Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
GEFActive_GEF GEF_activation default GeneralKinetics
Active_GEFGEF GEF_inactivation default GeneralKinetics
Activator Activator_degradation default GeneralKinetics

GEF_activation Universal ID's

GEF_activation Text Annotations

GEF_inactivation Universal ID's

GEF_inactivation Text Annotations

Activator_degradation Universal ID's

Activator_degradation Text Annotations

Expressions for GEF_activation

reaction rate

J

(Activator * GEF * k1) [umol.l-1.min-1]

global

k1

1.0 [l.umol-1.min-1]

Expressions for GEF_inactivation

reaction rate

J

(Active_GEF * k2) [umol.l-1.min-1]

global

k2

0.1 [min-1]

Expressions for Activator_degradation

reaction rate

J

(Activator * k3) [umol.l-1.min-1]

global

k3

0.5 [min-1]

Structures

Name
Type
Electrical
default Compartment (+)   (-)

default Universal ID's

default Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
Activator default Activator(). default
GEF default RhoGEF(Active~no!-,). default
Active_GEF default RhoGEF(Active~yes!-,). default

Activator Universal ID's

Activator Text Annotations

GEF Universal ID's

GEF Text Annotations

Active_GEF Universal ID's

Active_GEF Text Annotations

Molecules

Name
BioNetGen Definition
DEPICTION
Activator Activator()
RhoGEF RhoGEF(Active~no~yes,)

Activator Universal ID's

Activator Text Annotations

RhoGEF Universal ID's

RhoGEF Text Annotations

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION
O0_Activator_tot default Molecules Activator(). Multimolecular
O0_RhoGEF_tot default Molecules RhoGEF(Active!?,). Multimolecular

O0_Activator_tot Universal ID's

O0_Activator_tot Text Annotations

O0_RhoGEF_tot Universal ID's

O0_RhoGEF_tot Text Annotations

Applications

Name
Properties Math Type
Annotation
Canonical Application Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Compartmental

Canonical Application Universal ID's

Canonical Application Text Annotations

Specifications (Species) - Canonical Application go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
Activator 1.0 [umol] 0.0 [m2/min] default
GEF 0.31 [umol] 0.0 [m2/min] default
Active_GEF 0.0 [umol] 0.0 [m2/min] default

Specifications (Reaction) - Canonical Application go to Simulations

Name
Enabled?
GEF_activation included
GEF_inactivation included
Activator_degradation included

Simulations - Canonical Application go to Specifications

Name
End Time
Output Options
Simulation0 600.0

KeepEvery 1

KeepAtMost 1000

Canonical Application Universal ID's

Canonical Application Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry Compartmental1466267146

(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 default

Events

Name Variable Rate Expression

Global Parameters

Name
Expression
k3 0.5[min-1]
k2 0.1[min-1]
kcatGEF 5.64[min-1]
KmGEFRho 24.5[umol.l-1]
KmGEFGDI 1.0[umol.l-1]
k1 1.0[l.umol-1.min-1]

Universal ID's

Text Annotations

Universal ID's

Text Annotations

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 Canonical Application.bngl
SBML Canonical Application.sbml
Matlab Canonical Application.m
NFSim XML Canonical Application.xml