Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
GEF Active_GEF GEF_activation default GeneralKinetics
Active_GEF GEF GEF_inactivation default GeneralKinetics
Activator Activator_degradation default GeneralKinetics

Structures

Name
Type
Electrical
default Compartment (+)   (-)

Species

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

Molecules

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

Observables

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

Applications

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

Specifications (Species) - Canonical Application go to Simulations

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

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

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]

Downloads

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BNGL
MatLab
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SEDML