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Name - EGF ras Sep 2012

BioModel ID - 83446023

Reaction Diagram

Physiology

Universal ID's	Text Annotations

Reactions See in Dashboard
Reaction	Name Structure	Kinetics	Depiction
SHC_p_cytoSHC_cyto	SHC dephosphorylation cyto	MassAction	SHC_p_cytoSHC_cyto
		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]
MEK_cytoMEK_active_cyto	MEk activation cyto	HMMIrreversible	MEK_cytoMEK_active_cyto
		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]
MAPK_active_cytoMAPK_active_N_nucleus	nuclear transport nuclear Membrane	MassAction	MAPK_active_cytoMAPK_active_N_nucleus
		reaction rate (J): ((Kf * MAPK_active_cyto) - (Kr * MAPK_active_N_nucleus))[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): kf[molecules.um-2.s-1.uM-1] reverse rate constant (Kr): kr[molecules.um-2.s-1.uM-1] user defined (kf): 0.13[s-1] user defined (kr): 0.012[s-1]
EGFR_cyto_mem+EGF_extraEGFR_active	receptor ligand binding cyto_mem	MassAction	EGFR_cyto_mem+EGF_extraEGFR_active
		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]
Ras_GDP_cyto_memRas_GTP_cyto_mem	Ras activation by Sos cyto_mem	HMMIrreversible	Ras_GDP_cyto_memRas_GTP_cyto_mem
		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] user defined (kcat): 0.01[s-1]
MAPK_active_cytoMAPK_cyto	MAPK inactivation cyto	HMMIrreversible	MAPK_active_cytoMAPK_cyto
		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] user defined (kcat): 0.636[s-1]
MAPK_cytoMAPK_active_cyto	MAPK activation cyto	HMMIrreversible	MAPK_cytoMAPK_active_cyto
		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]
PP2A_inactivePP2A_cyto	r0 cyto	MassAction	PP2A_inactivePP2A_cyto
		reaction rate (J): ((Kf * PP2A_inactive) - (Kr * PP2A_cyto))[uM.s-1] forward rate constant (Kf): 0.001[s-1] reverse rate constant (Kr): 0.001[s-1]
Raf_active_cytoRaf_cyto	Raf inactivation cyto	HMMIrreversible	Raf_active_cytoRaf_cyto
		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] user defined (kcat): 5.0[s-1]
Ras_GTP_cyto_memRas_GDP_cyto_mem	Ras GAP cyto_mem	HMMIrreversible	Ras_GTP_cyto_memRas_GDP_cyto_mem
		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] user defined (kcat): 0.01[s-1]
Raf_cytoRaf_active_cyto	Raf activation cyto_mem	HMMIrreversible	Raf_cytoRaf_active_cyto
		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] user defined (kcat): 0.01[1.0E-15 mol.item-1.m-1.s-1]
MEK_active_cytoMEK_cyto	MEK inactivation cyto	HMMIrreversible	MEK_active_cytoMEK_cyto
		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] user defined (kcat): 5.0[s-1]
EGFR_GAP_Grb2+Sos_cytoEGFR_GAP_GRb2_Sos	Sos binding cyto_mem	MassAction	EGFR_GAP_Grb2+Sos_cytoEGFR_GAP_GRb2_Sos
		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]
SHC_cytoSHC_p_cyto	Shc phosphorylation cyto_mem	HMMIrreversible	SHC_cytoSHC_p_cyto
		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]
GAP+EGFR_dimerEGFR_GAP	GAP binding cyto_mem	MassAction	GAP+EGFR_dimerEGFR_GAP
		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]
SHC_p_cyto+EGFR_GAP_GRb2_SosEGFR_Sos_Grb2_Shc_cyto_mem	Shc binding EGFR cyto_mem	MassAction	SHC_p_cyto+EGFR_GAP_GRb2_SosEGFR_Sos_Grb2_Shc_cyto_mem
		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]
EGFR_activeEGFR_dimer	dimerization cyto_mem	MassAction	EGFR_activeEGFR_dimer
		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]
EGFR_GAP+Grb2_cytoEGFR_GAP_Grb2	GRb2 binding cyto_mem	MassAction	EGFR_GAP+Grb2_cytoEGFR_GAP_Grb2
		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 See in Dashboard
Name	Type Electrical (Membrane Polarity)
extra	Compartment (+) (-)

nucleus	Compartment (+) (-)

cyto	Compartment (+) (-)

cyto_mem	Membrane N/A

nuclear Membrane	Membrane N/A

Species See in Dashboard
Name	Structure	BioNetGen Definition
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

Molecules See in Dashboard
Name	Text Annotations	BioNetGen Definition

Observables See in Dashboard
Name	Type Count	BioNetGen Definition

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]