Dashboard

Name - PDGF Src March 2012

BioModel ID - 82065439

Reaction Diagram

reactionDiagram

Physiology

Universal ID's Text Annotations

Applications

Applications See in Dashboard
Name Math Type Annotation
compartmental Deterministic (ODE) Compartmental cloned from 'compartmental' owned by user susana compartmental model used for Fig S1
ellipse 0999 Deterministic (ODE) Spatial (2D) (copied from compartmental) cloned from 'compartmental' owned by user susana compartmental model used for Fig S1
circle Deterministic (ODE) Spatial (2D) (copied from ellipse 0999) (copied from compartmental) cloned from 'compartmental' owned by user susana compartmental model used for Fig S1

Application - compartmental

Specifications(Species) - compartmental See in Dashboard
Species Initial Condition Diffusion Constant
PDGF_extra 1.0 [uM] 0.0 [um2/s]
PTP 0.1 [uM] 0.0 [um2/s]
Csk_cyto_active 0.0 [uM] 0.0 [um2/s]
Src_active_cyto 0.0 [uM] 0.0 [um2/s]
csk_cyto_inactive 0.1 [uM] 0.0 [um2/s]
Src_cyto 1.0 [uM] 0.0 [um2/s]
PDGFR_cyto_mem 250.0 [uM] 0.0 [um2/s]
PDGF_PDGFR_Srccyto_mem 0.0 [uM] 0.0 [um2/s]
PDGF_PDGFR 0.0 [uM] 0.0 [um2/s]
Specifications(Reaction) - compartmental See in Dashboard
Name Reaction Mapping
PDGF_binds_PDGFR included
Src activation included
Src dephosphorylation in cyto included
r0 included
Src association with receptor included
Simulations - compartmental See in Dashboard
Name End Time Output Options
compartmental 2700.0 [s]

OutputTimeStep 10.0

Geometry non-spatial969899354 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 cyto_mem

Application - ellipse 0999

Specifications(Species) - ellipse 0999 See in Dashboard
Species Initial Condition Diffusion Constant
PDGF_extra 1.0 [uM] 10.0 [um2/s]
PTP 0.1 [uM] 10.0 [um2/s]
Csk_cyto_active 0.0 [uM] 10.0 [um2/s]
Src_active_cyto 0.0 [uM] 1.0 [um2/s]
csk_cyto_inactive 0.1 [uM] 10.0 [um2/s]
Src_cyto 1.0 [uM] 10.0 [um2/s]
PDGFR_cyto_mem 250.0 [uM] 0.041 [um2/s]
PDGF_PDGFR_Srccyto_mem 0.0 [uM] 0.041 [um2/s]
PDGF_PDGFR 0.0 [uM] 0.0 [um2/s]
Specifications(Reaction) - ellipse 0999 See in Dashboard
Name Reaction Mapping
PDGF_binds_PDGFR included
Src activation included
Src dephosphorylation in cyto included
r0 included
Src association with receptor included
Simulations - ellipse 0999 See in Dashboard
Name End Time Output Options
Simulation0 1800.0 [s]

OutputTimeStep 10.0

Geometry ellipse sep 08 0999 See in Dashboard
(Origin: -23.5, -1.25, 0.0; Extent: 47.0, 2.5, 10.0[um])
Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Volume Analytical Cell 74.97675 [um2] cyto
Volume Analytical ECM 42.52324999999999 [um2] extra
Surface Cell_ECM_membrane Cell | ECM 93.46482136095845 [um] cyto_mem

Application - circle

Specifications(Species) - circle See in Dashboard
Species Initial Condition Diffusion Constant
PDGF_extra 1.0 [uM] 10.0 [um2/s]
PTP 0.1 [uM] 10.0 [um2/s]
Csk_cyto_active 0.0 [uM] 10.0 [um2/s]
Src_active_cyto 0.0 [uM] 1.0 [um2/s]
csk_cyto_inactive 0.1 [uM] 10.0 [um2/s]
Src_cyto 1.0 [uM] 10.0 [um2/s]
PDGFR_cyto_mem 250.0 [uM] 0.041 [um2/s]
PDGF_PDGFR_Srccyto_mem 0.0 [uM] 0.041 [um2/s]
PDGF_PDGFR 0.0 [uM] 0.0 [um2/s]
Specifications(Reaction) - circle See in Dashboard
Name Reaction Mapping
PDGF_binds_PDGFR included
Src activation included
Src dephosphorylation in cyto included
r0 included
Src association with receptor included
Simulations - circle See in Dashboard
Name End Time Output Options
Simulation1 1800.0 [s]

OutputTimeStep 10.0

Copy of Simulation1 300.0 [s]

OutputTimeStep 10.0

Geometry circle sep 08 See in Dashboard
(Origin: -5.0, -5.0, 0.0; Extent: 10.0, 10.0, 10.0[um])
Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Volume Analytical Cell 78.39 [um2] cyto
Volume Analytical ECM 5.4125000000000005 [um2] extra
Surface Cell_ECM_membrane Cell | ECM 7.704697811481667 [um] cyto_mem

Global Parameters

Global Parameters See in Dashboard
Name Expression
n 900.0[molecules.um-2.uM-1]