Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Structures

Name
Type
Electrical
env Compartment (+)   (-)

Species

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

Molecules

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

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

Applications

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

Specifications (Species) - Deterministic go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
R 0.0 [mol] 0.0 [m2/s] env
S 0.0 [mol] 0.0 [m2/s] env
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)))) [mol] 0.0 [m2/s] env
E (Et - Ep) [mol] 0.0 [m2/s] env

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

Assignments

Name Variable Assignment Function Expression
assignmentRule0 E (Et - Ep)
assignmentRule1 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))))

Events

Name Trigger Type Variable Assignment

Geometry Compartmental481736209

(Origin: 0.0, 0.0, 0.0; Extent: 10.0, 10.0, 10.0 [m])

Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Compartmental Compartment env

Events

Name Variable Rate Expression

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]

Downloads

Model Format
Model Downloads
Virtual Cell Markup Language VCML File
PDF Report Report
COMBINE Archive OMEX File
SEDML SEDML File
File Format
Application Downloads
BNGL Deterministic.bngl
SBML Deterministic.sbml
Matlab Deterministic.m
NFSim XML Deterministic.xml