Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction

Structures

Name
Type
Electrical
NM Membrane (+)   (-)
PM Membrane (+)   (-)
EC Compartment (+)   (-)
Cyto Compartment (+)   (-)
Nuc Compartment (+)   (-)

NM Universal ID's

NM Text Annotations

PM Universal ID's

PM Text Annotations

EC Universal ID's

EC Text Annotations

Cyto Universal ID's

Cyto Text Annotations

Nuc Universal ID's

Nuc Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
DiffMol Cyto Cyto

DiffMol Universal ID's

DiffMol Text Annotations

Molecules

Name
BioNetGen Definition
DEPICTION

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION

Applications

Name
Properties Math Type
Annotation
01_06_2017 Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Spatial (3D) (copied from Myo2_04_07_2017) cloned from 'nuc_1.75radius' owned by user ACowan (copied from Application0)

01_06_2017 Universal ID's

01_06_2017 Text Annotations

Specifications (Species) - 01_06_2017 go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
DiffMol (0.8 * (x < 11.7)) [uM] 10.0 [um2/s] Cyto

Specifications (Reaction) - 01_06_2017 go to Simulations

Name
Enabled?

Simulations - 01_06_2017 go to Specifications

Name
End Time
Output Options
Simulation8 100.0

OutputTimeStep 1.0
Simulation9 100.0

OutputTimeStep 1.0

01_06_2017 Universal ID's

01_06_2017 Text Annotations

01_06_2017 Universal ID's

01_06_2017 Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry Geometry1315116102

(Origin: 0.0, 0.0, 0.0; Extent: 14.0, 4.0, 4.0 [um])

Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Volume CSGObject subdomain2 5.550618934886217 [um3] Nuc
Volume CSGObject subdomain1 98.51807261672559 [um3] Cyto
Volume Analytical subdomain0 119.9313084483882 [um3] EC
Surface subdomain0_subdomain1_membrane subdomain0 | subdomain1 131.95796777841093 [um2] PM
Surface subdomain1_subdomain2_membrane subdomain1 | subdomain2 15.044508258113671 [um2] NM

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 01_06_2017.bngl
SBML 01_06_2017.sbml
Matlab 01_06_2017.m
NFSim XML 01_06_2017.xml