Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
R R_synthesis env GeneralKinetics
R R_synthesis2 env GeneralKinetics
R R_degradation env GeneralKinetics
E Ep E_phosphorylation env GeneralKinetics
Ep E E_dephosphorylation env GeneralKinetics

R_synthesis Universal ID's

R_synthesis Text Annotations

R_synthesis2 Universal ID's

R_synthesis2 Text Annotations

R_degradation Universal ID's

R_degradation Text Annotations

E_phosphorylation Universal ID's

E_phosphorylation Text Annotations

E_dephosphorylation Universal ID's

E_dephosphorylation Text Annotations

Expressions for R_synthesis

reaction rate

J

(k0 * Ep) [mol.litre-1.s-1]

Expressions for R_synthesis2

reaction rate

J

(k1 * S) [mol.litre-1.s-1]

Expressions for R_degradation

reaction rate

J

(k2 * R) [mol.litre-1.s-1]

Expressions for E_phosphorylation

reaction rate

J

(k3 * R * E / (J3 + E)) [mol.litre-1.s-1]

Expressions for E_dephosphorylation

reaction rate

J

(k4 * Ep / (J4 + Ep)) [mol.litre-1.s-1]

Structures

Name
Type
Electrical
env Compartment (+)   (-)

env Universal ID's

env Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
R env R().
S env S().
Ep env E(mod~P!-,).
E env E(mod~U!-,).

R Universal ID's

R Text Annotations

S Universal ID's

S Text Annotations

Ep Universal ID's

Ep Text Annotations

E Universal ID's

E Text Annotations

Molecules

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

R Universal ID's

R Text Annotations

S Universal ID's

S Text Annotations

E Universal ID's

E Text Annotations

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION
O0_R_tot env Molecules R(). Multimolecular
O0_S_tot env Molecules S(). Multimolecular
O0_E_tot env Molecules E(mod!?,). Multimolecular

O0_R_tot Universal ID's

O0_R_tot Text Annotations

O0_S_tot Universal ID's

O0_S_tot Text Annotations

O0_E_tot Universal ID's

O0_E_tot Text Annotations

Applications

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

Deterministic Text Annotations

Deterministic Universal ID's

Annotations will come here

RFID | pubmed

Specifications (Species) - Deterministic go to Simulations

Species
Initial Condition
Diffusion Constant
R 0.0 0.0 [m2/s]
S 0.0 0.0 [m2/s]
Ep ((2.0 * (k3 * R) * J4) / ((k4 - (k3 * R)) + (J3 * k4) + (J4 * (k3 * R)) + pow((pow(((k4 - (k3 * R)) + (J3 * k4) + (J4 * (k3 * R))),2.0) - (4.0 * (k4 - (k3 * R)) * (k3 * R) * J4)),(1.0 / 2.0)))) 0.0 [m2/s]
E (Et - Ep) 0.0 [m2/s]

Specifications (Reaction) - Deterministic go to Simulations

Name
Enabled?
R_synthesis included
R_synthesis2 included
R_degradation included
E_phosphorylation included
E_dephosphorylation included

Simulations - Deterministic go to Specifications

Name
End Time
Output Options
Simulation0 1.0

KeepEvery 1

KeepAtMost 1000

Deterministic Universal ID's

Deterministic Text Annotations

Global Parameters

Name
Expression
k0 0.4[s-1]
k1 0.01[s-1]
k2 1.0[s-1]
k3 1.0[s-1]
J3 0.05[M]
k4 0.2[mol.s-1.l-1]
J4 0.05[M]
Et 1.0[M]

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

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Downloads

Format
File
VCML VCML File
BNGL
MatLab
SBML
Formatted XML
SEDML