Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
RPR protein_phos c0 HMMIrreversible
PRR protein_dephos c0 HMMIrreversible

protein_phos Universal ID's

protein_phos Text Annotations

protein_dephos Universal ID's

protein_dephos Text Annotations

Expressions for protein_phos

reaction rate

J

((Vmax * R) / (Km + R)) [uM.s-1]

Km (1/2 max)

Km

1.0 [uM]

max reaction rate

Vmax

S [uM.s-1]

Expressions for protein_dephos

reaction rate

J

((Vmax * PR) / (Km + PR)) [uM.s-1]

Km (1/2 max)

Km

1.0 [uM]

max reaction rate

Vmax

1.0 [uM.s-1]

Structures

Name
Type
Electrical
c0 Compartment (+)   (-)

c0 Universal ID's

c0 Text Annotations

Species

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

S Universal ID's

S Text Annotations

R Universal ID's

R Text Annotations

PR Universal ID's

PR 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
Sigmoidal Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Compartmental cloned from 'Sigmoidal' owned by user shreyasinha28 cloned from 'Sigmoidal' owned by user ModelBrick

Sigmoidal Universal ID's

Sigmoidal Text Annotations

Specifications (Species) - Sigmoidal go to Simulations

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

Specifications (Reaction) - Sigmoidal go to Simulations

Name
Enabled?
protein_phos included
protein_dephos included

Simulations - Sigmoidal go to Specifications

Name
End Time
Output Options
Simulation0 10.0

KeepEvery 1

KeepAtMost 1000

Sigmoidal Universal ID's

Sigmoidal Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry non-spatial1821159797

(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

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