Physiology
Reaction Diagram
Cross-References
Annotations
Reactions
| Reactions | Name | Structure | Kinetics | Depiction |
|---|---|---|---|---|
| SHC_p_cytoSHC_cyto | SHC dephosphorylation | cyto | MassAction | |
| MEK_cytoMEK_active_cyto | MEk activation | cyto | HMMIrreversible | |
| MAPK_active_cytoMAPK_active_N_nucleus | nuclear transport | nuclear Membrane | MassAction | |
| EGFR_cyto_mem+EGF_extraEGFR_active | receptor ligand binding | cyto_mem | MassAction | |
| Ras_GDP_cyto_memRas_GTP_cyto_mem | Ras activation by Sos | cyto_mem | HMMIrreversible | |
| MAPK_active_cytoMAPK_cyto | MAPK inactivation | cyto | HMMIrreversible | |
| MAPK_cytoMAPK_active_cyto | MAPK activation | cyto | HMMIrreversible | |
| PP2A_inactivePP2A_cyto | r0 | cyto | MassAction | |
| Raf_active_cytoRaf_cyto | Raf inactivation | cyto | HMMIrreversible | |
| Ras_GTP_cyto_memRas_GDP_cyto_mem | Ras GAP | cyto_mem | HMMIrreversible | |
| Raf_cytoRaf_active_cyto | Raf activation | cyto_mem | HMMIrreversible | |
| MEK_active_cytoMEK_cyto | MEK inactivation | cyto | HMMIrreversible | |
| EGFR_GAP_Grb2+Sos_cytoEGFR_GAP_GRb2_Sos | Sos binding | cyto_mem | MassAction | |
| SHC_cytoSHC_p_cyto | Shc phosphorylation | cyto_mem | HMMIrreversible | |
| GAP+EGFR_dimerEGFR_GAP | GAP binding | cyto_mem | MassAction | |
| SHC_p_cyto+EGFR_GAP_GRb2_SosEGFR_Sos_Grb2_Shc_cyto_mem | Shc binding EGFR | cyto_mem | MassAction | |
| EGFR_activeEGFR_dimer | dimerization | cyto_mem | MassAction | |
| EGFR_GAP+Grb2_cytoEGFR_GAP_Grb2 | GRb2 binding | cyto_mem | MassAction |
SHC dephosphorylation Universal ID's
SHC dephosphorylation Text Annotations
MEk activation Universal ID's
MEk activation Text Annotations
nuclear transport Universal ID's
nuclear transport Text Annotations
receptor ligand binding Universal ID's
receptor ligand binding Text Annotations
Ras activation by Sos Universal ID's
Ras activation by Sos Text Annotations
MAPK inactivation Universal ID's
MAPK inactivation Text Annotations
MAPK activation Universal ID's
MAPK activation Text Annotations
r0 Universal ID's
r0 Text Annotations
Raf inactivation Universal ID's
Raf inactivation Text Annotations
Ras GAP Universal ID's
Ras GAP Text Annotations
Raf activation Universal ID's
Raf activation Text Annotations
MEK inactivation Universal ID's
MEK inactivation Text Annotations
Sos binding Universal ID's
Sos binding Text Annotations
Shc phosphorylation Universal ID's
Shc phosphorylation Text Annotations
GAP binding Universal ID's
GAP binding Text Annotations
Shc binding EGFR Universal ID's
Shc binding EGFR Text Annotations
dimerization Universal ID's
dimerization Text Annotations
GRb2 binding Universal ID's
GRb2 binding Text Annotations
Expressions for SHC dephosphorylation
reaction rate
J
((Kf * SHC_p_cyto) - (Kr * SHC_cyto)) [uM.s-1]
forward rate constant
Kf
0.001 [s-1]
reverse rate constant
Kr
0.0 [s-1]
Expressions for MEk activation
reaction rate
J
((Vmax * MEK_cyto) / (Km + MEK_cyto)) [uM.s-1]
Km (1/2 max)
Km
0.1591 [uM]
max reaction rate
Vmax
(0.105 * Raf_active_cyto) [uM.s-1]
Expressions for nuclear transport
reaction rate
J
((Kf * MAPK_active_cyto) - (Kr * MAPK_active_N_nucleus)) [molecules.um-2.s-1]
global
n
1200.0 [molecules.um-2.uM-1]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
0.0 [1]
forward rate constant
Kf
kf [molecules.um-2.s-1.uM-1]
reverse rate constant
Kr
kr [molecules.um-2.s-1.uM-1]
local
kf
0.13 [s-1]
local
kr
0.012 [s-1]
Expressions for receptor ligand binding
reaction rate
J
(((Kf * EGFR_cyto_mem) * EGF_extra) - (Kr * EGFR_active)) [molecules.um-2.s-1]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
0.0 [1]
forward rate constant
Kf
30.0 [s-1.uM-1]
reverse rate constant
Kr
0.038 [s-1]
Expressions for Ras activation by Sos
reaction rate
J
((Vmax * Ras_GDP_cyto_mem) / (Km + Ras_GDP_cyto_mem)) [molecules.um-2.s-1]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
0.0 [1]
Km (1/2 max)
Km
0.5 [molecules.um-2]
max reaction rate
Vmax
(kcat * EGFR_Sos_Grb2_Shc_cyto_mem) [molecules.um-2.s-1]
local
kcat
0.01 [s-1]
Expressions for MAPK inactivation
reaction rate
J
((Vmax * MAPK_active_cyto) / (Km + MAPK_active_cyto)) [uM.s-1]
Km (1/2 max)
Km
0.77 [uM]
max reaction rate
Vmax
(kcat * PP2A_cyto) [uM.s-1]
local
kcat
0.636 [s-1]
Expressions for MAPK activation
reaction rate
J
((Vmax * MAPK_cyto) / (Km + MAPK_cyto)) [uM.s-1]
Km (1/2 max)
Km
0.1591 [uM]
max reaction rate
Vmax
(0.01 * Raf_active_cyto) [uM.s-1]
Expressions for r0
reaction rate
J
((Kf * PP2A_inactive) - (Kr * PP2A_cyto)) [uM.s-1]
global
n
1200.0 [molecules.um-2.uM-1]
forward rate constant
Kf
0.001 [s-1]
reverse rate constant
Kr
0.001 [s-1]
Expressions for Raf inactivation
reaction rate
J
((Vmax * Raf_active_cyto) / (Km + Raf_active_cyto)) [uM.s-1]
Km (1/2 max)
Km
15.7 [uM]
max reaction rate
Vmax
(kcat * PP2A_cyto) [uM.s-1]
local
kcat
5.0 [s-1]
Expressions for Ras GAP
reaction rate
J
((Vmax * Ras_GTP_cyto_mem) / (Km + Ras_GTP_cyto_mem)) [molecules.um-2.s-1]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
0.0 [1]
Km (1/2 max)
Km
1.0 [molecules.um-2]
max reaction rate
Vmax
(kcat * Ras_GAP_cyto) [molecules.um-2.s-1]
local
kcat
0.01 [s-1]
Expressions for Raf activation
reaction rate
J
((Vmax * Raf_cyto) / (Km + Raf_cyto)) [molecules.um-2.s-1]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
0.0 [1]
Km (1/2 max)
Km
2.0 [uM]
max reaction rate
Vmax
(kcat * Ras_GTP_cyto_mem) [molecules.um-2.s-1]
local
kcat
0.01 [1.0E-15 mol.item-1.m-1.s-1]
Expressions for MEK inactivation
reaction rate
J
((Vmax * MEK_active_cyto) / (Km + MEK_active_cyto)) [uM.s-1]
Km (1/2 max)
Km
15.7 [uM]
max reaction rate
Vmax
(kcat * PP2A_cyto) [uM.s-1]
local
kcat
5.0 [s-1]
Expressions for Sos binding
reaction rate
J
(((Kf * EGFR_GAP_Grb2) * Sos_cyto) - (Kr * EGFR_GAP_GRb2_Sos)) [molecules.um-2.s-1]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
0.0 [1]
forward rate constant
Kf
1.66 [s-1.uM-1]
reverse rate constant
Kr
0.06 [s-1]
Expressions for Shc phosphorylation
reaction rate
J
((Vmax * SHC_cyto) / (Km + SHC_cyto)) [molecules.um-2.s-1]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
0.0 [1]
Km (1/2 max)
Km
1.0 [uM]
max reaction rate
Vmax
(0.1 * EGFR_GAP_GRb2_Sos) [molecules.um-2.s-1]
Expressions for GAP binding
reaction rate
J
(((Kf * GAP) * EGFR_dimer) - (Kr * EGFR_GAP)) [molecules.um-2.s-1]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
0.0 [1]
forward rate constant
Kf
1.0 [s-1.uM-1]
reverse rate constant
Kr
0.001 [s-1]
Expressions for Shc binding EGFR
reaction rate
J
(((Kf * SHC_p_cyto) * EGFR_GAP_GRb2_Sos) - (Kr * EGFR_Sos_Grb2_Shc_cyto_mem)) [molecules.um-2.s-1]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
0.0 [1]
forward rate constant
Kf
1.0 [s-1.uM-1]
reverse rate constant
Kr
0.001 [s-1]
Expressions for dimerization
reaction rate
J
((Kf * pow(EGFR_active,2.0)) - (Kr * EGFR_dimer)) [molecules.um-2.s-1]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
0.0 [1]
forward rate constant
Kf
1.0 [um2.s-1.molecules-1]
reverse rate constant
Kr
0.1 [s-1]
Expressions for GRb2 binding
reaction rate
J
(((Kf * EGFR_GAP) * Grb2_cyto) - (Kr * EGFR_GAP_Grb2)) [molecules.um-2.s-1]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
0.0 [1]
forward rate constant
Kf
0.166 [s-1.uM-1]
reverse rate constant
Kr
0.0 [s-1]
Structures
| Name | Type | Electrical |
|---|---|---|
| cyto_mem | Membrane | cyto(+) extra(-) |
| nuclear Membrane | Membrane | nucleus(+) cyto(-) |
| extra | Compartment | (+) (-) |
| nucleus | Compartment | (+) (-) |
| cyto | Compartment | (+) (-) |
cyto_mem Universal ID's
cyto_mem Text Annotations
nuclear Membrane Universal ID's
nuclear Membrane Text Annotations
extra Universal ID's
extra Text Annotations
nucleus Universal ID's
nucleus Text Annotations
cyto Universal ID's
cyto Text Annotations
Species
| Name | Structure | BioNetGen Definition | Depiction |
|---|---|---|---|
| MAPK_active_N_nucleus | nucleus | ||
| Raf_active_cyto | cyto | ||
| ATP | cyto | ||
| EGFR_active | cyto_mem | ||
| GAP | cyto | ||
| EGFR_GAP | cyto_mem | ||
| MEK_cyto | cyto | ||
| MAPK_active_cyto | cyto | ||
| EGFR_cyto_mem | cyto_mem | ||
| EGFR_dimer | cyto_mem | ||
| Ras_GDP_cyto_mem | cyto_mem | ||
| Ras_GAP_cyto | cyto | ||
| MEK_active_cyto | cyto | ||
| MAPK_cyto | cyto | ||
| EGF_extra | extra | ||
| Sos_cyto | cyto | ||
| SHC_p_cyto | cyto | ||
| Ras_GTP_cyto_mem | cyto_mem | ||
| SHC_cyto | cyto | ||
| EGFR_GAP_GRb2_Sos | cyto_mem | ||
| Raf_cyto | cyto | ||
| EGFR_Sos_Grb2_Shc_cyto_mem | cyto_mem | ||
| Grb2_cyto | cyto | ||
| PP2A_cyto | cyto | ||
| EGFR_GAP_Grb2 | cyto_mem | ||
| PP2A_inactive | cyto |
MAPK_active_N_nucleus Universal ID's
MAPK_active_N_nucleus Text Annotations
Raf_active_cyto Universal ID's
Raf_active_cyto Text Annotations
ATP Universal ID's
ATP Text Annotations
EGFR_active Universal ID's
EGFR_active Text Annotations
GAP Universal ID's
GAP Text Annotations
EGFR_GAP Universal ID's
EGFR_GAP Text Annotations
MEK_cyto Universal ID's
MEK_cyto Text Annotations
MAPK_active_cyto Universal ID's
MAPK_active_cyto Text Annotations
EGFR_cyto_mem Universal ID's
EGFR_cyto_mem Text Annotations
EGFR_dimer Universal ID's
EGFR_dimer Text Annotations
Ras_GDP_cyto_mem Universal ID's
Ras_GDP_cyto_mem Text Annotations
Ras_GAP_cyto Universal ID's
Ras_GAP_cyto Text Annotations
MEK_active_cyto Universal ID's
MEK_active_cyto Text Annotations
MAPK_cyto Universal ID's
MAPK_cyto Text Annotations
EGF_extra Universal ID's
EGF_extra Text Annotations
Sos_cyto Universal ID's
Sos_cyto Text Annotations
SHC_p_cyto Universal ID's
SHC_p_cyto Text Annotations
Ras_GTP_cyto_mem Universal ID's
Ras_GTP_cyto_mem Text Annotations
SHC_cyto Universal ID's
SHC_cyto Text Annotations
EGFR_GAP_GRb2_Sos Universal ID's
EGFR_GAP_GRb2_Sos Text Annotations
Raf_cyto Universal ID's
Raf_cyto Text Annotations
EGFR_Sos_Grb2_Shc_cyto_mem Universal ID's
EGFR_Sos_Grb2_Shc_cyto_mem Text Annotations
Grb2_cyto Universal ID's
Grb2_cyto Text Annotations
PP2A_cyto Universal ID's
PP2A_cyto Text Annotations
EGFR_GAP_Grb2 Universal ID's
EGFR_GAP_Grb2 Text Annotations
PP2A_inactive Universal ID's
PP2A_inactive Text Annotations
Applications
| Name | Properties | Math Type | Annotation |
|---|---|---|---|
| compartmental |
Specs -
Species Specs - Reaction Simulations |
Deterministic (ODE) Compartmental | |
| ellipse_0999 receptor activation only |
Specs -
Species Specs - Reaction Simulations |
Deterministic (ODE) Spatial (2D) | (copied from ellipse_0999) (copied from compartmental) |
| circle |
Specs -
Species Specs - Reaction Simulations |
Deterministic (ODE) Spatial (2D) | (copied from ellipse_0999 receptor activation only) (copied from ellipse_0999) (copied from compartmental) |
| ellipse_099_nucleus1_1 |
Specs -
Species Specs - Reaction Simulations |
Deterministic (ODE) Spatial (2D) | (copied from ellipse_0999 receptor activation only) (copied from ellipse_0999) (copied from compartmental) |
| ellipse_099_nucleus3_1 |
Specs -
Species Specs - Reaction Simulations |
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 |
Specs -
Species Specs - Reaction Simulations |
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 |
Specs -
Species Specs - Reaction Simulations |
Deterministic (ODE) Spatial (2D) | (copied from ellipse_0999 receptor activation only) (copied from ellipse_0999) (copied from compartmental) |
| circle fine mesh |
Specs -
Species Specs - Reaction Simulations |
Deterministic (ODE) Spatial (2D) | (copied from circle) (copied from ellipse_0999 receptor activation only) (copied from ellipse_0999) (copied from compartmental) |
| ellipse fine mesh |
Specs -
Species Specs - Reaction Simulations |
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) |
compartmental Universal ID's
compartmental Text Annotations
ellipse_0999 receptor activation only Universal ID's
ellipse_0999 receptor activation only Text Annotations
circle Universal ID's
circle Text Annotations
ellipse_099_nucleus1_1 Universal ID's
ellipse_099_nucleus1_1 Text Annotations
ellipse_099_nucleus3_1 Universal ID's
ellipse_099_nucleus3_1 Text Annotations
ellipse_099_nucleus5_1 Universal ID's
ellipse_099_nucleus5_1 Text Annotations
circle fine mesh Universal ID's
circle fine mesh Text Annotations
ellipse fine mesh Universal ID's
ellipse fine mesh Text Annotations
Specifications (Species) - compartmental go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| EGF_extra | 1.0 [uM] | 0.0 [um2/s] | extra |
| MAPK_active_N_nucleus | 0.0 [uM] | 0.0 [um2/s] | nucleus |
| Raf_active_cyto | 0.0 [uM] | 0.0 [um2/s] | cyto |
| ATP | 5000.0 [uM] | 0.0 [um2/s] | cyto |
| GAP | 0.1 [uM] | 0.0 [um2/s] | cyto |
| MEK_cyto | 0.18 [uM] | 0.0 [um2/s] | cyto |
| MAPK_active_cyto | 0.0 [uM] | 0.0 [um2/s] | cyto |
| Ras_GAP_cyto | 0.002 [uM] | 0.0 [um2/s] | cyto |
| MEK_active_cyto | 0.0 [uM] | 0.0 [um2/s] | cyto |
| MAPK_cyto | 0.36 [uM] | 0.0 [um2/s] | cyto |
| Sos_cyto | 0.1 [uM] | 0.0 [um2/s] | cyto |
| SHC_p_cyto | 0.0 [uM] | 0.0 [um2/s] | cyto |
| SHC_cyto | 0.5 [uM] | 0.0 [um2/s] | cyto |
| Raf_cyto | 0.2 [uM] | 0.0 [um2/s] | cyto |
| Grb2_cyto | 1.0 [uM] | 0.0 [um2/s] | cyto |
| PP2A_cyto | 0.0 [uM] | 0.0 [um2/s] | cyto |
| PP2A_inactive | 0.1 [uM] | 0.0 [um2/s] | cyto |
| EGFR_active | 0.0 [uM] | 0.0 [um2/s] | cyto_mem |
| EGFR_GAP | 0.0 [uM] | 0.0 [um2/s] | cyto_mem |
| EGFR_cyto_mem | 400.0 [uM] | 0.0 [um2/s] | cyto_mem |
| EGFR_dimer | 0.0 [uM] | 0.0 [um2/s] | cyto_mem |
| Ras_GDP_cyto_mem | 500.0 [uM] | 0.0 [um2/s] | cyto_mem |
| Ras_GTP_cyto_mem | 0.0 [uM] | 0.0 [um2/s] | cyto_mem |
| EGFR_GAP_GRb2_Sos | 0.0 [uM] | 0.0 [um2/s] | cyto_mem |
| EGFR_Sos_Grb2_Shc_cyto_mem | 0.0 [uM] | 0.0 [um2/s] | cyto_mem |
| EGFR_GAP_Grb2 | 0.0 [uM] | 0.0 [um2/s] | cyto_mem |
Specifications (Reaction) - compartmental go to Simulations
| Name | Enabled? |
|---|---|
| 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 go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| Simulation0 | 3600.0 |
OutputTimeStep 10.0 |
| Simulation13 | 1.0 |
OutputTimeStep 10.0 |
compartmental Universal ID's
compartmental Text Annotations
compartmental Universal ID's
compartmental Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|
Geometry non-spatial107399510
(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 |
Events
| Name | Variable | Rate Expression |
|---|
Specifications (Species) - ellipse_0999 receptor activation only go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| EGF_extra | 1.0 [uM] | 1.0 [um2/s] | extra |
| MAPK_active_N_nucleus | 0.0 [uM] | 7.0 [um2/s] | nucleus |
| Raf_active_cyto | 0.0 [uM] | 7.0 [um2/s] | cyto |
| ATP | 5000.0 [uM] | 10.0 [um2/s] | cyto |
| GAP | 0.1 [uM] | 10.0 [um2/s] | cyto |
| MEK_cyto | 0.18 [uM] | 6.0 [um2/s] | cyto |
| MAPK_active_cyto | 0.0 [uM] | 7.0 [um2/s] | cyto |
| Ras_GAP_cyto | 0.002 [uM] | 4.14 [um2/s] | cyto |
| MEK_active_cyto | 0.0 [uM] | 6.0 [um2/s] | cyto |
| MAPK_cyto | 0.36 [uM] | 7.0 [um2/s] | cyto |
| Sos_cyto | 1.0 [uM] | 3.7 [um2/s] | cyto |
| SHC_p_cyto | 0.0 [uM] | 6.4 [um2/s] | cyto |
| SHC_cyto | 1.0 [uM] | 6.4 [um2/s] | cyto |
| Raf_cyto | 0.2 [uM] | 7.0 [um2/s] | cyto |
| Grb2_cyto | 1.0 [uM] | 8.5 [um2/s] | cyto |
| PP2A_cyto | 0.0 [uM] | 0.0 [um2/s] | cyto |
| PP2A_inactive | 0.05 [uM] | 0.0 [um2/s] | cyto |
| EGFR_active | 0.0 [uM] | 0.0 [um2/s] | cyto_mem |
| EGFR_GAP | 0.0 [uM] | 0.08 [um2/s] | cyto_mem |
| EGFR_cyto_mem | 400.0 [uM] | 0.112 [um2/s] | cyto_mem |
| EGFR_dimer | 0.0 [uM] | 0.08 [um2/s] | cyto_mem |
| Ras_GDP_cyto_mem | 500.0 [uM] | 0.16 [um2/s] | cyto_mem |
| Ras_GTP_cyto_mem | 0.0 [uM] | 0.16 [um2/s] | cyto_mem |
| EGFR_GAP_GRb2_Sos | 0.0 [uM] | 0.0 [um2/s] | cyto_mem |
| EGFR_Sos_Grb2_Shc_cyto_mem | 0.0 [uM] | 0.08 [um2/s] | cyto_mem |
| EGFR_GAP_Grb2 | 0.0 [uM] | 0.0 [um2/s] | cyto_mem |
Specifications (Reaction) - ellipse_0999 receptor activation only go to Simulations
| Name | Enabled? |
|---|---|
| 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 go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| Simulation12 | 60.0 |
OutputTimeStep 10.0 |
| Copy of Simulation12 1 | 3600.0 |
OutputTimeStep 10.0 |
| Copy of Copy of Simulation12 1 | 7200.0 |
OutputTimeStep 10.0 |
| varying diffusion of EGFR | 3600.0 |
OutputTimeStep 10.0 |
| varying receptor density | 3600.0 |
OutputTimeStep 10.0 |
ellipse_0999 receptor activation only Universal ID's
ellipse_0999 receptor activation only Text Annotations
ellipse_0999 receptor activation only Universal ID's
ellipse_0999 receptor activation only Text Annotations
ellipse_0999 receptor activation only Universal ID's
ellipse_0999 receptor activation only Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|
Geometry Mathieu ellipse 0999 with nucleus ratio 6
(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 |
Events
| Name | Variable | Rate Expression |
|---|
Specifications (Species) - circle go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| EGF_extra | 1.0 [uM] | 1.0 [um2/s] | extra |
| MAPK_active_N_nucleus | 0.0 [uM] | 7.0 [um2/s] | nucleus |
| Raf_active_cyto | 0.0 [uM] | 7.0 [um2/s] | cyto |
| ATP | 5000.0 [uM] | 10.0 [um2/s] | cyto |
| GAP | 0.1 [uM] | 10.0 [um2/s] | cyto |
| MEK_cyto | 0.18 [uM] | 6.0 [um2/s] | cyto |
| MAPK_active_cyto | 0.0 [uM] | 7.0 [um2/s] | cyto |
| Ras_GAP_cyto | 0.002 [uM] | 4.14 [um2/s] | cyto |
| MEK_active_cyto | 0.0 [uM] | 6.0 [um2/s] | cyto |
| MAPK_cyto | 0.36 [uM] | 7.0 [um2/s] | cyto |
| Sos_cyto | 1.0 [uM] | 10.0 [um2/s] | cyto |
| SHC_p_cyto | 0.0 [uM] | 6.4 [um2/s] | cyto |
| SHC_cyto | 1.0 [uM] | 6.4 [um2/s] | cyto |
| Raf_cyto | 0.2 [uM] | 7.0 [um2/s] | cyto |
| Grb2_cyto | 1.0 [uM] | 8.5 [um2/s] | cyto |
| PP2A_cyto | 0.0 [uM] | 0.0 [um2/s] | cyto |
| PP2A_inactive | 0.05 [uM] | 0.0 [um2/s] | cyto |
| EGFR_active | 0.0 [uM] | 0.0 [um2/s] | cyto_mem |
| EGFR_GAP | 0.0 [uM] | 0.08 [um2/s] | cyto_mem |
| EGFR_cyto_mem | 400.0 [uM] | 0.04 [um2/s] | cyto_mem |
| EGFR_dimer | 0.0 [uM] | 0.08 [um2/s] | cyto_mem |
| Ras_GDP_cyto_mem | 500.0 [uM] | 0.16 [um2/s] | cyto_mem |
| Ras_GTP_cyto_mem | 0.0 [uM] | 0.16 [um2/s] | cyto_mem |
| EGFR_GAP_GRb2_Sos | 0.0 [uM] | 0.0 [um2/s] | cyto_mem |
| EGFR_Sos_Grb2_Shc_cyto_mem | 0.0 [uM] | 0.08 [um2/s] | cyto_mem |
| EGFR_GAP_Grb2 | 0.0 [uM] | 0.0 [um2/s] | cyto_mem |
Specifications (Reaction) - circle go to Simulations
| Name | Enabled? |
|---|---|
| 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 go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| Simulation1 | 480.0 |
OutputTimeStep 10.0 |
| Simulation2 | 7200.0 |
OutputTimeStep 10.0 |
| Copy of Simulation1 | 60.0 |
OutputTimeStep 10.0 |
circle Universal ID's
circle Text Annotations
circle Universal ID's
circle Text Annotations
circle Universal ID's
circle Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|
Geometry circle with nucleus ratio 6 feb 2009
(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 |
Events
| Name | Variable | Rate Expression |
|---|
Specifications (Species) - ellipse_099_nucleus1_1 go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| EGF_extra | 1.0 [uM] | 1.0 [um2/s] | extra |
| MAPK_active_N_nucleus | 0.0 [uM] | 7.0 [um2/s] | nucleus |
| Raf_active_cyto | 0.0 [uM] | 7.0 [um2/s] | cyto |
| ATP | 5000.0 [uM] | 10.0 [um2/s] | cyto |
| GAP | 0.1 [uM] | 10.0 [um2/s] | cyto |
| MEK_cyto | 0.18 [uM] | 6.0 [um2/s] | cyto |
| MAPK_active_cyto | 0.0 [uM] | 7.0 [um2/s] | cyto |
| Ras_GAP_cyto | 0.002 [uM] | 4.14 [um2/s] | cyto |
| MEK_active_cyto | 0.0 [uM] | 6.0 [um2/s] | cyto |
| MAPK_cyto | 0.36 [uM] | 7.0 [um2/s] | cyto |
| Sos_cyto | 1.0 [uM] | 10.0 [um2/s] | cyto |
| SHC_p_cyto | 0.0 [uM] | 6.4 [um2/s] | cyto |
| SHC_cyto | 1.0 [uM] | 6.4 [um2/s] | cyto |
| Raf_cyto | 0.2 [uM] | 7.0 [um2/s] | cyto |
| Grb2_cyto | 1.0 [uM] | 8.5 [um2/s] | cyto |
| PP2A_cyto | 0.0 [uM] | 0.0 [um2/s] | cyto |
| PP2A_inactive | 0.05 [uM] | 0.0 [um2/s] | cyto |
| EGFR_active | 0.0 [uM] | 0.0 [um2/s] | cyto_mem |
| EGFR_GAP | 0.0 [uM] | 0.08 [um2/s] | cyto_mem |
| EGFR_cyto_mem | 400.0 [uM] | 0.04 [um2/s] | cyto_mem |
| EGFR_dimer | 0.0 [uM] | 0.08 [um2/s] | cyto_mem |
| Ras_GDP_cyto_mem | 500.0 [uM] | 0.16 [um2/s] | cyto_mem |
| Ras_GTP_cyto_mem | 0.0 [uM] | 0.16 [um2/s] | cyto_mem |
| EGFR_GAP_GRb2_Sos | 0.0 [uM] | 0.0 [um2/s] | cyto_mem |
| EGFR_Sos_Grb2_Shc_cyto_mem | 0.0 [uM] | 0.08 [um2/s] | cyto_mem |
| EGFR_GAP_Grb2 | 0.0 [uM] | 0.0 [um2/s] | cyto_mem |
Specifications (Reaction) - ellipse_099_nucleus1_1 go to Simulations
| Name | Enabled? |
|---|---|
| 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 go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| Simulation5 | 15000.0 |
OutputTimeStep 10.0 |
ellipse_099_nucleus1_1 Universal ID's
ellipse_099_nucleus1_1 Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|
Geometry ellipse sep 08 0999 with cyt-n 2:1
(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 |
Events
| Name | Variable | Rate Expression |
|---|
Specifications (Species) - ellipse_099_nucleus3_1 go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| EGF_extra | 1.0 [uM] | 1.0 [um2/s] | extra |
| MAPK_active_N_nucleus | 0.0 [uM] | 7.0 [um2/s] | nucleus |
| Raf_active_cyto | 0.0 [uM] | 7.0 [um2/s] | cyto |
| ATP | 5000.0 [uM] | 10.0 [um2/s] | cyto |
| GAP | 0.1 [uM] | 10.0 [um2/s] | cyto |
| MEK_cyto | 0.18 [uM] | 6.0 [um2/s] | cyto |
| MAPK_active_cyto | 0.0 [uM] | 7.0 [um2/s] | cyto |
| Ras_GAP_cyto | 0.002 [uM] | 4.14 [um2/s] | cyto |
| MEK_active_cyto | 0.0 [uM] | 6.0 [um2/s] | cyto |
| MAPK_cyto | 0.36 [uM] | 7.0 [um2/s] | cyto |
| Sos_cyto | 1.0 [uM] | 10.0 [um2/s] | cyto |
| SHC_p_cyto | 0.0 [uM] | 6.4 [um2/s] | cyto |
| SHC_cyto | 1.0 [uM] | 6.4 [um2/s] | cyto |
| Raf_cyto | 0.2 [uM] | 7.0 [um2/s] | cyto |
| Grb2_cyto | 1.0 [uM] | 8.5 [um2/s] | cyto |
| PP2A_cyto | 0.0 [uM] | 0.0 [um2/s] | cyto |
| PP2A_inactive | 0.05 [uM] | 0.0 [um2/s] | cyto |
| EGFR_active | 0.0 [uM] | 0.0 [um2/s] | cyto_mem |
| EGFR_GAP | 0.0 [uM] | 0.08 [um2/s] | cyto_mem |
| EGFR_cyto_mem | 400.0 [uM] | 0.04 [um2/s] | cyto_mem |
| EGFR_dimer | 0.0 [uM] | 0.08 [um2/s] | cyto_mem |
| Ras_GDP_cyto_mem | 500.0 [uM] | 0.16 [um2/s] | cyto_mem |
| Ras_GTP_cyto_mem | 0.0 [uM] | 0.16 [um2/s] | cyto_mem |
| EGFR_GAP_GRb2_Sos | 0.0 [uM] | 0.0 [um2/s] | cyto_mem |
| EGFR_Sos_Grb2_Shc_cyto_mem | 0.0 [uM] | 0.08 [um2/s] | cyto_mem |
| EGFR_GAP_Grb2 | 0.0 [uM] | 0.0 [um2/s] | cyto_mem |
Specifications (Reaction) - ellipse_099_nucleus3_1 go to Simulations
| Name | Enabled? |
|---|---|
| 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 go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| Simulation3 | 15000.0 |
OutputTimeStep 10.0 |
ellipse_099_nucleus3_1 Universal ID's
ellipse_099_nucleus3_1 Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|
Geometry ellipse sep 08 0999 with cyt-n 4:1
(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 |
Events
| Name | Variable | Rate Expression |
|---|
Specifications (Species) - ellipse_099_nucleus5_1 go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| EGF_extra | 1.0 [uM] | 1.0 [um2/s] | extra |
| MAPK_active_N_nucleus | 0.0 [uM] | 7.0 [um2/s] | nucleus |
| Raf_active_cyto | 0.0 [uM] | 7.0 [um2/s] | cyto |
| ATP | 5000.0 [uM] | 10.0 [um2/s] | cyto |
| GAP | 0.1 [uM] | 10.0 [um2/s] | cyto |
| MEK_cyto | 0.18 [uM] | 6.0 [um2/s] | cyto |
| MAPK_active_cyto | 0.0 [uM] | 7.0 [um2/s] | cyto |
| Ras_GAP_cyto | 0.002 [uM] | 4.14 [um2/s] | cyto |
| MEK_active_cyto | 0.0 [uM] | 6.0 [um2/s] | cyto |
| MAPK_cyto | 0.36 [uM] | 7.0 [um2/s] | cyto |
| Sos_cyto | 1.0 [uM] | 10.0 [um2/s] | cyto |
| SHC_p_cyto | 0.0 [uM] | 6.4 [um2/s] | cyto |
| SHC_cyto | 1.0 [uM] | 6.4 [um2/s] | cyto |
| Raf_cyto | 0.2 [uM] | 7.0 [um2/s] | cyto |
| Grb2_cyto | 1.0 [uM] | 8.5 [um2/s] | cyto |
| PP2A_cyto | 0.0 [uM] | 0.0 [um2/s] | cyto |
| PP2A_inactive | 0.05 [uM] | 0.0 [um2/s] | cyto |
| EGFR_active | 0.0 [uM] | 0.0 [um2/s] | cyto_mem |
| EGFR_GAP | 0.0 [uM] | 0.08 [um2/s] | cyto_mem |
| EGFR_cyto_mem | 400.0 [uM] | 0.04 [um2/s] | cyto_mem |
| EGFR_dimer | 0.0 [uM] | 0.08 [um2/s] | cyto_mem |
| Ras_GDP_cyto_mem | 500.0 [uM] | 0.16 [um2/s] | cyto_mem |
| Ras_GTP_cyto_mem | 0.0 [uM] | 0.16 [um2/s] | cyto_mem |
| EGFR_GAP_GRb2_Sos | 0.0 [uM] | 0.0 [um2/s] | cyto_mem |
| EGFR_Sos_Grb2_Shc_cyto_mem | 0.0 [uM] | 0.08 [um2/s] | cyto_mem |
| EGFR_GAP_Grb2 | 0.0 [uM] | 0.0 [um2/s] | cyto_mem |
Specifications (Reaction) - ellipse_099_nucleus5_1 go to Simulations
| Name | Enabled? |
|---|---|
| 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 go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| Simulation4 | 15000.0 |
OutputTimeStep 10.0 |
| Copy of Simulation4 | 60.0 |
OutputTimeStep 10.0 |
ellipse_099_nucleus5_1 Universal ID's
ellipse_099_nucleus5_1 Text Annotations
ellipse_099_nucleus5_1 Universal ID's
ellipse_099_nucleus5_1 Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|
Geometry ellipse sep 08 0999 with cyt-n 6:1
(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 |
Events
| Name | Variable | Rate Expression |
|---|
Specifications (Species) - spatially varying diffusion and receptor number go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| EGF_extra | 1.0 [uM] | 1.0 [um2/s] | extra |
| MAPK_active_N_nucleus | 0.0 [uM] | 7.0 [um2/s] | nucleus |
| Raf_active_cyto | 0.0 [uM] | 7.0 [um2/s] | cyto |
| ATP | 5000.0 [uM] | 10.0 [um2/s] | cyto |
| GAP | 0.1 [uM] | 10.0 [um2/s] | cyto |
| MEK_cyto | 0.18 [uM] | 6.0 [um2/s] | cyto |
| MAPK_active_cyto | 0.0 [uM] | 7.0 [um2/s] | cyto |
| Ras_GAP_cyto | 0.002 [uM] | 4.14 [um2/s] | cyto |
| MEK_active_cyto | 0.0 [uM] | 6.0 [um2/s] | cyto |
| MAPK_cyto | 0.36 [uM] | 7.0 [um2/s] | cyto |
| Sos_cyto | 1.0 [uM] | 3.7 [um2/s] | cyto |
| SHC_p_cyto | 0.0 [uM] | 6.4 [um2/s] | cyto |
| SHC_cyto | 1.0 [uM] | 6.4 [um2/s] | cyto |
| Raf_cyto | 0.2 [uM] | 7.0 [um2/s] | cyto |
| Grb2_cyto | 1.0 [uM] | 8.5 [um2/s] | cyto |
| PP2A_cyto | 0.0 [uM] | 0.0 [um2/s] | cyto |
| PP2A_inactive | 0.05 [uM] | 0.0 [um2/s] | cyto |
| EGFR_active | 0.0 [uM] | 0.0 [um2/s] | cyto_mem |
| EGFR_GAP | 0.0 [uM] | 0.08 [um2/s] | cyto_mem |
| EGFR_cyto_mem | (213.0 * (1.0 + (0.018 * abs(x)))) [uM] | (0.112 * (1.0 + (0.018 * abs(x)))) [um2/s] | cyto_mem |
| EGFR_dimer | 0.0 [uM] | 0.08 [um2/s] | cyto_mem |
| Ras_GDP_cyto_mem | 500.0 [uM] | 0.16 [um2/s] | cyto_mem |
| Ras_GTP_cyto_mem | 0.0 [uM] | 0.16 [um2/s] | cyto_mem |
| EGFR_GAP_GRb2_Sos | 0.0 [uM] | 0.0 [um2/s] | cyto_mem |
| EGFR_Sos_Grb2_Shc_cyto_mem | 0.0 [uM] | (0.08 * (1.0 + (0.03 * abs(x)))) [um2/s] | cyto_mem |
| EGFR_GAP_Grb2 | 0.0 [uM] | 0.0 [um2/s] | cyto_mem |
Specifications (Reaction) - spatially varying diffusion and receptor number go to Simulations
| Name | Enabled? |
|---|---|
| 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 go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| Simulation6 | 60.0 |
OutputTimeStep 10.0 |
| Simulation7 | 3600.0 |
OutputTimeStep 10.0 |
| Simulation8 | 7200.0 |
OutputTimeStep 10.0 |
| Simulation9 | 3600.0 |
OutputTimeStep 10.0 |
| Simulation10 | 3600.0 |
OutputTimeStep 10.0 |
| Copy of Simulation6 | 480.0 |
OutputTimeStep 10.0 |
spatially varying diffusion and receptor number Universal ID's
spatially varying diffusion and receptor number Text Annotations
spatially varying diffusion and receptor number Universal ID's
spatially varying diffusion and receptor number Text Annotations
spatially varying diffusion and receptor number Universal ID's
spatially varying diffusion and receptor number Text Annotations
spatially varying diffusion and receptor number Universal ID's
spatially varying diffusion and receptor number Text Annotations
spatially varying diffusion and receptor number Universal ID's
spatially varying diffusion and receptor number Text Annotations
spatially varying diffusion and receptor number Universal ID's
spatially varying diffusion and receptor number Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|
Geometry Mathieu ellipse 0999 with nucleus ratio 6
(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 |
Events
| Name | Variable | Rate Expression |
|---|
Specifications (Species) - circle fine mesh go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| EGF_extra | 1.0 [uM] | 1.0 [um2/s] | extra |
| MAPK_active_N_nucleus | 0.0 [uM] | 7.0 [um2/s] | nucleus |
| Raf_active_cyto | 0.0 [uM] | 7.0 [um2/s] | cyto |
| ATP | 5000.0 [uM] | 10.0 [um2/s] | cyto |
| GAP | 0.1 [uM] | 10.0 [um2/s] | cyto |
| MEK_cyto | 0.18 [uM] | 6.0 [um2/s] | cyto |
| MAPK_active_cyto | 0.0 [uM] | 7.0 [um2/s] | cyto |
| Ras_GAP_cyto | 0.002 [uM] | 4.14 [um2/s] | cyto |
| MEK_active_cyto | 0.0 [uM] | 6.0 [um2/s] | cyto |
| MAPK_cyto | 0.36 [uM] | 7.0 [um2/s] | cyto |
| Sos_cyto | 1.0 [uM] | 10.0 [um2/s] | cyto |
| SHC_p_cyto | 0.0 [uM] | 6.4 [um2/s] | cyto |
| SHC_cyto | 1.0 [uM] | 6.4 [um2/s] | cyto |
| Raf_cyto | 0.2 [uM] | 7.0 [um2/s] | cyto |
| Grb2_cyto | 1.0 [uM] | 8.5 [um2/s] | cyto |
| PP2A_cyto | 0.0 [uM] | 0.0 [um2/s] | cyto |
| PP2A_inactive | 0.05 [uM] | 0.0 [um2/s] | cyto |
| EGFR_active | 0.0 [uM] | 0.0 [um2/s] | cyto_mem |
| EGFR_GAP | 0.0 [uM] | 0.08 [um2/s] | cyto_mem |
| EGFR_cyto_mem | 400.0 [uM] | 0.04 [um2/s] | cyto_mem |
| EGFR_dimer | 0.0 [uM] | 0.08 [um2/s] | cyto_mem |
| Ras_GDP_cyto_mem | 500.0 [uM] | 0.16 [um2/s] | cyto_mem |
| Ras_GTP_cyto_mem | 0.0 [uM] | 0.16 [um2/s] | cyto_mem |
| EGFR_GAP_GRb2_Sos | 0.0 [uM] | 0.0 [um2/s] | cyto_mem |
| EGFR_Sos_Grb2_Shc_cyto_mem | 0.0 [uM] | 0.08 [um2/s] | cyto_mem |
| EGFR_GAP_Grb2 | 0.0 [uM] | 0.0 [um2/s] | cyto_mem |
Specifications (Reaction) - circle fine mesh go to Simulations
| Name | Enabled? |
|---|---|
| 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 go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| Simulation11 | 60.0 |
OutputTimeStep 10.0 |
| Simulation14 | 7200.0 |
OutputTimeStep 10.0 |
circle fine mesh Universal ID's
circle fine mesh Text Annotations
circle fine mesh Universal ID's
circle fine mesh Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|
Geometry circle with nucleus ratio 6 feb 2009
(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 |
Events
| Name | Variable | Rate Expression |
|---|
Specifications (Species) - ellipse fine mesh go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| EGF_extra | 1.0 [uM] | 1.0 [um2/s] | extra |
| MAPK_active_N_nucleus | 0.0 [uM] | 7.0 [um2/s] | nucleus |
| Raf_active_cyto | 0.0 [uM] | 7.0 [um2/s] | cyto |
| ATP | 5000.0 [uM] | 10.0 [um2/s] | cyto |
| GAP | 0.1 [uM] | 10.0 [um2/s] | cyto |
| MEK_cyto | 0.18 [uM] | 6.0 [um2/s] | cyto |
| MAPK_active_cyto | 0.0 [uM] | 7.0 [um2/s] | cyto |
| Ras_GAP_cyto | 0.002 [uM] | 4.14 [um2/s] | cyto |
| MEK_active_cyto | 0.0 [uM] | 6.0 [um2/s] | cyto |
| MAPK_cyto | 0.36 [uM] | 7.0 [um2/s] | cyto |
| Sos_cyto | 1.0 [uM] | 10.0 [um2/s] | cyto |
| SHC_p_cyto | 0.0 [uM] | 6.4 [um2/s] | cyto |
| SHC_cyto | 1.0 [uM] | 6.4 [um2/s] | cyto |
| Raf_cyto | 0.2 [uM] | 7.0 [um2/s] | cyto |
| Grb2_cyto | 1.0 [uM] | 8.5 [um2/s] | cyto |
| PP2A_cyto | 0.0 [uM] | 0.0 [um2/s] | cyto |
| PP2A_inactive | 0.05 [uM] | 0.0 [um2/s] | cyto |
| EGFR_active | 0.0 [uM] | 0.0 [um2/s] | cyto_mem |
| EGFR_GAP | 0.0 [uM] | 0.08 [um2/s] | cyto_mem |
| EGFR_cyto_mem | 400.0 [uM] | 0.04 [um2/s] | cyto_mem |
| EGFR_dimer | 0.0 [uM] | 0.08 [um2/s] | cyto_mem |
| Ras_GDP_cyto_mem | 500.0 [uM] | 0.16 [um2/s] | cyto_mem |
| Ras_GTP_cyto_mem | 0.0 [uM] | 0.16 [um2/s] | cyto_mem |
| EGFR_GAP_GRb2_Sos | 0.0 [uM] | 0.0 [um2/s] | cyto_mem |
| EGFR_Sos_Grb2_Shc_cyto_mem | 0.0 [uM] | 0.08 [um2/s] | cyto_mem |
| EGFR_GAP_Grb2 | 0.0 [uM] | 0.0 [um2/s] | cyto_mem |
Specifications (Reaction) - ellipse fine mesh go to Simulations
| Name | Enabled? |
|---|---|
| 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 go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| Simulation15 | 60.0 |
OutputTimeStep 10.0 |
ellipse fine mesh Universal ID's
ellipse fine mesh Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|
Geometry ellipse sep 08 0999 with cyt-n 6:1
(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 |
Events
| Name | Variable | Rate Expression |
|---|