Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Structures

Name
Type
Electrical
env Compartment (+)   (-)

Species

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

Molecules

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

Observables

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

Applications

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

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 (Et - E) 0.0 [m2/s]
E (Et * ((2.0 * k3 * J4) / (((k4 * R) - k3) + (J3 * (k4 * R)) + (J4 * k3) + pow((pow((((k4 * R) - k3) + (J3 * (k4 * R)) + (J4 * k3)),2.0) - (4.0 * ((k4 * R) - k3) * k3 * J4)),(1.0 / 2.0))))) 0.0 [m2/s]

Specifications (Reaction) - Deterministic go to Simulations

Name
Enabled?
R_synthesis included
R_degradation included
E_dephosphorylation included
E_phosphorylation included

Simulations - Deterministic go to Specifications

Name
End Time
Output Options
Simulation0 1.0

KeepEvery 1

KeepAtMost 1000

Global Parameters

Name
Expression
k0 0.0[mol.s-1.l-1]
k1 0.05[s-1]
k2 0.1[s-1]
k2_prime 0.5[M-1.s-1]
k3 0.2[mol.s-1.l-1]
J3 0.05[1]
k4 1.0[s-1]
J4 0.05[1]
Et 1.0[M]
Km3 (J3 * Et)[M]
Km4 (J4 * Et)[M]

Downloads

Format
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VCML VCML File
BNGL
MatLab
SBML
Formatted XML
SEDML