Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Structures

Name
Type
Electrical
env Compartment (+)   (-)

Species

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

Molecules

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

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION
O0_E_tot env Molecules E(mod!?,). Multimolecular
O0_S_tot env Molecules S(). Multimolecular
O0_R_tot env Molecules R(). Multimolecular
O0_X_tot env Molecules X(). Multimolecular

Applications

Specifications (Species) - Deterministic go to Simulations

Species
Initial Condition
Diffusion Constant
R 0.0 0.0
X 0.0 0.0
S 0.0 0.0
E (Et - Ep) 0.0
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)))) * Et) 0.0

Specifications (Reaction) - Deterministic go to Simulations

Name
Enabled?
R_synthesis included
R_synthesis2 included
R_degradation included
R_degradation_by_X included
E_phosphorylation included
E_dephosphorylation included
X_synthesis included
X_degradation included

Simulations - Deterministic go to Specifications

Name
End Time
Output Options
Simulation0 10.0 every

Global Parameters

Name
Expression
k0 4.0[s-1]
k1 1.0[s-1]
k2 1.0[s-1]
k2_prime 1.0[M-1.s-1]
k3 1.0[s-1]
J3 0.3[1]
k4 1.0[mol.s-1.l-1]
J4 0.3[1]
k5 0.1[s-1]
k6 0.075[s-1]
Et 1.0[M]
Km3 (J3 * Et)[M]
Km4 (J4 * Et)[M]

Downloads

Format
File
VCML VCML File
BNGL
MatLab
SBML
Formatted XML
SEDML