Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
RRP R_phosphorylation c0 GeneralKinetics
RPR R_dephosphorylation c0 GeneralKinetics

R_phosphorylation Universal ID's

R_phosphorylation Text Annotations

R_dephosphorylation Universal ID's

R_dephosphorylation Text Annotations

Expressions for R_phosphorylation

reaction rate

J

(kf_R_phos * R * S) [uM.s-1]

global

kf_R_phos

1.0 [s-1.uM-1]

Expressions for R_dephosphorylation

reaction rate

J

(kf_phosp * RP) [uM.s-1]

global

kf_phosp

1.0 [s-1]

Structures

Name
Type
Electrical
c0 Compartment (+)   (-)

c0 Universal ID's

c0 Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
R c0 R(mod~U!-,). c0
RP c0 R(mod~P!-,). c0
S c0 S(). c0

R Universal ID's

R Text Annotations

RP Universal ID's

RP Text Annotations

S Universal ID's

S Text Annotations

Molecules

Name
BioNetGen Definition
DEPICTION
R R(mod~P~U,)
S S()

R Universal ID's

R Text Annotations

S Universal ID's

S Text Annotations

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION
O0_R_tot c0 Molecules R(mod!?,). Multimolecular
O0_S_tot c0 Molecules S(). Multimolecular

O0_R_tot Universal ID's

O0_R_tot Text Annotations

O0_S_tot Universal ID's

O0_S_tot Text Annotations

Applications

Name
Properties Math Type
Annotation
Hyperbolic Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Compartmental cloned from 'Hyperbolic' owned by user shreyasinha28 cloned from 'Hyperbolic' owned by user ModelBrick

Hyperbolic Universal ID's

Hyperbolic Text Annotations

Specifications (Species) - Hyperbolic go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
R 1.0 [uM] 0.0 [um2/s] c0
RP 0.0 [uM] 0.0 [um2/s] c0
S t [uM] 0.0 [um2/s] c0

Specifications (Reaction) - Hyperbolic go to Simulations

Name
Enabled?
R_phosphorylation included
R_dephosphorylation included

Simulations - Hyperbolic go to Specifications

Name
End Time
Output Options
Simulation0 10.0

KeepEvery 1

KeepAtMost 1000

Hyperbolic Universal ID's

Hyperbolic Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry non-spatial1832886354

(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 c0

Events

Name Variable Rate Expression

Global Parameters

Name
Expression
kf_R_phos 1.0[s-1.uM-1]
kf_phosp 1.0[s-1]

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 Hyperbolic.bngl
SBML Hyperbolic.sbml
Matlab Hyperbolic.m
NFSim XML Hyperbolic.xml