Physiology
Reaction Diagram
Cross-References
Annotations
Reactions
Reactions | Name | Structure | Kinetics | Depiction |
---|---|---|---|---|
Rab7_GDP | Recruitment of Rab7_GDP | endosome | GeneralLumpedKinetics | |
Rab7_GDPRab7_GTP | activation of Rab7 by GEF7 | endosome | GeneralLumpedKinetics | |
Rab7_GDPRab7_GTP | activation of Rab7 by GEF5 | endosome | GeneralLumpedKinetics | |
Rab7_GDP | Extraction of Rab7_GDP | endosome | GeneralLumpedKinetics | |
Rab7_GTPRab7_GDP | Hydrolysis of Rab7_GTP | endosome | GeneralLumpedKinetics |
Recruitment of Rab7_GDP Universal ID's
Recruitment of Rab7_GDP Text Annotations
activation of Rab7 by GEF7 Universal ID's
activation of Rab7 by GEF7 Text Annotations
activation of Rab7 by GEF5 Universal ID's
activation of Rab7 by GEF5 Text Annotations
Extraction of Rab7_GDP Universal ID's
Extraction of Rab7_GDP Text Annotations
Hydrolysis of Rab7_GTP Universal ID's
Hydrolysis of Rab7_GTP Text Annotations
Expressions for Recruitment of Rab7_GDP
lumped reaction rate
LumpedJ
(endosome * K1) [mole.s-1]
local
K1
0.483 [mol.s-1.l-1]
Expressions for activation of Rab7 by GEF7
lumped reaction rate
LumpedJ
(endosome * ((Rab7_GDP * ke * pow(Rab7_GTP,h)) / (kg + pow(Rab7_GTP,h)))) [mole.s-1]
local
h
3.0 [1]
local
ke
0.21 [s-1]
local
kg
0.1 [tbd]
Expressions for activation of Rab7 by GEF5
lumped reaction rate
LumpedJ
(endosome * ((ke * Rab7_GDP) / (1.0 + exp(((kg - Rab5_GTP) * kf))))) [mole.s-1]
local
ke
0.021 [s-1]
local
kf
3.0 [M-1]
local
kg
1.0 [M]
Expressions for Extraction of Rab7_GDP
lumped reaction rate
LumpedJ
(endosome * (kminus1 * Rab7_GDP)) [mole.s-1]
local
kminus1
0.483 [s-1]
Expressions for Hydrolysis of Rab7_GTP
lumped reaction rate
LumpedJ
(endosome * (kh * Rab7_GTP)) [mole.s-1]
local
kh
0.15 [s-1]
Structures
Name | Type | Electrical |
---|---|---|
endosome | Compartment | (+) (-) |
endosome Universal ID's
endosome Text Annotations
Species
Name | Structure | BioNetGen Definition | Depiction |
---|---|---|---|
Rab5_GTP | endosome | RAB5(BS!1,).GTP(BS!1,). | |
Rab7_GDP | endosome | Rab7(bs!1,).GDP(BS!1,). | |
Rab7_GTP | endosome | Rab7(bs!1,).GTP(BS!1,). |
Rab5_GTP Universal ID's
Rab5_GTP Text Annotations
Rab7_GDP Universal ID's
Rab7_GDP Text Annotations
Rab7_GTP Universal ID's
Rab7_GTP Text Annotations
Molecules
RAB5 Universal ID's
RAB5 Text Annotations
Rab7 Universal ID's
Rab7 Text Annotations
GTP Universal ID's
GTP Text Annotations
GDP Universal ID's
GDP Text Annotations
Observables
Name | Structure | Count | BNGL Definition | Sequence Type | DEPICTION |
---|---|---|---|---|---|
O0_RAB5_tot | endosome | Molecules | RAB5(BS!?,). | Multimolecular | |
O0_Rab7_tot | endosome | Molecules | Rab7(bs!?,). | Multimolecular | |
O0_GTP_tot | endosome | Molecules | GTP(BS!?,). | Multimolecular | |
O0_GDP_tot | endosome | Molecules | GDP(BS!?,). | Multimolecular |
O0_RAB5_tot Universal ID's
O0_RAB5_tot Text Annotations
O0_Rab7_tot Universal ID's
O0_Rab7_tot Text Annotations
O0_GTP_tot Universal ID's
O0_GTP_tot Text Annotations
O0_GDP_tot Universal ID's
O0_GDP_tot Text Annotations
Applications
Name | Properties | Math Type | Annotation |
---|---|---|---|
Deterministic |
Specs -
Species Specs - Reaction Simulations |
Deterministic (ODE) Compartmental |
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 |
---|---|---|
Simulation0 | 1000.0 |
KeepEvery 1 KeepAtMost 1000 |
Deterministic Universal ID's
Deterministic Text Annotations
Assignments
Name | Variable | Assignment Function Expression |
---|
Events
Name | Trigger Type | Variable Assignment |
---|
Geometry Compartmental1388779149
(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 | endosome |
Events
Name | Variable | Rate Expression |
---|
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 |