Physiology
Reaction Diagram
Cross-References
Annotations
Reactions
Reactions | Name | Structure | Kinetics | Depiction |
---|---|---|---|---|
EGFR+EGFLR | EGF_Binding_Unbinding | compartment | GeneralKinetics | |
LREGFR_deg | EGFReceptor_Degradation | compartment | GeneralKinetics | |
proEGFREGFR | EGFReceptor_Production | compartment | GeneralKinetics | |
EGFREGFR_deg | EGFReceptor_Degradation_Free | compartment | GeneralKinetics |
EGF_Binding_Unbinding Universal ID's
EGF_Binding_Unbinding Text Annotations
EGFReceptor_Degradation Universal ID's
EGFReceptor_Degradation Text Annotations
EGFReceptor_Production Universal ID's
EGFReceptor_Production Text Annotations
EGFReceptor_Degradation_Free Universal ID's
EGFReceptor_Degradation_Free Text Annotations
Expressions for EGF_Binding_Unbinding
reaction rate
J
((k1_EGFR * EGF * EGFR) - (k2_EGFR * LR)) [mmol.ml-1.min-1]
global
k1_EGFR
2.18503E-5 [ml.min-1.mmol-1]
global
k2_EGFR
0.121008 [min-1]
Expressions for EGFReceptor_Degradation
reaction rate
J
(k1_deg * LR) [mmol.ml-1.min-1]
global
k1_deg
0.2 [min-1]
Expressions for EGFReceptor_Production
reaction rate
J
v_EGFR [mmol.ml-1.min-1]
global
v_EGFR
100.0 [mmol.min-1.ml-1]
Expressions for EGFReceptor_Degradation_Free
reaction rate
J
(k1_deg * EGFR) [mmol.ml-1.min-1]
global
k1_deg
0.2 [min-1]
Structures
Name | Type | Electrical |
---|---|---|
compartment | Compartment | (+) (-) |
compartment Universal ID's
compartment Text Annotations
Species
Name | Structure | BioNetGen Definition | Depiction |
---|---|---|---|
LR | compartment | EGFR(Y~U!1,State~active!-,).EGF(Site0!1,). | |
EGFR | compartment | EGFR(Y~U!-,State~active!-,). | |
EGFR_deg | compartment | EGFR(Y~U!-,State~deg!-,). | |
EGF | compartment | EGF(Site0!-,). | |
proEGFR | compartment | EGFR(Y~U!-,State~deg!-,). |
LR Universal ID's
LR Text Annotations
EGFR Universal ID's
EGFR Text Annotations
EGFR_deg Universal ID's
EGFR_deg Text Annotations
EGF Universal ID's
EGF Text Annotations
proEGFR Universal ID's
proEGFR Text Annotations
Molecules
Name | BioNetGen Definition | DEPICTION |
---|---|---|
EGFR | EGFR(Y~P~U,State~deg~active,) | |
EGF | EGF(Site0,) | |
SOS | SOS(Active~yes~no,) | |
Ras | Ras(Active~yes~no,) | |
Raf | Raf(Active~yes~no,) | |
MEK | MEK(Active~yes~no,) | |
ERK | ERK(Active~yes~no,) | |
P90Rsk | P90Rsk(Active~yes~no,) | |
PI3K | PI3K(Active~yes~no,) | |
Akt | Akt(Active~yes~no,) | |
C3G | C3G(Active~yes~no,) | |
Rap1 | Rap1(Active~yes~no,) | |
B_Raf | B_Raf(Active~yes~no,) | |
PP2A | PP2A(Active~yes~no,) | |
P_tase | P_tase() | |
GAP | GAP() |
EGFR Universal ID's
EGFR Text Annotations
EGF Universal ID's
EGF Text Annotations
SOS Universal ID's
SOS Text Annotations
Ras Universal ID's
Ras Text Annotations
Raf Universal ID's
Raf Text Annotations
MEK Universal ID's
MEK Text Annotations
ERK Universal ID's
ERK Text Annotations
P90Rsk Universal ID's
P90Rsk Text Annotations
PI3K Universal ID's
PI3K Text Annotations
Akt Universal ID's
Akt Text Annotations
C3G Universal ID's
C3G Text Annotations
Rap1 Universal ID's
Rap1 Text Annotations
B_Raf Universal ID's
B_Raf Text Annotations
PP2A Universal ID's
PP2A Text Annotations
P_tase Universal ID's
P_tase Text Annotations
GAP Universal ID's
GAP Text Annotations
Applications
Name | Properties | Math Type | Annotation |
---|---|---|---|
Deterministic |
Specs -
Species Specs - Reaction Simulations |
Deterministic (ODE) Compartmental | cloned from 'Deterministic' owned by user PraneetDangol cloned from 'Deterministic' owned by user ModelBrick cloned from 'Deterministic' owned by user mblinov cloned from 'Deterministic' owned by user savi06 cloned from 'Deterministic' owned by user mblinov cloned from 'Deterministic' owned by user cab15130 |
Deterministic Universal ID's
Deterministic Text Annotations
Specifications (Species) - Deterministic go to Simulations
Specifications (Reaction) - Deterministic go to Simulations
Simulations - Deterministic go to Specifications
Name | End Time | Output Options |
---|---|---|
test | 60.0 |
KeepEvery 1 KeepAtMost 1000 |
Deterministic Universal ID's
Deterministic Text Annotations
Assignments
Name | Variable | Assignment Function Expression |
---|
Events
Name | Trigger Type | Variable Assignment |
---|
Geometry Compartmental1940725914
(Origin: 0.0, 0.0, 0.0; Extent: 10.0, 10.0, 10.0 [m])
Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
---|---|---|---|---|---|
Compartmental | Compartment | compartment |
Events
Name | Variable | Rate Expression |
---|
Global Parameters
Name | Expression |
---|---|
k1_deg | 0.2[min-1] |
v_EGFR | 100.0[mmol.min-1.ml-1] |
k1_EGFR | 2.18503E-5[ml.min-1.mmol-1] |
k2_EGFR | 0.121008[min-1] |
Universal ID's
Text Annotations
Universal ID's
Text Annotations
Universal ID's
Text Annotations
Universal ID's
Text Annotations
Downloads
Model Format | Model Downloads |
---|---|
Virtual Cell Markup Language | VCML File |
PDF Report | Report |
COMBINE Archive | OMEX File |
SEDML | SEDML File |
File Format | Application Downloads |
BNGL | Deterministic.bngl |
SBML | Deterministic.sbml |
Matlab | Deterministic.m |
NFSim XML | Deterministic.xml |