Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
R PR protein_phos c0 HMMIrreversible
PR R 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().
R c0 R(mod~U!-,).
PR c0 R(mod~P!-,).

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
Sigmoidal Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Compartmental

Sigmoidal Text Annotations

Sigmoidal Universal ID's

Annotations will come here

RFID | pubmed

Specifications (Species) - Sigmoidal go to Simulations

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

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

Global Parameters

Name
Expression

Downloads

Format
File
VCML VCML File
BNGL
MatLab
SBML
Formatted XML
SEDML