Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
AB r0 CM MassAction

r0 Universal ID's

r0 Text Annotations

Expressions for r0

reaction rate

J

((Kf * A) - (Kr * B)) [molecules.um-2.s-1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

0.0 [1]

forward rate constant

Kf

1.0 [s-1]

reverse rate constant

Kr

1.0 [s-1]

Structures

Name
Type
Electrical
CM Membrane IC(+)   EC(-)
IC Compartment (+)   (-)
EC Compartment (+)   (-)

CM Universal ID's

CM Text Annotations

IC Universal ID's

IC Text Annotations

EC Universal ID's

EC Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
A CM CM
B CM CM

A Universal ID's

A Text Annotations

B Universal ID's

B Text Annotations

Molecules

Name
BioNetGen Definition
DEPICTION

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION

Applications

Name
Properties Math Type
Annotation
Det Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Spatial (3D)
stoch Specs - Species
Specs - Reaction
Simulations 		Stochastic (SSA) Spatial (3D) (copied from Det)

Det Universal ID's

Det Text Annotations

stoch Universal ID's

stoch Text Annotations

Specifications (Species) - Det go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
A 0.1 [uM] 0.1 [um2/s] CM
B 0.0 [uM] 0.1 [um2/s] CM

Specifications (Reaction) - Det go to Simulations

Name
Enabled?
r0 included

Simulations - Det go to Specifications

Name
End Time
Output Options
Simulation1 10.0

OutputTimeStep 0.05

Det Universal ID's

Det Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry 3DLEGIStoch_Sayak

(Origin: 0.0, 0.0, 0.0; Extent: 5.0, 5.0, 5.0 [um])

Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Volume Analytical IC 11.821125 [um3] IC
Volume Analytical EC 113.17887499999999 [um3] EC
Surface EC_IC_membrane EC | IC 25.03574790171551 [um2] CM

Events

Name Variable Rate Expression

Specifications (Species) - stoch go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
A 0.1 [uM] 0.1 [um2/s] CM
B 0.0 [uM] 0.1 [um2/s] CM

Specifications (Reaction) - stoch go to Simulations

Name
Enabled?
r0 included

Simulations - stoch go to Specifications

Name
End Time
Output Options
Simulation0 10.0

OutputTimeStep 0.05

stoch Universal ID's

stoch Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry 3DLEGIStoch_Sayak

(Origin: 0.0, 0.0, 0.0; Extent: 5.0, 5.0, 5.0 [um])

Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Volume Analytical IC 11.821125 [um3] IC
Volume Analytical EC 113.17887499999999 [um3] EC
Surface EC_IC_membrane EC | IC 25.03574790171551 [um2] CM

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 Det.bngl , stoch.bngl
SBML Det.sbml , stoch.sbml
Matlab Det.m , stoch.m
NFSim XML Det.xml , stoch.xml