Dashboard

Name - Falkenberg_GTPases_Rac_betaCell

BioModel ID - 60113862

Reaction Diagram

reactionDiagram

Physiology

Universal ID's Text Annotations

Applications

Applications See in Dashboard
Name Math Type Annotation
psGDIfactor_R1=0.1; find SS with no gluc Deterministic (ODE) Compartmental (copied from C:\Documents and Settings\cfalkenberg\.vcell\BioNetGen\vcell_bng_1222\vcell_bng_1222_Compartmental)
psGDIfactor_R1=0.1+change konM+coefonGR; transient studies Deterministic (ODE) Compartmental (copied from psGDIfactor_R1=0.1; transient studies) (copied from psGDIfactor_R1=0; transient studies) (copied from C:\Documents and Settings\cfalkenberg\.vcell\BioNetGen\vcell_bng_1222\vcell_bng_1222_Compartmental)

Application - psGDIfactor_R1=0.1; find SS with no gluc

Specifications(Species) - psGDIfactor_R1=0.1; find SS with no gluc See in Dashboard
Species Initial Condition Diffusion Constant
GDIuuco_Rac1cgTp 0.0 [uM] 0.0 [um2/s]
pakuc 0.5 [uM] 0.0 [um2/s]
NonGlucLc 1.0 [uM] 0.0 [um2/s]
glucc 0.0 [uM] 0.0 [um2/s]
GlucLc 0.0 [uM] 0.0 [um2/s]
PLDci 0.0 [uM] 0.0 [um2/s]
pakpc 0.0 [uM] 0.0 [um2/s]
Rac1cgTp 0.0 [uM] 0.0 [um2/s]
GDIpuco_Rac1cgDp 0.0 [uM] 0.0 [um2/s]
GDIpuco_Rac1cgTp 0.0 [uM] 0.0 [um2/s]
GDIuuco 0.07 [uM] 0.0 [um2/s]
GDIpuco 0.06 [uM] 0.0 [um2/s]
Rac1cgDp 0.0427 [uM] 0.0 [um2/s]
GDIuuco_Rac1cgDp 0.11 [uM] 0.0 [um2/s]
PLDgi 2.7777777777777777 [uM] 0.0 [um2/s]
GDIuugo 0.0 [uM] 0.0 [um2/s]
GDIpugo 0.0 [uM] 0.0 [um2/s]
Rac1ggDp 0.0 [uM] 0.0 [um2/s]
Rac1ggTp 0.0 [uM] 0.0 [um2/s]
GDIuumo_Rac1mgDp 0.0 [uM] 0.0 [um2/s]
GDIuumo_Rac1mgTp 0.0 [uM] 0.0 [um2/s]
Rac1mgDp 0.0 [uM] 0.0 [um2/s]
Rac1mgTp 0.0 [uM] 0.0 [um2/s]
Trashm 601999.9999999999 [uM] 0.0 [um2/s]
GDIuumo 0.0 [uM] 0.0 [um2/s]
GDIpumo 0.0 [uM] 0.0 [um2/s]
PLDmi 0.0 [uM] 0.0 [um2/s]
PLDma 0.0 [uM] 0.0 [um2/s]
Specifications(Reaction) - psGDIfactor_R1=0.1; find SS with no gluc See in Dashboard
Name Reaction Mapping
R20 included
R14 included
R15 included
R11 included
R13 included
R21 included
R31 included
R35 included
R17 included
R18 included
R41 included
R1 included
R2 included
R4 included
R5 included
R6 included
R7 included
R9 included
R3 included
R30 included
R36 included
R22 included
R37 included
Simulations - psGDIfactor_R1=0.1; find SS with no gluc See in Dashboard
Name End Time Output Options
find SS 5000.0 [s]

KeepEvery 500

KeepAtMost 1000

Events - psGDIfactor_R1=0.1; find SS with no gluc See in Dashboard
Name Trigger Type Variable Assignment
event0 on condition: (t > tgluc) glucc --> 20000.0, actPak --> (0.116 + (0.116 * changePsGDI)), gef_R1 --> (gef0_R1 + (((gef0_R1 * coef_gef) - gef0_R1) * change_gef_only))
Geometry Compartmental1146174258 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 Membrane

Application - psGDIfactor_R1=0.1+change konM+coefonGR; transient studies

Specifications(Species) - psGDIfactor_R1=0.1+change konM+coefonGR; transient studies See in Dashboard
Species Initial Condition Diffusion Constant
GDIuuco_Rac1cgTp 1.6563957705568633E-4 [uM] 0.0 [um2/s]
pakuc 0.11240310077519382 [uM] 0.0 [um2/s]
NonGlucLc 1.0 [uM] 0.0 [um2/s]
glucc 0.0 [uM] 0.0 [um2/s]
GlucLc 0.0 [uM] 0.0 [um2/s]
PLDci 0.0 [uM] 0.0 [um2/s]
pakpc 0.38759689922480617 [uM] 0.0 [um2/s]
Rac1cgTp 3.622850570650371E-7 [uM] 0.0 [um2/s]
GDIpuco_Rac1cgDp 0.011582451335819324 [uM] 0.0 [um2/s]
GDIpuco_Rac1cgTp 1.9214186222063993E-5 [uM] 0.0 [um2/s]
GDIuuco 0.05943702212607566 [uM] 0.0 [um2/s]
GDIpuco 0.06894692985331065 [uM] 0.0 [um2/s]
Rac1cgDp 2.183880698389099E-4 [uM] 0.0 [um2/s]
GDIuuco_Rac1cgDp 0.09984874292151663 [uM] 0.0 [um2/s]
PLDgi 2.7777777777777777 [uM] 0.0 [um2/s]
GDIuugo 0.0 [uM] 0.0 [um2/s]
GDIpugo 0.0 [uM] 0.0 [um2/s]
Rac1ggDp 4.770672010383799 [uM] 0.0 [um2/s]
Rac1ggTp 0.0031608535148760723 [uM] 0.0 [um2/s]
GDIuumo_Rac1mgDp 0.0 [uM] 0.0 [um2/s]
GDIuumo_Rac1mgTp 0.0 [uM] 0.0 [um2/s]
Rac1mgDp 4.554384740079095 [uM] 0.0 [um2/s]
Rac1mgTp 2.9446676851097253 [uM] 0.0 [um2/s]
Trashm 601999.9999999999 [uM] 0.0 [um2/s]
GDIuumo 0.0 [uM] 0.0 [um2/s]
GDIpumo 0.0 [uM] 0.0 [um2/s]
PLDmi 0.0 [uM] 0.0 [um2/s]
PLDma 0.0 [uM] 0.0 [um2/s]
Specifications(Reaction) - psGDIfactor_R1=0.1+change konM+coefonGR; transient studies See in Dashboard
Name Reaction Mapping
R20 included
R14 included
R15 included
R11 included
R13 included
R21 included
R31 included
R35 included
R17 included
R18 included
R41 included
R1 included
R2 included
R4 included
R5 included
R6 included
R7 included
R9 included
R3 included
R30 included
R36 included
R22 included
R37 included
Simulations - psGDIfactor_R1=0.1+change konM+coefonGR; transient studies See in Dashboard
Name End Time Output Options
effect of ps-gdi only 4000.0 [s]

KeepEvery 500

KeepAtMost 1000

effect of increase konM over t; coef on Gr=0; coef pld0=1.5 4000.0 [s]

KeepEvery 500

KeepAtMost 1000

effect of increase konM and konGr: coef on Gr=1.5; coef pld0=[1,1.5,2] 4000.0 [s]

KeepEvery 500

KeepAtMost 1000

effect of increase konM and konGr: coef on Gr=2; coef pld0=[1,1.5,2] 4000.0 [s]

KeepEvery 500

KeepAtMost 1000

Events - psGDIfactor_R1=0.1+change konM+coefonGR; transient studies See in Dashboard
Name Trigger Type Variable Assignment
event0 on condition: (t > tgluc) glucc --> 20000.0, actPak --> (0.116 + (0.116 * changePsGDI)), gef_R1 --> (gef0_R1 + (((gef0_R1 * coef_gef) - gef0_R1) * change_gef_only))
Geometry Compartmental1146174258 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 Membrane

Global Parameters

Global Parameters See in Dashboard
Name Expression
SfRAVolNIH3T3 0.524[tbd]
SfRAVol 0.587[tbd]
toexport2 1.0E-12[tbd]
FR 1.0[tbd]
fusRate ((1.67E-5 * (t >= (600.0 + tgluc))) + (2.779166666666666E-7 * (t > (60.0 + tgluc)) * (t < (300.0 + tgluc)) * ( - (60.0 + tgluc) + t)) + ((t >= (300.0 + tgluc)) * (t < (600.0 + tgluc)) * (6.67E-5 - (1.6666666666666668E-7 * ( - (300.0 + tgluc) + t)))))[tbd]
coef_on_Gr 1.0[tbd]
actPLD 0.1[tbd]
inacPLD 0.1[tbd]
actPak 0.116[tbd]
coefP_G_s 0.02[tbd]
changePsGDI 0.0[tbd]
gluc0 glucc[tbd]
KDM_G 10.0[tbd]
koffM_G 1.0[tbd]
KDMp_G 0.1[tbd]
koffMp_G 0.1[tbd]
KDGr_G 10.0[tbd]
koffGr_G 1.0[tbd]
KDGrp_G 0.1[tbd]
koffGrp_G 0.1[tbd]
kon_Pak_G 1.0[tbd]
koff_Pak_G 1.0[tbd]
alphaPak 1.0[tbd]
KD_pak_C2 2.9[tbd]
KD_pak_R1 0.7[tbd]
koffPak_C2 1.0[tbd]
koffPak_R1 1.0[tbd]
gtpm_C2 1.0[tbd]
gtpm_R1 1.0[tbd]
dP_pak 0.1[tbd]
P_R1 0.0[tbd]
dP_R1 0.0[tbd]
pld0 (changekonM * PLDma / (0.1 + PLDma))[tbd]
koffMD_R1 0.1496[tbd]
koffMT_R1 0.011[tbd]
koffGrD_R1 0.1496[tbd]
koffGrT_R1 0.011[tbd]
gef_R1 gef0_R1[tbd]
gef_Cyt_R1 0.0[tbd]
gef_Gr_R1 0.01[tbd]
KDD_2d_R1 1.0[tbd]
KDT_2d_R1 1.0[tbd]
koff1_2d_R1 0.0[tbd]
phospFactor2_R1 1.0[tbd]
koff1P_2d_R1 0.0[tbd]
geomFac25_R1 1.0[tbd]
koff1_25d_R1 0.0[tbd]
phospFactor25_R1 1.0[tbd]
koff1P_25d_R1 0.0[tbd]
alpha_R1 1.0[tbd]
koff1_3d_R1 0.044[tbd]
phospFactor3_R1 1.0[tbd]
koff1P_3d_R1 0.044[tbd]
koffMD_gG_R1 0.1496[tbd]
koffMT_gG_R1 0.1496[tbd]
konM_gG_R1 0.0[tbd]
konE_R1 0.1[tbd]
koffE_R1 0.1[tbd]
pGdifactor_R1 0.1[tbd]
psGdifactor_R1 0.1[tbd]
konGluc 1.0E-7[tbd]
koffGluc 0.001[tbd]
Vol2Sfc (1.0 / SfRAVol)[tbd]
SfcGr 4.230317273795534[tbd]
VolGr 0.23501762632197415[tbd]
VolCyt2SfcGr (1.0 / SfcGr)[tbd]
toexportM 0.0019083969465648854[tbd]
toexport1 (0.001 * Vol2Sfc)[tbd]
toexport1gr (0.001 * VolCyt2SfcGr)[tbd]
pmp (toexportM * toexport2)[tbd]
pmp0 toexport2[tbd]
pmpGr (toexportM * toexport2)[tbd]
P_G_s (actPak * coefP_G_s)[tbd]
dP_G_s (0.1 * coefP_G_s)[tbd]
konM_G 0.0[tbd]
konMp_G 0.0[tbd]
konGr_G 0.0[tbd]
konGrp_G 0.0[tbd]
konPak_C2 (koffPak_C2 / KD_pak_C2)[tbd]
konPak_R1 (koffPak_R1 / KD_pak_R1)[tbd]
P_pak (alphaPak * gtpm_C2 / KD_pak_C2)[tbd]
konM_R1 (2.84 * (1.0 + (coef_pld0 * pld0)))[tbd]
konGr_R1 (2.84 * (1.0 + (coef_on_Gr * pld0)))[tbd]
gap_R1 (1.5455950540958268 * gef0_R1)[tbd]
gap_Cyt_R1 (4.0 * gap_R1)[tbd]
gap_Gr_R1 gap_R1[tbd]
koffD_2d_R1 koff1_2d_R1[tbd]
koffT_2d_R1 koff1_2d_R1[tbd]
konD_2d_R1 (koffD_2d_R1 / KDD_2d_R1)[tbd]
konT_2d_R1 (koffT_2d_R1 / KDT_2d_R1)[tbd]
KDDP_2d_R1 (KDD_2d_R1 / phospFactor2_R1)[tbd]
KDTP_2d_R1 (KDD_2d_R1 / phospFactor2_R1)[tbd]
koffDP_2d_R1 koff1P_2d_R1[tbd]
koffTP_2d_R1 koff1P_2d_R1[tbd]
konDP_2d_R1 (koffDP_2d_R1 / KDDP_2d_R1)[tbd]
konTP_2d_R1 (koffTP_2d_R1 / KDTP_2d_R1)[tbd]
KDD_25d_R1 (5.2E-4 / geomFac25_R1)[tbd]
KDT_25d_R1 (5.2E-4 / geomFac25_R1)[tbd]
koffD_25d_R1 koff1_25d_R1[tbd]
koffT_25d_R1 koff1_25d_R1[tbd]
konD_25d_R1 (koffD_25d_R1 / KDD_25d_R1)[tbd]
konT_25d_R1 (koffT_25d_R1 / KDT_25d_R1)[tbd]
KDDP_25d_R1 (KDD_25d_R1 / phospFactor25_R1)[tbd]
KDTP_25d_R1 (KDD_25d_R1 / phospFactor25_R1)[tbd]
koffDP_25d_R1 koff1P_25d_R1[tbd]
koffTP_25d_R1 koff1P_25d_R1[tbd]
konDP_25d_R1 (koffDP_25d_R1 / KDDP_25d_R1)[tbd]
konTP_25d_R1 (koffTP_25d_R1 / KDTP_25d_R1)[tbd]
KDD_3d_R1 (1.3E-4 * alpha_R1)[tbd]
KDT_3d_R1 (1.3E-4 * alpha_R1)[tbd]
koffD_3d_R1 koff1_3d_R1[tbd]
koffT_3d_R1 koff1_3d_R1[tbd]
konD_3d_R1 (koffD_3d_R1 / KDD_3d_R1)[tbd]
konT_3d_R1 (koffT_3d_R1 / KDT_3d_R1)[tbd]
KDDP_3d_R1 (KDD_3d_R1 / phospFactor3_R1)[tbd]
KDTP_3d_R1 (KDD_3d_R1 / phospFactor3_R1)[tbd]
koffDP_3d_R1 koff1P_3d_R1[tbd]
koffTP_3d_R1 koff1P_3d_R1[tbd]
konDP_3d_R1 (koffDP_3d_R1 / KDDP_3d_R1)[tbd]
konTP_3d_R1 (koffTP_3d_R1 / KDTP_3d_R1)[tbd]
ppGdifactor_R1 (pGdifactor_R1 * psGdifactor_R1)[tbd]
InitialConc1 0.0[tbd]
InitialConc2 0.0[tbd]
InitialConc3 0.0[tbd]
InitialConc4 0.0[tbd]
InitialConc5 (pmpGr / pmp0)[tbd]
rateParam1 (fusRate * pmp0)[tbd]
rateParam2 (1.0E10 * fusRate * pmpGr)[tbd]
rateParam3 (7.2 * fusRate * pmp0)[tbd]
rateParam4 (koffM_G * pmp0)[tbd]
rateParam5 (konM_G * pmp)[tbd]
rateParam6 (koffMp_G * pmp0)[tbd]
rateParam7 (konMp_G * pmp)[tbd]
rateParam8 (koffGr_G * pmp0)[tbd]
rateParam9 (konGr_G * pmp)[tbd]
rateParam10 (koffGrp_G * pmp0)[tbd]
rateParam11 (konGrp_G * pmp)[tbd]
rateParam12 (konGluc * gluc0)[tbd]
rateParam13 (konM_R1 * pmp)[tbd]
rateParam14 (koffMD_R1 * pmp0)[tbd]
rateParam15 (konM_R1 * pmp)[tbd]
rateParam16 (koffMT_R1 * pmp0)[tbd]
rateParam17 (konGr_R1 * pmpGr)[tbd]
rateParam18 (koffGrD_R1 * pmp0)[tbd]
rateParam19 (konGr_R1 * pmpGr)[tbd]
rateParam20 (koffGrT_R1 * pmp0)[tbd]
rateParam21 (gef_R1 * pmp0)[tbd]
rateParam22 (gap_R1 * pmp0)[tbd]
rateParam23 (gef_Gr_R1 * pmp0)[tbd]
rateParam24 (gap_Gr_R1 * pmp0)[tbd]
rateParam25 (pGdifactor_R1 * konD_3d_R1)[tbd]
rateParam26 (pGdifactor_R1 * konT_3d_R1)[tbd]
rateParam27 (psGdifactor_R1 * konD_3d_R1)[tbd]
rateParam28 (psGdifactor_R1 * konT_3d_R1)[tbd]
Group_nonG NonGlucLc[tbd]
Group_glucL GlucLc[tbd]
VC_SpConcFactor_1000_0 1.6611295681063123E-6 [1000]
Group_Rac1 (Rac1cgDp + GDIuuco_Rac1cgDp + GDIuuco_Rac1cgTp + (GDIuumo_Rac1mgDp * VC_SpConcFactor_1000_0) + (GDIuumo_Rac1mgTp * VC_SpConcFactor_1000_0) + (Rac1mgDp * VC_SpConcFactor_1000_0) + (Rac1mgTp * VC_SpConcFactor_1000_0) + Rac1cgTp + (Rac1ggDp * VC_SpConcFactor_1000_0) + GDIpuco_Rac1cgDp + (Rac1ggTp * VC_SpConcFactor_1000_0) + GDIpuco_Rac1cgTp)[tbd]
Group_GDI (GDIuuco + GDIpuco + GDIuuco_Rac1cgDp + GDIuuco_Rac1cgTp + (GDIuumo_Rac1mgDp * VC_SpConcFactor_1000_0) + (GDIuumo_Rac1mgTp * VC_SpConcFactor_1000_0) + (GDIuumo * VC_SpConcFactor_1000_0) + (GDIpumo * VC_SpConcFactor_1000_0) + (GDIuugo * VC_SpConcFactor_1000_0) + (GDIpugo * VC_SpConcFactor_1000_0) + GDIpuco_Rac1cgDp + GDIpuco_Rac1cgTp)[tbd]
Group_pak (pakuc + pakpc)[tbd]
Group_tot_Rac1_M (((GDIuumo_Rac1mgDp * VC_SpConcFactor_1000_0) + (GDIuumo_Rac1mgTp * VC_SpConcFactor_1000_0) + (Rac1mgDp * VC_SpConcFactor_1000_0) + (Rac1mgTp * VC_SpConcFactor_1000_0)) / VC_SpConcFactor_1000_0)[tbd]
Group_tot_Rac1_G (((Rac1ggDp * VC_SpConcFactor_1000_0) + (Rac1ggTp * VC_SpConcFactor_1000_0)) / VC_SpConcFactor_1000_0)[tbd]
Group_tot_Rac1_C (Rac1cgDp + GDIuuco_Rac1cgDp + GDIuuco_Rac1cgTp + Rac1cgTp + GDIpuco_Rac1cgDp + GDIpuco_Rac1cgTp)[tbd]
Group_Rac1_Mfree (((Rac1mgDp * VC_SpConcFactor_1000_0) + (Rac1mgTp * VC_SpConcFactor_1000_0)) / VC_SpConcFactor_1000_0)[tbd]
Group_Rac1_GDP_m (((GDIuumo_Rac1mgDp * VC_SpConcFactor_1000_0) + (Rac1mgDp * VC_SpConcFactor_1000_0)) / VC_SpConcFactor_1000_0)[tbd]
Group_Rac1_GTP_m (((GDIuumo_Rac1mgTp * VC_SpConcFactor_1000_0) + (Rac1mgTp * VC_SpConcFactor_1000_0)) / VC_SpConcFactor_1000_0)[tbd]
Group_Rac1_GDP_c (Rac1cgDp + GDIuuco_Rac1cgDp + GDIpuco_Rac1cgDp)[tbd]
Group_Rac1_GTP_c (GDIuuco_Rac1cgTp + Rac1cgTp + GDIpuco_Rac1cgTp)[tbd]
Group_Rac1_c_g (GDIuuco_Rac1cgDp + GDIpuco_Rac1cgDp)[tbd]
Group_GDI_c (GDIuuco + GDIpuco + GDIuuco_Rac1cgDp + GDIuuco_Rac1cgTp + GDIpuco_Rac1cgDp + GDIpuco_Rac1cgTp)[tbd]
Group_GDI_m (((GDIuumo_Rac1mgDp * VC_SpConcFactor_1000_0) + (GDIuumo_Rac1mgTp * VC_SpConcFactor_1000_0) + (GDIuumo * VC_SpConcFactor_1000_0) + (GDIpumo * VC_SpConcFactor_1000_0)) / VC_SpConcFactor_1000_0)[tbd]
Group_GDI_g (((GDIuugo * VC_SpConcFactor_1000_0) + (GDIpugo * VC_SpConcFactor_1000_0)) / VC_SpConcFactor_1000_0)[tbd]
Group_GDI_mb_g (((GDIuumo_Rac1mgDp * VC_SpConcFactor_1000_0) + (GDIuumo_Rac1mgTp * VC_SpConcFactor_1000_0)) / VC_SpConcFactor_1000_0)[tbd]
Group_GDI_mf (((GDIuumo * VC_SpConcFactor_1000_0) + (GDIpumo * VC_SpConcFactor_1000_0)) / VC_SpConcFactor_1000_0)[tbd]
Group_GDI_cb (GDIuuco_Rac1cgDp + GDIuuco_Rac1cgTp + GDIpuco_Rac1cgDp + GDIpuco_Rac1cgTp)[tbd]
Group_GDI_cf (GDIuuco + GDIpuco)[tbd]
Group_GDI_py_m 0.0[tbd]
Group_GDI_py_c 0.0[tbd]
Group_gdiSp_m (GDIpumo * VC_SpConcFactor_1000_0 / VC_SpConcFactor_1000_0)[tbd]
Group_gdiSp_c (GDIpuco + GDIpuco_Rac1cgDp + GDIpuco_Rac1cgTp)[tbd]
Group_pak_m 0.0[tbd]
Group_pak_Ac_m 0.0[tbd]
Group_pak_Ac_c pakpc[tbd]
g0 0.0[tbd]
tgluc 60.0[tbd]
gef0_R1 10.0[tbd]
changekonM 0.0[tbd]
coef_pld0 2.0[tbd]
change_gef_only 0.0[tbd]
coef_gef 5.0[tbd]
KD4_sys (koff_granule * koff_membrane * SfRAVolNIH3T3 / (1.0E-20 + (koff_membrane * konGr_R1 * SfcGr) + (koff_granule * konM_R1 * SfRAVol)))[tbd]
koff_granule (((koffGrD_R1 * Rac1ggDp) + (koffGrT_R1 * Rac1ggTp)) / (1.0E-20 + Rac1ggDp + Rac1ggTp))[tbd]
koff_membrane (((koffMD_R1 * Rac1mgDp) + (koffMT_R1 * Rac1mgTp)) / (1.0E-20 + Rac1mgDp + Rac1mgTp))[tbd]
KD4_sys_c ((Rac1cgDp + Rac1cgTp) / (0.0016611295681063123 * (((Rac1mgDp + Rac1mgTp) * SfRAVol) + ((Rac1ggDp + Rac1ggTp) * SfcGr))))[tbd]