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 |