.0

DA1.0+BDNF 5400.0 [s]

OutputTimeStep 60.0

Events - Application0 See in Dashboard
Name Trigger Type Variable Assignment
t3600 on condition: 3600.0 Da --> 0.1, U0126 --> 0.0, Rolipram --> 0.0, BDNF --> 0.0
t5400 on condition: 5400.0 IBMX --> 10.0, Fsk --> 10.0
Geometry non-spatial1634669173 See in Dashboard
(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 ER_Membrane

Global Parameters

Global Parameters See in Dashboard
Name Expression