Physiology
Reaction Diagram
Cross-References
Annotations
Structures
| Name | Type | Electrical |
|---|---|---|
| plasma membrane | Membrane | muscle(+) Extracellular(-) |
| muscle | Compartment | (+) (-) |
| Extracellular | Compartment | (+) (-) |
plasma membrane Universal ID's
plasma membrane Text Annotations
muscle Universal ID's
muscle Text Annotations
Extracellular Universal ID's
Extracellular Text Annotations
Species
| Name | Structure | BioNetGen Definition | Depiction |
|---|---|---|---|
| GluR_plasma_membrane | plasma membrane | ||
| Leak_plasma_membrane | plasma membrane | ||
| ion_muscle | muscle | ||
| Sion_Extracellular | Extracellular | ||
| ion_Extracellular | Extracellular | ||
| Sion_muscle | muscle |
GluR_plasma_membrane Universal ID's
GluR_plasma_membrane Text Annotations
Leak_plasma_membrane Universal ID's
Leak_plasma_membrane Text Annotations
ion_muscle Universal ID's
ion_muscle Text Annotations
Sion_Extracellular Universal ID's
Sion_Extracellular Text Annotations
ion_Extracellular Universal ID's
ion_Extracellular Text Annotations
Sion_muscle Universal ID's
Sion_muscle Text Annotations
Applications
| Name | Properties | Math Type | Annotation |
|---|---|---|---|
| compartment |
Specs -
Species Specs - Reaction Simulations |
Deterministic (ODE) Compartmental |
compartment Universal ID's
compartment Text Annotations
Specifications (Species) - compartment go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| ion_muscle | 100000.0 [uM] | 0.0 [um2/s] | muscle |
| Sion_muscle | 100000.0 [uM] | 0.0 [um2/s] | muscle |
| Sion_Extracellular | 100000.0 [uM] | 0.0 [um2/s] | Extracellular |
| ion_Extracellular | 100000.0 [uM] | 0.0 [um2/s] | Extracellular |
| GluR_plasma_membrane | 0.0 [uM] | 0.0 [um2/s] | plasma membrane |
| Leak_plasma_membrane | 0.0 [uM] | 0.0 [um2/s] | plasma membrane |
Specifications (Reaction) - compartment go to Simulations
Simulations - compartment go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| Simulation1 | 0.2 |
KeepEvery 1 KeepAtMost 5000 |
compartment Universal ID's
compartment Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|
Geometry non-spatial350451321
(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 | plasma membrane |
Events
| Name | Variable | Rate Expression |
|---|
Global Parameters
| Name | Expression |
|---|---|
| gL | -0.00116[nS.um-2] |
| VL | -63.0[mV] |
| Gs | 7.29[nS] |
| alpha | 0.0[s-1] |
| Vs | -1.0[mV] |
| gcs | 0.0[nS.um-2] |
| Ek | 0.0[mV] |
| onset | 0.0065[s] |
Universal ID's
Text Annotations
Universal ID's
Text Annotations
Universal ID's
Text Annotations
Universal ID's
Text Annotations
Universal ID's
Text Annotations
Universal ID's
Text Annotations
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 | compartment.bngl |
| SBML | compartment.sbml |
| Matlab | compartment.m |
| NFSim XML | compartment.xml |