Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
X X_degradation c0 MassAction
X X_synthesis c0 GeneralKinetics
R R_synthesis c0 GeneralKinetics
R R_degradation c0 GeneralKinetics

X_degradation Universal ID's

X_degradation Text Annotations

X_synthesis Universal ID's

X_synthesis Text Annotations

R_synthesis Universal ID's

R_synthesis Text Annotations

R_degradation Universal ID's

R_degradation Text Annotations

Expressions for X_degradation

reaction rate

J

(Kf * X) [uM.s-1]

forward rate constant

Kf

k4 [s-1]

reverse rate constant

Kr

0.0 [uM.s-1]

local

k4

1.0 [s-1]

Expressions for X_synthesis

reaction rate

J

(k3 * S) [uM.s-1]

local

k3

1.0 [s-1]

Expressions for R_synthesis

reaction rate

J

(k1 * S) [uM.s-1]

local

k1

2.0 [s-1]

Expressions for R_degradation

reaction rate

J

(k2 * X * R) [uM.s-1]

local

k2

2.0 [s-1.uM-1]

Structures

Name
Type
Electrical
c0 Compartment (+)   (-)

c0 Universal ID's

c0 Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
S c0 S(). c0
R c0 R(). c0
X c0 X(). c0

S Universal ID's

S Text Annotations

R Universal ID's

R Text Annotations

X Universal ID's

X Text Annotations

Molecules

Name
BioNetGen Definition
DEPICTION
S S()
R R()
X X()

S Universal ID's

S Text Annotations

R Universal ID's

R Text Annotations

X Universal ID's

X Text Annotations

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION
O0_S_tot c0 Molecules S(). Multimolecular
O0_R_tot c0 Molecules R(). Multimolecular
O0_X_tot c0 Molecules X(). Multimolecular

O0_S_tot Universal ID's

O0_S_tot Text Annotations

O0_R_tot Universal ID's

O0_R_tot Text Annotations

O0_X_tot Universal ID's

O0_X_tot Text Annotations

Applications

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

PerfectlyAdapted Universal ID's

PerfectlyAdapted Text Annotations

Specifications (Species) - PerfectlyAdapted go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
S 1.0 [uM] 0.0 [um2/s] c0
R 0.0 [uM] 0.0 [um2/s] c0
X 0.0 [uM] 0.0 [um2/s] c0

Specifications (Reaction) - PerfectlyAdapted go to Simulations

Name
Enabled?
X_degradation included
X_synthesis included
R_synthesis included
R_degradation included

Simulations - PerfectlyAdapted go to Specifications

Name
End Time
Output Options
Simulation0 20.0

KeepEvery 1

KeepAtMost 1000

PerfectlyAdapted Universal ID's

PerfectlyAdapted Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment
event0 at times: [4.0,8.0,12.0,16.0] S --> (S + 0.2)

Geometry non-spatial1422527727

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

Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Compartmental Compartment c0

Events

Name Variable Rate Expression

Global Parameters

Name
Expression

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 PerfectlyAdapted.bngl
SBML PerfectlyAdapted.sbml
Matlab PerfectlyAdapted.m
NFSim XML PerfectlyAdapted.xml