Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction

Structures

Name
Type
Electrical
ecMem Membrane c(+)   EC(-)
lMem Membrane l(+)   c(-)
mMem Membrane m(+)   c(-)
l Compartment (+)   (-)
m Compartment (+)   (-)
EC Compartment (+)   (-)
c Compartment (+)   (-)

ecMem Universal ID's

ecMem Text Annotations

lMem Universal ID's

lMem Text Annotations

mMem Universal ID's

mMem Text Annotations

l Universal ID's

l Text Annotations

m Universal ID's

m Text Annotations

EC Universal ID's

EC Text Annotations

c Universal ID's

c Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
Mt_m m m
Mt_l l l
Mt_e EC EC
Mt_c c c

Mt_m Universal ID's

Mt_m Text Annotations

Mt_l Universal ID's

Mt_l Text Annotations

Mt_e Universal ID's

Mt_e Text Annotations

Mt_c Universal ID's

Mt_c Text Annotations

Molecules

Name
BioNetGen Definition
DEPICTION

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION

Applications

Name
Properties Math Type
Annotation
Matching w/ Matlab data Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Compartmental cloned from 'Matching w/ Matlab data' owned by user jsbaik Monobasic molecule M transport simulator v.1 Mt is total concentration of M in each compartment. a = apical lumen of intestine, where drug initially is introduced as high concentration. pH = 6.8 aMem = apical side membrane of enterocyte. Membrane potential Eam. -9.3mV c = cytosolic compartment of enterocyte. pH = 7.0 m = mitochondria of enterocyte. pH = 8.0 mMem = mitochondrial membrane Membrane potential Emm = -160mV b = basolateral lumen of enterocyte. pH = 7.4 bMem = basolateral side membrane of enterocyte. Membrane potential Ebm = 119mV

Matching w/ Matlab data Universal ID's

Matching w/ Matlab data Text Annotations

Specifications (Species) - Matching w/ Matlab data go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
Mt_l 0.0 [uM] 0.0 [um2/s] l
Mt_m 0.0 [uM] 0.0 [um2/s] m
Mt_e 4.75 [uM] 0.0 [um2/s] EC
Mt_c 0.0 [uM] 0.0 [um2/s] c

Specifications (Reaction) - Matching w/ Matlab data go to Simulations

Name
Enabled?
flux_ac included
flux_cl included
flux_cm included

Simulations - Matching w/ Matlab data go to Specifications

Name
End Time
Output Options
Clofazimine 30.0

KeepEvery 1

KeepAtMost 1000
Amiodarone 30.0

KeepEvery 1

KeepAtMost 1000
Bupivacaine 30.0

KeepEvery 1

KeepAtMost 1000
Chlorprothixene 300.0

KeepEvery 1

KeepAtMost 1000
Lidocaine 30.0

KeepEvery 1

KeepAtMost 1000
Celiprolol 300.0

KeepEvery 1

KeepAtMost 1000

Matching w/ Matlab data Universal ID's

Matching w/ Matlab data Text Annotations

Matching w/ Matlab data Universal ID's

Matching w/ Matlab data Text Annotations

Matching w/ Matlab data Universal ID's

Matching w/ Matlab data Text Annotations

Matching w/ Matlab data Universal ID's

Matching w/ Matlab data Text Annotations

Matching w/ Matlab data Universal ID's

Matching w/ Matlab data Text Annotations

Matching w/ Matlab data Universal ID's

Matching w/ Matlab data Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry non-spatial1067581628

(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 mMem

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 Matching w/ Matlab data.bngl
SBML Matching w/ Matlab data.sbml
Matlab Matching w/ Matlab data.m
NFSim XML Matching w/ Matlab data.xml