Dashboard

Name - Kruse_Kohout_Hille_CiVSP

BioModel ID - 145545992

Reaction Diagram

reactionDiagram

Physiology

Universal ID's Text Annotations

Applications

Applications See in Dashboard
Name Math Type Annotation
modelinOct2010 Deterministic (ODE) Compartmental cloned from 'modelinOct2010' owned by user hillelab cloned from 'modelinOct2010' owned by user bfalken (copied from PBio519 talk) (copied from M1R activation, manuscript 1) (copied from M1R activation) (copied from PipDecay) cloned from 'PipDecay' owned by user hillelab cloned from 'PipDecay' owned by user bfalken cloned from 'PipDecay' owned by user hillelab cloned from 'PipDecay' owned by user bfalken cloned from 'PipDecay' owned by user hillelab

Application - modelinOct2010

Specifications(Species) - modelinOct2010 See in Dashboard
Species Initial Condition Diffusion Constant
Ca_Ca_store 400.0 [uM] 0.0 [um2/s]
IP3_PH_YFP_C 0.0 [uM] 0.0 [um2/s]
C1_dom_C 0.0 [uM] 0.0 [um2/s]
K_C 100000.0 [uM] 0.0 [um2/s]
Ca_C 0.13 [uM] 0.0 [um2/s]
IP3_LibraVIII_C 0.0 [uM] 0.0 [um2/s]
LibraVIII_C 0.0 [uM] 0.0 [um2/s]
PH_YFP_C 0.0 [uM] 0.0 [um2/s]
Ca_Fura4F_C 0.0 [uM] 0.0 [um2/s]
Fura4F_C 0.0 [uM] 0.0 [um2/s]
IP3_C 0.02 [uM] 0.0 [um2/s]
Palk_C1 1.0 [uM] 0.0 [um2/s]
Palk_C2 0.0 [uM] 0.0 [um2/s]
Palk_C3 0.0 [uM] 0.0 [um2/s]
Palk_O4 0.0 [uM] 0.0 [um2/s]
TAPP1_dom_C 0.0 [uM] 0.0 [um2/s]
PH_Btk_dom_C 0.0 [uM] 0.0 [um2/s]
P4M_dom_C 0.0 [uM] 0.0 [um2/s]
IP3_pipette 0.0 [uM] 0.0 [um2/s]
oxoM_EX 0.0 [uM] 0.0 [um2/s]
OxoM_conc_EX 10.0 [uM] 0.0 [um2/s]
K_EX 0.0 [uM] 0.0 [um2/s]
PI4P_M 4000.0 [uM] 0.0 [um2/s]
PH_YFP_PIP2_M 0.0 [uM] 0.0 [um2/s]
KCNQ_M 4.0 [uM] 0.0 [um2/s]
PI_M 140000.0 [uM] 0.0 [um2/s]
RLG_GDP_M 0.0 [uM] 0.0 [um2/s]
RL_M 0.0 [uM] 0.0 [um2/s]
GaGTP_PLC_M 0.0 [uM] 0.0 [um2/s]
GaGTP_M 0.0 [uM] 0.0 [um2/s]
RLGbeta_M 0.0 [uM] 0.0 [um2/s]
Gbeta_M 0.0 [uM] 0.0 [um2/s]
RGbeta_M 0.0 [uM] 0.0 [um2/s]
R_M 500.0 [uM] 0.0 [um2/s]
boundPIP2_M (( - 1.0 + foldPIP2) * PIP2_M) [uM] 0.0 [um2/s]
G_GDP_M 40.0 [uM] 0.0 [um2/s]
RG_GDP_M 0.0 [uM] 0.0 [um2/s]
Ga_GDP_M 0.0 [uM] 0.0 [um2/s]
DAG_M 13.0 [uM] 0.0 [um2/s]
PA_2AG_M 0.0 [uM] 0.0 [um2/s]
PLC_M 10.0 [uM] 0.0 [um2/s]
PIP2_M 5000.0 [uM] 0.0 [um2/s]
C1_DAG_M 0.0 [uM] 0.0 [um2/s]
GaGDP_PLC_M 0.0 [uM] 0.0 [um2/s]
KCNQ_PIP2_M 0.0 [uM] 0.0 [um2/s]
PIP3 1338.0 [uM] 0.0 [um2/s]
PI3_4_P2 1200.0 [uM] 0.0 [um2/s]
TAPP1_PI34P2_M 0.0 [uM] 0.0 [um2/s]
PH_Btk_PIP3_M 0.0 [uM] 0.0 [um2/s]
P4M_PI4P_M 0.0 [uM] 0.0 [um2/s]
PI4P_VSPbound 0.0 [uM] 0.0 [um2/s]
inactiveIP3R 0.0 [uM] 0.0 [um2/s]
noninactiveIP3R 1.0 [uM] 0.0 [um2/s]
Specifications(Reaction) - modelinOct2010 See in Dashboard
Name Reaction Mapping
Cabind_Fura4F included
IP3_LibraVIII included
PLC_on_PI4P included
NE_RG included
L1 included
h_reaction_IP3Rinactivation included
PIP5K_5Pase included
NE_G included
GTPase_Ga included
IP3deg_Palk excluded
r12 excluded
r23 excluded
r24 excluded
PIP2_buffering included
L2beta included
NE_RLG included
NE_GaP included
PH_YFP_PIP2 included
VSP included
G1beta included
DAGPase included
PI4K_4Pase included
PH_YFP_IP3 included
IP3Pase_FDH included
G2beta included
PLCdiss included
L2 included
PLCassoc included
G1 included
PIP2bindKCNQ included
PIP2hydr included
IP3_dialysis included
GTPase_GaP included
Oxo_appl included
G2 included
reconstitution included
C1bindDAG included
VSP_PIP3 included
PI3K_PTEN included
TAPP1_binding included
PH_Btk_binding included
PI3K_on_PIP4P included
P4M_PI4P_binding included
VSP_5P_PIP3 included
PIPKIgamma_PIP included
PIPKIgamma_PI34P2 included
VSP_PI34P2 included
PI4P_VSPbound_release included
RyR_Palk excluded
leak_Palk excluded
SERCA_Palk excluded
KCNQ2/3 included
ER_leak_flux_FDH included
IP3R_flux_FDH included
SERCA_flux_FDH included
IP3R_Palk excluded
Simulations - modelinOct2010 See in Dashboard
Name End Time Output Options
DFH Figures 4C and 5A "Oxo" 600.0 [s]

KeepEvery 10

KeepAtMost 1000

DFH Figures 4D and 5B "Oxo" and 6F 600.0 [s]

KeepEvery 10

KeepAtMost 1000

DFH Figure 5A "UTP" 600.0 [s]

KeepEvery 10

KeepAtMost 1000

DFH Figure 5B "UTP" 600.0 [s]

KeepEvery 10

KeepAtMost 1000

DFH Figure 6B "Oxo" 600.0 [s]

KeepEvery 10

KeepAtMost 1000

DFH Figure 6B pipette dialysis 600.0 [s]

KeepEvery 10

KeepAtMost 1000

DFH Figure 6E 600.0 [s]

KeepEvery 10

KeepAtMost 1000

DFH Figure 7B 600.0 [s]

KeepEvery 10

KeepAtMost 1000

VSP 60.0 [s]

KeepEvery 10

KeepAtMost 1000

DFH Figure 8C 600.0 [s]

KeepEvery 10

KeepAtMost 1000

DFH Figure 8D "4K at resting rate" 600.0 [s]

KeepEvery 10

KeepAtMost 1000

DFH Figure 8D "4K turned off" 600.0 [s]

KeepEvery 10

KeepAtMost 1000

FDH Figure 1E 600.0 [s]

KeepEvery 10

KeepAtMost 1000

FDH Figure 1F 600.0 [s]

KeepEvery 10

KeepAtMost 1000

FDH Figures 4G and 4H 600.0 [s]

KeepEvery 10

KeepAtMost 1000

FDH Figure 6B 600.0 [s]

KeepEvery 10

KeepAtMost 1000

FDH Figures 6C and 6D 600.0 [s]

KeepEvery 10

KeepAtMost 1000

FDH Figure 8A except Fura, Libra, C1 600.0 [s]

KeepEvery 10

KeepAtMost 1000

FDH Figure 8A Fura 600.0 [s]

KeepEvery 10

KeepAtMost 1000

FDH Figure 8A Libra, C1 600.0 [s]

KeepEvery 10

KeepAtMost 1000

FDH Figure 8B except Fura, Libra, C1 600.0 [s]

KeepEvery 10

KeepAtMost 1000

FDH Figure 8C except Fura, Libra, C1 600.0 [s]

KeepEvery 10

KeepAtMost 1000

Geometry non-spatial61971900 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 ERM

Global Parameters

Global Parameters See in Dashboard
Name Expression
KfL1 (KrL1 / KL1)[uM-1.s-1]
KrL1 5.555555555555555[s-1]
KfG1 (0.1 * KfG2)[um2.molecules-1.s-1]
KfG2 0.0026666[um2.molecules-1.s-1]
KrG2 0.68[s-1]
KfL2 KfL1[uM-1.s-1]
KrL2 (KL2 * KfL2)[s-1]
allRL (RL_M + RLG_GDP_M + RLGbeta_M)[molecules.um-2]
KrG1 (KfG1 * KG1)[s-1]
alpha 100.0[1]
KL1 2.0[uM]
KL2 (KL1 / alpha)[uM]
KG1 (KG2 * alpha)[molecules.um-2]
KG2 (KrG2 / KfG2)[molecules.um-2]
allRGbeta (RG_GDP_M + RLG_GDP_M + RLGbeta_M + RGbeta_M)[molecules.um-2]
allGabg (G_GDP_M + RG_GDP_M + RLG_GDP_M)[molecules.um-2]
allGaPLC (GaGTP_PLC_M + GaGDP_PLC_M)[molecules.um-2]
allPIP2M (PIP2_M + KCNQ_PIP2_M + PH_YFP_PIP2_M + boundPIP2_M)[molecules.um-2]
allPH_cytoplasm (PH_YFP_C + IP3_PH_YFP_C)[uM]
speed_PH_PIP2 1.0[uM-1.s-1]
KD_PH_PIP2 2.0[uM]
speed_PH_IP3 10.0[uM-1.s-1]
KD_PH_IP3 0.1[uM]
K_plc 0.2[um2.molecules-1.s-1]
PLC_basal 0.0[s-1]
start 0.0[s]
end 0.0[s]
foldPIP2 3.0[1]
KD_act_Ca_IP3R 0.2[uM]
KD_IP3_IP3R 0.1[uM]
IP3R pow((h * IP3_C * Ca_C / (IP3_C + KD_IP3_IP3R) / (Ca_C + KD_act_Ca_IP3R)),3.0)[1]
KD_DAG_C1 0.2[uM]
speed_DAG_C1 10.0[uM-1.s-1]
activePKC (DAG_M * PIP2_M / ((DAG_M + (1000.0 * KD_DAG_C1)) * (PIP2_M + (1000.0 * KD_PH_PIP2))))[1]
h (noninactiveIP3R / (noninactiveIP3R + inactiveIP3R))[1]
stim_4k (stim_4k_max / (1.0 + exp( - (277.77777777777777 * ( - 0.0175 + OxoMforKinases)))))[s-1]
stim_4k_max 0.0023647[s-1]
stim_5K_max 0.1819[s-1]
stim_5k (stim_5K_max / (1.0 + exp( - (277.77777777777777 * ( - 0.0175 + OxoMforKinases)))))[s-1]
tau_stim_onset 1.0[s]
tau_stim_recovery 5.0[s]
k5k_base 0.0181[s-1]
OxoMforKinases 0.0[uM]
all_IP3 (IP3_C + IP3_LibraVIII_C + IP3_PH_YFP_C)[uM]
r_FDH 1.0[1]
r_Palk 0.0[1]
perms2pers 1000.0[s-1]
uM2nM 1000.0[uM-1]
removeuM 1.0[uM-1]
qKT -40.5898[tbd]
VSP_conc 1.6[1]
Vstep 0.16[V]
Vhold -0.1[V]
Vcommand 0.16[V]