Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Structures

Name
Type
Electrical
env Compartment (+)   (-)

Species

Name
Structure
BioNetGen Definition
Depiction
Rp env R(mod~P!-,).
X env X().
Yp env Y(mod~P!-,).
S env S().
Y env Y(mod~U!-,).
R env R(mod~U!-,).

Molecules

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

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION
O0_R_tot env Molecules R(mod!?,). Multimolecular
O0_X_tot env Molecules X(). Multimolecular
O0_Y_tot env Molecules Y(mod!?,). Multimolecular
O0_S_tot env Molecules S(). Multimolecular

Applications

Specifications (Species) - Deterministic go to Simulations

Species
Initial Condition
Diffusion Constant
Rp 0.0 0.0
X 0.0 0.0
Yp 0.0 0.0
S 0.0 0.0
Y (Yt - Yp) 0.0
R (Rt - Rp) 0.0

Specifications (Reaction) - Deterministic go to Simulations

Name
Enabled?
X_synthesis included
X_degradation included
Y_phosphorylation included
Y_dephosphorylation included
R_phosphorylation included
R_dephosphorylation included

Simulations - Deterministic go to Specifications

Name
End Time
Output Options
Simulation0 1.0 every

Global Parameters

Name
Expression
k0 0.0[mol.s-1.l-1]
k1 1.0[s-1]
k2 0.01[s-1]
k2_prime 10.0[M-1.s-1]
k3 0.1[s-1]
Yt 1.0[M]
Km3 0.01[M]
k4 0.2[mol.s-1.l-1]
Km4 0.01[M]
k5 0.1[s-1]
Rt 1.0[M]
Km5 0.01[M]
k6 0.05[mol.s-1.l-1]
Km6 0.01[M]

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BNGL
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