Physiology
Reaction Diagram
Cross-References
Annotations
Reactions
Reactions | Name | Structure | Kinetics | Depiction |
---|---|---|---|---|
R | R_degradation | c0 | MassAction | |
R | R_synthesis | c0 | GeneralKinetics |
R_degradation Universal ID's
R_degradation Text Annotations
R_synthesis Universal ID's
R_synthesis Text Annotations
Expressions for R_degradation
reaction rate
J
(Kf * R) [uM.s-1]
forward rate constant
Kf
kd_R_degrad [s-1]
global
kd_R_degrad
5.0 [s-1]
reverse rate constant
Kr
0.0 [uM.s-1]
Expressions for R_synthesis
reaction rate
J
(k_R_synth * S) [uM.s-1]
global
k_R_synth
1.0 [s-1]
Species
R Universal ID's
R Text Annotations
S Universal ID's
S Text Annotations
Molecules
S Universal ID's
S Text Annotations
R Universal ID's
R 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_S_tot Universal ID's
O0_S_tot Text Annotations
O0_R_tot Universal ID's
O0_R_tot Text Annotations
Applications
Name | Properties | Math Type | Annotation |
---|---|---|---|
Linear |
Specs -
Species Specs - Reaction Simulations |
Deterministic (ODE) Compartmental | cloned from 'Linear' owned by user shreyasinha28 cloned from 'Linear' owned by user ModelBrick |
Linear Universal ID's
Linear Text Annotations
Specifications (Species) - Linear go to Simulations
Specifications (Reaction) - Linear go to Simulations
Simulations - Linear go to Specifications
Name | End Time | Output Options |
---|---|---|
Simulation0 | 3.0 |
KeepEvery 1 KeepAtMost 1000 |
Linear Universal ID's
Linear Text Annotations
Assignments
Name | Variable | Assignment Function Expression |
---|
Events
Name | Trigger Type | Variable Assignment |
---|
Geometry non-spatial1766805835
(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 |
---|---|
k_R_synth | 1.0[s-1] |
kd_R_degrad | 5.0[s-1] |
Universal ID's
Text Annotations
Universal ID's
Text Annotations
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 | Linear.bngl |
SBML | Linear.sbml |
Matlab | Linear.m |
NFSim XML | Linear.xml |