Dashboard

Name - Boras-Diffusional Study-100xPDEtest6 for images

BioModel ID - 95675197

Reaction Diagram

reactionDiagram

Physiology

Universal ID's Text Annotations

Applications

Applications See in Dashboard
Name Math Type Annotation
Correct PDE conc. with new geo with crop correct size Deterministic (ODE) Spatial (3D) cloned from 'Correct PDE conc. with new geo with crop correct size' owned by user schaff cloned from 'Correct PDE conc. with new geo with crop correct size' owned by user bboras (copied from PDE's with new geo with crop correct size) (copied from PDE's with new geo with crop) (copied from PDE's with new geo) (copied from Copy of test 3) (copied from test 3) (copied from test)
Copy of Correct PDE conc. with new geo with crop correct size Deterministic (ODE) Spatial (3D) cloned from 'Copy of Correct PDE conc. with new geo with crop correct size' owned by user schaff cloned from 'Copy of Correct PDE conc. with new geo with crop correct size' owned by user bboras (copied from Correct PDE conc. with new geo with crop correct size) (copied from PDE's with new geo with crop correct size) (copied from PDE's with new geo with crop) (copied from PDE's with new geo) (copied from Copy of test 3) (copied from test 3) (copied from test)
ode Deterministic (ODE) Compartmental cloned from 'ode' owned by user schaff (copied from Correct PDE conc. with new geo with crop correct size) cloned from 'Correct PDE conc. with new geo with crop correct size' owned by user bboras (copied from PDE's with new geo with crop correct size) (copied from PDE's with new geo with crop) (copied from PDE's with new geo) (copied from Copy of test 3) (copied from test 3) (copied from test)

Application - Correct PDE conc. with new geo with crop correct size

Specifications(Species) - Correct PDE conc. with new geo with crop correct size See in Dashboard
Species Initial Condition Diffusion Constant
PDE_cAMP (8400.0 * ((((x - 0.57) ^ 2.0) + ((y - 0.35) ^ 2.0) + ((z - 0.18) ^ 2.0)) < (0.025 ^ 2.0))) [uM] 0.0 [um2/s]
PDE_Cyto (51600.0 * ((((x - 0.57) ^ 2.0) + ((y - 0.35) ^ 2.0) + ((z - 0.18) ^ 2.0)) < (0.025 ^ 2.0))) [uM] 0.0 [um2/s]
cAMP_best 1.0 [uM] 9.0 [um2/s]
Specifications(Reaction) - Correct PDE conc. with new geo with crop correct size See in Dashboard
Name Reaction Mapping
r0 included
r1 included
Simulations - Correct PDE conc. with new geo with crop correct size See in Dashboard
Name End Time Output Options
Simulation0 360000 elements 10.0 [s]

OutputTimeStep 0.5

Simulation0 137826 elements diffusion 9 10.0 [s]

OutputTimeStep 0.5

Copy of Simulation0 137826 elements diffusion 75 10.0 [s]

OutputTimeStep 0.5

Copy of Simulation0 137826 elements diffusion 300 10.0 [s]

OutputTimeStep 0.5

Copy of Simulation0 137826 elements diffusion 9 10.0 [s]

OutputTimeStep 0.5

Copy of Copy of Simulation0 137826 elements diffusion 9 10.0 [s]

OutputTimeStep 0.5

Copy of Copy of Copy of Simulation0 137826 elements diffusion 9 10.0 [s]

OutputTimeStep 0.5

Copy of Copy of Copy of Copy of Simulation0 137826 elements diffusion 10 10.0 [s]

OutputTimeStep 0.5

Copy of Copy of Copy of Copy of Copy of Simulation0 137826 elements diffusion 10 10.0 [s]

OutputTimeStep 0.5

Geometry geom_20150608_114218 See in Dashboard
(Origin: 0.0, 0.0, 0.0; Extent: 1.04, 0.765, 0.41500000000000004[um])
Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Volume Image cytosol 0.2878215261413742 [um3] Cyto
Volume Image rest 0.014342978016688063 [um3]
Surface cytosol_rest_membrane cytosol | rest 0.36025610812006187 [um2]

Application - Copy of Correct PDE conc. with new geo with crop correct size

Specifications(Species) - Copy of Correct PDE conc. with new geo with crop correct size See in Dashboard
Species Initial Condition Diffusion Constant
PDE_cAMP 0.0 [uM] 0.0 [um2/s]
PDE_Cyto ((600.0 * (0.41 < x) * (x < 0.6) * (y > 0.28) * (y < 0.43) * (z > 0.03) * (z < 0.22)) - (600.0 * (0.46 < x) * (x < 0.55) * (y > 0.33) * (y < 0.38) * (z > 0.08) * (z < 0.17))) [uM] 0.0 [um2/s]
cAMP_best 0.0 [uM] 200.0 [um2/s]
Specifications(Reaction) - Copy of Correct PDE conc. with new geo with crop correct size See in Dashboard
Name Reaction Mapping
r0 included
r1 included
Simulations - Copy of Correct PDE conc. with new geo with crop correct size See in Dashboard
Name End Time Output Options
Simulation5 5.0 [s]

OutputTimeStep 0.5

Simulation6 1.0 [s]

OutputTimeStep 0.5

Simulation7 1.0 [s]

OutputTimeStep 0.5

Simulation8 10.0 [s]

OutputTimeStep 0.5

Simulation9 10.0 [s]

OutputTimeStep 0.5

Simulation10 10.0 [s]

OutputTimeStep 0.5

Simulation11 10.0 [s]

OutputTimeStep 0.5

Simulation12 1000.0 [s]

OutputTimeStep 0.5

Simulation13 10.0 [s]

OutputTimeStep 0.5

Copy of Simulation12 700.0 [s]

OutputTimeStep 0.5

Copy of Copy of Simulation12 700.0 [s]

OutputTimeStep 0.5

Copy of Simulation12 1 10.0 [s]

OutputTimeStep 0.5

Geometry cAMP-diffusion_with EPAC_V_cell_short11_including PKA_Correct PDE conc. with new geo with crop correct size_20110706_826393532 See in Dashboard
(Origin: 0.0, 0.0, 0.0; Extent: 1.04, 0.765, 0.41500000000000004[um])
Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Volume Image background 0.2878215261413742 [um3] Cyto
Volume Image roi_255 0.00507383535190043 [um3] ttube
Volume Image mito 0.006815278841323884 [um3] mito
Volume Image mito2 0.014342978016688063 [um3] mito2
Volume Image SR 0.011513772206563602 [um3] SR
Volume Image ttube2 0.004606609442149914 [um3] ttube2
Surface background_roi_255_membrane background | roi_255 0.18949064675557042 [um2] tttt
Surface SR_background_membrane SR | background 0.9515156362075461 [um2] Membrane3
Surface background_ttube2_membrane background | ttube2 0.23305999926855114 [um2] Membrane2
Surface background_mito_membrane background | mito 0.19753629961257163 [um2] Membrane0
Surface background_mito2_membrane background | mito2 0.36025610812006187 [um2] Membrane1

Application - ode

Specifications(Species) - ode See in Dashboard
Species Initial Condition Diffusion Constant
PDE_cAMP 0.0 [uM] 0.0 [um2/s]
PDE_Cyto 7.0 [uM] 0.0 [um2/s]
cAMP_best 1.0 [uM] 0.0 [um2/s]
Specifications(Reaction) - ode See in Dashboard
Name Reaction Mapping
r0 included
r1 included
Simulations - ode See in Dashboard
Name End Time Output Options
Simulation0 1.0 [s]

OutputTimeStep 0.5

Geometry nonspatial1893829213 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 Membrane3

Global Parameters

Global Parameters See in Dashboard
Name Expression
g0 0.0[tbd]
C_kr 2.3[s-1]
C_kd 3.8E-4[uM]
B_factor 5.0[tbd]
F_B_binding 3.175[s-1]
B_kd 0.013[tbd]
A_kd 0.03[tbd]
spots 2.0[tbd]
F_A_binding 0.3[s-1]
A_factor 23.0[tbd]