Dashboard

Name - EGF ras Sep 2012

BioModel ID - 83446023

Reaction Diagram

reactionDiagram

Physiology

Universal ID's Text Annotations

Applications

Applications See in Dashboard
Name Math Type Annotation
compartmental Deterministic (ODE) Compartmental
ellipse_0999 receptor activation only Deterministic (ODE) Spatial (2D) (copied from ellipse_0999) (copied from compartmental)
circle Deterministic (ODE) Spatial (2D) (copied from ellipse_0999 receptor activation only) (copied from ellipse_0999) (copied from compartmental)
ellipse_099_nucleus1_1 Deterministic (ODE) Spatial (2D) (copied from ellipse_0999 receptor activation only) (copied from ellipse_0999) (copied from compartmental)
ellipse_099_nucleus3_1 Deterministic (ODE) Spatial (2D) (copied from ellipse_099_nucleus1_1) (copied from ellipse_0999 receptor activation only) (copied from ellipse_0999) (copied from compartmental)
ellipse_099_nucleus5_1 Deterministic (ODE) Spatial (2D) (copied from ellipse_099_nucleus3_1) (copied from ellipse_099_nucleus1_1) (copied from ellipse_0999 receptor activation only) (copied from ellipse_0999) (copied from compartmental)
spatially varying diffusion and receptor number Deterministic (ODE) Spatial (2D) (copied from ellipse_0999 receptor activation only) (copied from ellipse_0999) (copied from compartmental)
circle fine mesh Deterministic (ODE) Spatial (2D) (copied from circle) (copied from ellipse_0999 receptor activation only) (copied from ellipse_0999) (copied from compartmental)
ellipse fine mesh Deterministic (ODE) Spatial (2D) (copied from ellipse_099_nucleus5_1) (copied from ellipse_099_nucleus3_1) (copied from ellipse_099_nucleus1_1) (copied from ellipse_0999 receptor activation only) (copied from ellipse_0999) (copied from compartmental)

Application - compartmental

Specifications(Species) - compartmental See in Dashboard
Species Initial Condition Diffusion Constant
EGF_extra 1.0 [uM] 0.0 [um2/s]
MAPK_active_N_nucleus 0.0 [uM] 0.0 [um2/s]
Raf_active_cyto 0.0 [uM] 0.0 [um2/s]
ATP 5000.0 [uM] 0.0 [um2/s]
GAP 0.1 [uM] 0.0 [um2/s]
MEK_cyto 0.18 [uM] 0.0 [um2/s]
MAPK_active_cyto 0.0 [uM] 0.0 [um2/s]
Ras_GAP_cyto 0.002 [uM] 0.0 [um2/s]
MEK_active_cyto 0.0 [uM] 0.0 [um2/s]
MAPK_cyto 0.36 [uM] 0.0 [um2/s]
Sos_cyto 0.1 [uM] 0.0 [um2/s]
SHC_p_cyto 0.0 [uM] 0.0 [um2/s]
SHC_cyto 0.5 [uM] 0.0 [um2/s]
Raf_cyto 0.2 [uM] 0.0 [um2/s]
Grb2_cyto 1.0 [uM] 0.0 [um2/s]
PP2A_cyto 0.0 [uM] 0.0 [um2/s]
PP2A_inactive 0.1 [uM] 0.0 [um2/s]
EGFR_active 0.0 [uM] 0.0 [um2/s]
EGFR_GAP 0.0 [uM] 0.0 [um2/s]
EGFR_cyto_mem 400.0 [uM] 0.0 [um2/s]
EGFR_dimer 0.0 [uM] 0.0 [um2/s]
Ras_GDP_cyto_mem 500.0 [uM] 0.0 [um2/s]
Ras_GTP_cyto_mem 0.0 [uM] 0.0 [um2/s]
EGFR_GAP_GRb2_Sos 0.0 [uM] 0.0 [um2/s]
EGFR_Sos_Grb2_Shc_cyto_mem 0.0 [uM] 0.0 [um2/s]
EGFR_GAP_Grb2 0.0 [uM] 0.0 [um2/s]
Specifications(Reaction) - compartmental See in Dashboard
Name Reaction Mapping
SHC dephosphorylation included
MEk activation included
nuclear transport included
receptor ligand binding included
Ras activation by Sos included
MAPK inactivation included
MAPK activation included
r0 included
Raf inactivation included
Ras GAP included
Raf activation included
MEK inactivation included
Sos binding included
Shc phosphorylation included
GAP binding included
Shc binding EGFR included
dimerization included
GRb2 binding included
Simulations - compartmental See in Dashboard
Name End Time Output Options
Simulation0 3600.0 [s]

OutputTimeStep 10.0

Simulation13 1.0 [s]

OutputTimeStep 10.0

Geometry non-spatial107399510 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 nuclear Membrane

Application - ellipse_0999 receptor activation only

Specifications(Species) - ellipse_0999 receptor activation only See in Dashboard
Species Initial Condition Diffusion Constant
EGF_extra 1.0 [uM] 1.0 [um2/s]
MAPK_active_N_nucleus 0.0 [uM] 7.0 [um2/s]
Raf_active_cyto 0.0 [uM] 7.0 [um2/s]
ATP 5000.0 [uM] 10.0 [um2/s]
GAP 0.1 [uM] 10.0 [um2/s]
MEK_cyto 0.18 [uM] 6.0 [um2/s]
MAPK_active_cyto 0.0 [uM] 7.0 [um2/s]
Ras_GAP_cyto 0.002 [uM] 4.14 [um2/s]
MEK_active_cyto 0.0 [uM] 6.0 [um2/s]
MAPK_cyto 0.36 [uM] 7.0 [um2/s]
Sos_cyto 1.0 [uM] 3.7 [um2/s]
SHC_p_cyto 0.0 [uM] 6.4 [um2/s]
SHC_cyto 1.0 [uM] 6.4 [um2/s]
Raf_cyto 0.2 [uM] 7.0 [um2/s]
Grb2_cyto 1.0 [uM] 8.5 [um2/s]
PP2A_cyto 0.0 [uM] 0.0 [um2/s]
PP2A_inactive 0.05 [uM] 0.0 [um2/s]
EGFR_active 0.0 [uM] 0.0 [um2/s]
EGFR_GAP 0.0 [uM] 0.08 [um2/s]
EGFR_cyto_mem 400.0 [uM] 0.112 [um2/s]
EGFR_dimer 0.0 [uM] 0.08 [um2/s]
Ras_GDP_cyto_mem 500.0 [uM] 0.16 [um2/s]
Ras_GTP_cyto_mem 0.0 [uM] 0.16 [um2/s]
EGFR_GAP_GRb2_Sos 0.0 [uM] 0.0 [um2/s]
EGFR_Sos_Grb2_Shc_cyto_mem 0.0 [uM] 0.08 [um2/s]
EGFR_GAP_Grb2 0.0 [uM] 0.0 [um2/s]
Specifications(Reaction) - ellipse_0999 receptor activation only See in Dashboard
Name Reaction Mapping
SHC dephosphorylation included
MEk activation included
nuclear transport included
receptor ligand binding included
Ras activation by Sos included
MAPK inactivation included
MAPK activation included
r0 included
Raf inactivation included
Ras GAP included
Raf activation included
MEK inactivation included
Sos binding included
Shc phosphorylation included
GAP binding included
Shc binding EGFR included
dimerization included
GRb2 binding included
Simulations - ellipse_0999 receptor activation only See in Dashboard
Name End Time Output Options
Simulation12 60.0 [s]

OutputTimeStep 10.0

Copy of Simulation12 1 3600.0 [s]

OutputTimeStep 10.0

Copy of Copy of Simulation12 1 7200.0 [s]

OutputTimeStep 10.0

varying diffusion of EGFR 3600.0 [s]

OutputTimeStep 10.0

varying receptor density 3600.0 [s]

OutputTimeStep 10.0

Geometry Mathieu ellipse 0999 with nucleus ratio 6 See in Dashboard
(Origin: -30.0, -3.0, 0.0; Extent: 60.0, 6.0, 10.0[um])
Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Volume Analytical nucleus 11.673486088379706 [um2] nucleus
Volume Analytical cell 158.12602291325695 [um2] cyto
Volume Analytical ECM 190.20049099836334 [um2] extra
Surface ECM_cell_membrane ECM | cell 109.6318051248791 [um] cyto_mem
Surface cell_nucleus_membrane cell | nucleus 37.823588052652646 [um] nuclear Membrane

Application - circle

Specifications(Species) - circle See in Dashboard
Species Initial Condition Diffusion Constant
EGF_extra 1.0 [uM] 1.0 [um2/s]
MAPK_active_N_nucleus 0.0 [uM] 7.0 [um2/s]
Raf_active_cyto 0.0 [uM] 7.0 [um2/s]
ATP 5000.0 [uM] 10.0 [um2/s]
GAP 0.1 [uM] 10.0 [um2/s]
MEK_cyto 0.18 [uM] 6.0 [um2/s]
MAPK_active_cyto 0.0 [uM] 7.0 [um2/s]
Ras_GAP_cyto 0.002 [uM] 4.14 [um2/s]
MEK_active_cyto 0.0 [uM] 6.0 [um2/s]
MAPK_cyto 0.36 [uM] 7.0 [um2/s]
Sos_cyto 1.0 [uM] 10.0 [um2/s]
SHC_p_cyto 0.0 [uM] 6.4 [um2/s]
SHC_cyto 1.0 [uM] 6.4 [um2/s]
Raf_cyto 0.2 [uM] 7.0 [um2/s]
Grb2_cyto 1.0 [uM] 8.5 [um2/s]
PP2A_cyto 0.0 [uM] 0.0 [um2/s]
PP2A_inactive 0.05 [uM] 0.0 [um2/s]
EGFR_active 0.0 [uM] 0.0 [um2/s]
EGFR_GAP 0.0 [uM] 0.08 [um2/s]
EGFR_cyto_mem 400.0 [uM] 0.04 [um2/s]
EGFR_dimer 0.0 [uM] 0.08 [um2/s]
Ras_GDP_cyto_mem 500.0 [uM] 0.16 [um2/s]
Ras_GTP_cyto_mem 0.0 [uM] 0.16 [um2/s]
EGFR_GAP_GRb2_Sos 0.0 [uM] 0.0 [um2/s]
EGFR_Sos_Grb2_Shc_cyto_mem 0.0 [uM] 0.08 [um2/s]
EGFR_GAP_Grb2 0.0 [uM] 0.0 [um2/s]
Specifications(Reaction) - circle See in Dashboard
Name Reaction Mapping
SHC dephosphorylation included
MEk activation included
nuclear transport included
receptor ligand binding included
Ras activation by Sos included
MAPK inactivation included
MAPK activation included
r0 included
Raf inactivation included
Ras GAP included
Raf activation included
MEK inactivation included
Sos binding included
Shc phosphorylation included
GAP binding included
Shc binding EGFR included
dimerization included
GRb2 binding included
Simulations - circle See in Dashboard
Name End Time Output Options
Simulation1 480.0 [s]

OutputTimeStep 10.0

Simulation2 7200.0 [s]

OutputTimeStep 10.0

Copy of Simulation1 60.0 [s]

OutputTimeStep 10.0

Geometry circle with nucleus ratio 6 feb 2009 See in Dashboard
(Origin: -8.0, -8.0, 0.0; Extent: 16.0, 16.0, 10.0[um])
Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Volume Analytical nucleus 12.313600000000001 [um2] nucleus
Volume Analytical cyto 156.97920000000002 [um2] cyto
Volume Analytical ecm 86.7072 [um2] extra
Surface cyto_ecm_membrane cyto | ecm 46.21278101811295 [um] cyto_mem
Surface cyto_nucleus_membrane cyto | nucleus 12.415157207294083 [um] nuclear Membrane

Application - ellipse_099_nucleus1_1

Specifications(Species) - ellipse_099_nucleus1_1 See in Dashboard
Species Initial Condition Diffusion Constant
EGF_extra 1.0 [uM] 1.0 [um2/s]
MAPK_active_N_nucleus 0.0 [uM] 7.0 [um2/s]
Raf_active_cyto 0.0 [uM] 7.0 [um2/s]
ATP 5000.0 [uM] 10.0 [um2/s]
GAP 0.1 [uM] 10.0 [um2/s]
MEK_cyto 0.18 [uM] 6.0 [um2/s]
MAPK_active_cyto 0.0 [uM] 7.0 [um2/s]
Ras_GAP_cyto 0.002 [uM] 4.14 [um2/s]
MEK_active_cyto 0.0 [uM] 6.0 [um2/s]
MAPK_cyto 0.36 [uM] 7.0 [um2/s]
Sos_cyto 1.0 [uM] 10.0 [um2/s]
SHC_p_cyto 0.0 [uM] 6.4 [um2/s]
SHC_cyto 1.0 [uM] 6.4 [um2/s]
Raf_cyto 0.2 [uM] 7.0 [um2/s]
Grb2_cyto 1.0 [uM] 8.5 [um2/s]
PP2A_cyto 0.0 [uM] 0.0 [um2/s]
PP2A_inactive 0.05 [uM] 0.0 [um2/s]
EGFR_active 0.0 [uM] 0.0 [um2/s]
EGFR_GAP 0.0 [uM] 0.08 [um2/s]
EGFR_cyto_mem 400.0 [uM] 0.04 [um2/s]
EGFR_dimer 0.0 [uM] 0.08 [um2/s]
Ras_GDP_cyto_mem 500.0 [uM] 0.16 [um2/s]
Ras_GTP_cyto_mem 0.0 [uM] 0.16 [um2/s]
EGFR_GAP_GRb2_Sos 0.0 [uM] 0.0 [um2/s]
EGFR_Sos_Grb2_Shc_cyto_mem 0.0 [uM] 0.08 [um2/s]
EGFR_GAP_Grb2 0.0 [uM] 0.0 [um2/s]
Specifications(Reaction) - ellipse_099_nucleus1_1 See in Dashboard
Name Reaction Mapping
SHC dephosphorylation included
MEk activation included
nuclear transport included
receptor ligand binding included
Ras activation by Sos included
MAPK inactivation included
MAPK activation included
r0 included
Raf inactivation included
Ras GAP included
Raf activation included
MEK inactivation included
Sos binding included
Shc phosphorylation included
GAP binding included
Shc binding EGFR included
dimerization included
GRb2 binding included
Simulations - ellipse_099_nucleus1_1 See in Dashboard
Name End Time Output Options
Simulation5 15000.0 [s]

OutputTimeStep 10.0

Geometry ellipse sep 08 0999 with cyt-n 2:1 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 subdomain0 37.682249999999996 [um2] nucleus
Volume Analytical Cell 37.29449999999999 [um2] cyto
Volume Analytical ECM 42.52324999999999 [um2] extra
Surface Cell_ECM_membrane Cell | ECM 93.46482136095845 [um] cyto_mem
Surface Cell_subdomain0_membrane Cell | subdomain0 65.35262936922854 [um] nuclear Membrane

Application - ellipse_099_nucleus3_1

Specifications(Species) - ellipse_099_nucleus3_1 See in Dashboard
Species Initial Condition Diffusion Constant
EGF_extra 1.0 [uM] 1.0 [um2/s]
MAPK_active_N_nucleus 0.0 [uM] 7.0 [um2/s]
Raf_active_cyto 0.0 [uM] 7.0 [um2/s]
ATP 5000.0 [uM] 10.0 [um2/s]
GAP 0.1 [uM] 10.0 [um2/s]
MEK_cyto 0.18 [uM] 6.0 [um2/s]
MAPK_active_cyto 0.0 [uM] 7.0 [um2/s]
Ras_GAP_cyto 0.002 [uM] 4.14 [um2/s]
MEK_active_cyto 0.0 [uM] 6.0 [um2/s]
MAPK_cyto 0.36 [uM] 7.0 [um2/s]
Sos_cyto 1.0 [uM] 10.0 [um2/s]
SHC_p_cyto 0.0 [uM] 6.4 [um2/s]
SHC_cyto 1.0 [uM] 6.4 [um2/s]
Raf_cyto 0.2 [uM] 7.0 [um2/s]
Grb2_cyto 1.0 [uM] 8.5 [um2/s]
PP2A_cyto 0.0 [uM] 0.0 [um2/s]
PP2A_inactive 0.05 [uM] 0.0 [um2/s]
EGFR_active 0.0 [uM] 0.0 [um2/s]
EGFR_GAP 0.0 [uM] 0.08 [um2/s]
EGFR_cyto_mem 400.0 [uM] 0.04 [um2/s]
EGFR_dimer 0.0 [uM] 0.08 [um2/s]
Ras_GDP_cyto_mem 500.0 [uM] 0.16 [um2/s]
Ras_GTP_cyto_mem 0.0 [uM] 0.16 [um2/s]
EGFR_GAP_GRb2_Sos 0.0 [uM] 0.0 [um2/s]
EGFR_Sos_Grb2_Shc_cyto_mem 0.0 [uM] 0.08 [um2/s]
EGFR_GAP_Grb2 0.0 [uM] 0.0 [um2/s]
Specifications(Reaction) - ellipse_099_nucleus3_1 See in Dashboard
Name Reaction Mapping
SHC dephosphorylation included
MEk activation included
nuclear transport included
receptor ligand binding included
Ras activation by Sos included
MAPK inactivation included
MAPK activation included
r0 included
Raf inactivation included
Ras GAP included
Raf activation included
MEK inactivation included
Sos binding included
Shc phosphorylation included
GAP binding included
Shc binding EGFR included
dimerization included
GRb2 binding included
Simulations - ellipse_099_nucleus3_1 See in Dashboard
Name End Time Output Options
Simulation3 15000.0 [s]

OutputTimeStep 10.0

Geometry ellipse sep 08 0999 with cyt-n 4:1 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 subdomain0 18.858749999999997 [um2] nucleus
Volume Analytical Cell 56.117999999999995 [um2] cyto
Volume Analytical ECM 42.52324999999999 [um2] extra
Surface Cell_ECM_membrane Cell | ECM 93.46482136095845 [um] cyto_mem
Surface Cell_subdomain0_membrane Cell | subdomain0 46.33232970167217 [um] nuclear Membrane

Application - ellipse_099_nucleus5_1

Specifications(Species) - ellipse_099_nucleus5_1 See in Dashboard
Species Initial Condition Diffusion Constant
EGF_extra 1.0 [uM] 1.0 [um2/s]
MAPK_active_N_nucleus 0.0 [uM] 7.0 [um2/s]
Raf_active_cyto 0.0 [uM] 7.0 [um2/s]
ATP 5000.0 [uM] 10.0 [um2/s]
GAP 0.1 [uM] 10.0 [um2/s]
MEK_cyto 0.18 [uM] 6.0 [um2/s]
MAPK_active_cyto 0.0 [uM] 7.0 [um2/s]
Ras_GAP_cyto 0.002 [uM] 4.14 [um2/s]
MEK_active_cyto 0.0 [uM] 6.0 [um2/s]
MAPK_cyto 0.36 [uM] 7.0 [um2/s]
Sos_cyto 1.0 [uM] 10.0 [um2/s]
SHC_p_cyto 0.0 [uM] 6.4 [um2/s]
SHC_cyto 1.0 [uM] 6.4 [um2/s]
Raf_cyto 0.2 [uM] 7.0 [um2/s]
Grb2_cyto 1.0 [uM] 8.5 [um2/s]
PP2A_cyto 0.0 [uM] 0.0 [um2/s]
PP2A_inactive 0.05 [uM] 0.0 [um2/s]
EGFR_active 0.0 [uM] 0.0 [um2/s]
EGFR_GAP 0.0 [uM] 0.08 [um2/s]
EGFR_cyto_mem 400.0 [uM] 0.04 [um2/s]
EGFR_dimer 0.0 [uM] 0.08 [um2/s]
Ras_GDP_cyto_mem 500.0 [uM] 0.16 [um2/s]
Ras_GTP_cyto_mem 0.0 [uM] 0.16 [um2/s]
EGFR_GAP_GRb2_Sos 0.0 [uM] 0.0 [um2/s]
EGFR_Sos_Grb2_Shc_cyto_mem 0.0 [uM] 0.08 [um2/s]
EGFR_GAP_Grb2 0.0 [uM] 0.0 [um2/s]
Specifications(Reaction) - ellipse_099_nucleus5_1 See in Dashboard
Name Reaction Mapping
SHC dephosphorylation included
MEk activation included
nuclear transport included
receptor ligand binding included
Ras activation by Sos included
MAPK inactivation included
MAPK activation included
r0 included
Raf inactivation included
Ras GAP included
Raf activation included
MEK inactivation included
Sos binding included
Shc phosphorylation included
GAP binding included
Shc binding EGFR included
dimerization included
GRb2 binding included
Simulations - ellipse_099_nucleus5_1 See in Dashboard
Name End Time Output Options
Simulation4 15000.0 [s]

OutputTimeStep 10.0

Copy of Simulation4 60.0 [s]

OutputTimeStep 10.0

Geometry ellipse sep 08 0999 with cyt-n 6:1 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 subdomain0 12.560749999999999 [um2] nucleus
Volume Analytical Cell 62.41599999999999 [um2] cyto
Volume Analytical ECM 42.52324999999999 [um2] extra
Surface Cell_ECM_membrane Cell | ECM 93.46482136095845 [um] cyto_mem
Surface Cell_subdomain0_membrane Cell | subdomain0 38.29432490973859 [um] nuclear Membrane

Application - spatially varying diffusion and receptor number

Specifications(Species) - spatially varying diffusion and receptor number See in Dashboard
Species Initial Condition Diffusion Constant
EGF_extra 1.0 [uM] 1.0 [um2/s]
MAPK_active_N_nucleus 0.0 [uM] 7.0 [um2/s]
Raf_active_cyto 0.0 [uM] 7.0 [um2/s]
ATP 5000.0 [uM] 10.0 [um2/s]
GAP 0.1 [uM] 10.0 [um2/s]
MEK_cyto 0.18 [uM] 6.0 [um2/s]
MAPK_active_cyto 0.0 [uM] 7.0 [um2/s]
Ras_GAP_cyto 0.002 [uM] 4.14 [um2/s]
MEK_active_cyto 0.0 [uM] 6.0 [um2/s]
MAPK_cyto 0.36 [uM] 7.0 [um2/s]
Sos_cyto 1.0 [uM] 3.7 [um2/s]
SHC_p_cyto 0.0 [uM] 6.4 [um2/s]
SHC_cyto 1.0 [uM] 6.4 [um2/s]
Raf_cyto 0.2 [uM] 7.0 [um2/s]
Grb2_cyto 1.0 [uM] 8.5 [um2/s]
PP2A_cyto 0.0 [uM] 0.0 [um2/s]
PP2A_inactive 0.05 [uM] 0.0 [um2/s]
EGFR_active 0.0 [uM] 0.0 [um2/s]
EGFR_GAP 0.0 [uM] 0.08 [um2/s]
EGFR_cyto_mem (213.0 * (1.0 + (0.018 * abs(x)))) [uM] (0.112 * (1.0 + (0.018 * abs(x)))) [um2/s]
EGFR_dimer 0.0 [uM] 0.08 [um2/s]
Ras_GDP_cyto_mem 500.0 [uM] 0.16 [um2/s]
Ras_GTP_cyto_mem 0.0 [uM] 0.16 [um2/s]
EGFR_GAP_GRb2_Sos 0.0 [uM] 0.0 [um2/s]
EGFR_Sos_Grb2_Shc_cyto_mem 0.0 [uM] (0.08 * (1.0 + (0.03 * abs(x)))) [um2/s]
EGFR_GAP_Grb2 0.0 [uM] 0.0 [um2/s]
Specifications(Reaction) - spatially varying diffusion and receptor number See in Dashboard
Name Reaction Mapping
SHC dephosphorylation included
MEk activation included
nuclear transport included
receptor ligand binding included
Ras activation by Sos included
MAPK inactivation included
MAPK activation included
r0 included
Raf inactivation included
Ras GAP included
Raf activation included
MEK inactivation included
Sos binding included
Shc phosphorylation included
GAP binding included
Shc binding EGFR included
dimerization included
GRb2 binding included
Simulations - spatially varying diffusion and receptor number See in Dashboard
Name End Time Output Options
Simulation6 60.0 [s]

OutputTimeStep 10.0

Simulation7 3600.0 [s]

OutputTimeStep 10.0

Simulation8 7200.0 [s]

OutputTimeStep 10.0

Simulation9 3600.0 [s]

OutputTimeStep 10.0

Simulation10 3600.0 [s]

OutputTimeStep 10.0

Copy of Simulation6 480.0 [s]

OutputTimeStep 10.0

Geometry Mathieu ellipse 0999 with nucleus ratio 6 See in Dashboard
(Origin: -30.0, -3.0, 0.0; Extent: 60.0, 6.0, 10.0[um])
Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Volume Analytical nucleus 12.308944744072456 [um2] nucleus
Volume Analytical cell 156.20637020453853 [um2] cyto
Volume Analytical ECM 191.48468505138905 [um2] extra
Surface ECM_cell_membrane ECM | cell 108.81799234890245 [um] cyto_mem
Surface cell_nucleus_membrane cell | nucleus 36.43730612082122 [um] nuclear Membrane

Application - circle fine mesh

Specifications(Species) - circle fine mesh See in Dashboard
Species Initial Condition Diffusion Constant
EGF_extra 1.0 [uM] 1.0 [um2/s]
MAPK_active_N_nucleus 0.0 [uM] 7.0 [um2/s]
Raf_active_cyto 0.0 [uM] 7.0 [um2/s]
ATP 5000.0 [uM] 10.0 [um2/s]
GAP 0.1 [uM] 10.0 [um2/s]
MEK_cyto 0.18 [uM] 6.0 [um2/s]
MAPK_active_cyto 0.0 [uM] 7.0 [um2/s]
Ras_GAP_cyto 0.002 [uM] 4.14 [um2/s]
MEK_active_cyto 0.0 [uM] 6.0 [um2/s]
MAPK_cyto 0.36 [uM] 7.0 [um2/s]
Sos_cyto 1.0 [uM] 10.0 [um2/s]
SHC_p_cyto 0.0 [uM] 6.4 [um2/s]
SHC_cyto 1.0 [uM] 6.4 [um2/s]
Raf_cyto 0.2 [uM] 7.0 [um2/s]
Grb2_cyto 1.0 [uM] 8.5 [um2/s]
PP2A_cyto 0.0 [uM] 0.0 [um2/s]
PP2A_inactive 0.05 [uM] 0.0 [um2/s]
EGFR_active 0.0 [uM] 0.0 [um2/s]
EGFR_GAP 0.0 [uM] 0.08 [um2/s]
EGFR_cyto_mem 400.0 [uM] 0.04 [um2/s]
EGFR_dimer 0.0 [uM] 0.08 [um2/s]
Ras_GDP_cyto_mem 500.0 [uM] 0.16 [um2/s]
Ras_GTP_cyto_mem 0.0 [uM] 0.16 [um2/s]
EGFR_GAP_GRb2_Sos 0.0 [uM] 0.0 [um2/s]
EGFR_Sos_Grb2_Shc_cyto_mem 0.0 [uM] 0.08 [um2/s]
EGFR_GAP_Grb2 0.0 [uM] 0.0 [um2/s]
Specifications(Reaction) - circle fine mesh See in Dashboard
Name Reaction Mapping
SHC dephosphorylation included
MEk activation included
nuclear transport included
receptor ligand binding included
Ras activation by Sos included
MAPK inactivation included
MAPK activation included
r0 included
Raf inactivation included
Ras GAP included
Raf activation included
MEK inactivation included
Sos binding included
Shc phosphorylation included
GAP binding included
Shc binding EGFR included
dimerization included
GRb2 binding included
Simulations - circle fine mesh See in Dashboard
Name End Time Output Options
Simulation11 60.0 [s]

OutputTimeStep 10.0

Simulation14 7200.0 [s]

OutputTimeStep 10.0

Geometry circle with nucleus ratio 6 feb 2009 See in Dashboard
(Origin: -8.0, -8.0, 0.0; Extent: 16.0, 16.0, 10.0[um])
Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Volume Analytical nucleus 12.313600000000001 [um2] nucleus
Volume Analytical cyto 156.97920000000002 [um2] cyto
Volume Analytical ecm 86.7072 [um2] extra
Surface cyto_ecm_membrane cyto | ecm 46.21278101811295 [um] cyto_mem
Surface cyto_nucleus_membrane cyto | nucleus 12.415157207294083 [um] nuclear Membrane

Application - ellipse fine mesh

Specifications(Species) - ellipse fine mesh See in Dashboard
Species Initial Condition Diffusion Constant
EGF_extra 1.0 [uM] 1.0 [um2/s]
MAPK_active_N_nucleus 0.0 [uM] 7.0 [um2/s]
Raf_active_cyto 0.0 [uM] 7.0 [um2/s]
ATP 5000.0 [uM] 10.0 [um2/s]
GAP 0.1 [uM] 10.0 [um2/s]
MEK_cyto 0.18 [uM] 6.0 [um2/s]
MAPK_active_cyto 0.0 [uM] 7.0 [um2/s]
Ras_GAP_cyto 0.002 [uM] 4.14 [um2/s]
MEK_active_cyto 0.0 [uM] 6.0 [um2/s]
MAPK_cyto 0.36 [uM] 7.0 [um2/s]
Sos_cyto 1.0 [uM] 10.0 [um2/s]
SHC_p_cyto 0.0 [uM] 6.4 [um2/s]
SHC_cyto 1.0 [uM] 6.4 [um2/s]
Raf_cyto 0.2 [uM] 7.0 [um2/s]
Grb2_cyto 1.0 [uM] 8.5 [um2/s]
PP2A_cyto 0.0 [uM] 0.0 [um2/s]
PP2A_inactive 0.05 [uM] 0.0 [um2/s]
EGFR_active 0.0 [uM] 0.0 [um2/s]
EGFR_GAP 0.0 [uM] 0.08 [um2/s]
EGFR_cyto_mem 400.0 [uM] 0.04 [um2/s]
EGFR_dimer 0.0 [uM] 0.08 [um2/s]
Ras_GDP_cyto_mem 500.0 [uM] 0.16 [um2/s]
Ras_GTP_cyto_mem 0.0 [uM] 0.16 [um2/s]
EGFR_GAP_GRb2_Sos 0.0 [uM] 0.0 [um2/s]
EGFR_Sos_Grb2_Shc_cyto_mem 0.0 [uM] 0.08 [um2/s]
EGFR_GAP_Grb2 0.0 [uM] 0.0 [um2/s]
Specifications(Reaction) - ellipse fine mesh See in Dashboard
Name Reaction Mapping
SHC dephosphorylation included
MEk activation included
nuclear transport included
receptor ligand binding included
Ras activation by Sos included
MAPK inactivation included
MAPK activation included
r0 included
Raf inactivation included
Ras GAP included
Raf activation included
MEK inactivation included
Sos binding included
Shc phosphorylation included
GAP binding included
Shc binding EGFR included
dimerization included
GRb2 binding included
Simulations - ellipse fine mesh See in Dashboard
Name End Time Output Options
Simulation15 60.0 [s]

OutputTimeStep 10.0

Geometry ellipse sep 08 0999 with cyt-n 6:1 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 subdomain0 12.40975935828877 [um2] nucleus
Volume Analytical Cell 62.52005347593583 [um2] cyto
Volume Analytical ECM 42.5701871657754 [um2] extra
Surface Cell_ECM_membrane Cell | ECM 93.03794179617861 [um] cyto_mem
Surface Cell_subdomain0_membrane Cell | subdomain0 37.60040211638436 [um] nuclear Membrane

Global Parameters

Global Parameters See in Dashboard
Name Expression
n 1200.0[molecules.um-2.uM-1]