Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
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]

reverse rate constant

Kr

0.0 [uM.s-1]

Expressions for R_synthesis

reaction rate

J

(k_R_synth * S) [uM.s-1]

Structures

Name
Type
Electrical
c0 Compartment (+)   (-)

c0 Universal ID's

c0 Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
R c0 R().
S c0 S().

R Universal ID's

R Text Annotations

S Universal ID's

S Text Annotations

Molecules

Name
BioNetGen Definition
DEPICTION
S S()
R R()

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
Linear Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Compartmental

Linear Text Annotations

Linear Universal ID's

Annotations will come here

RFID | pubmed

Specifications (Species) - Linear go to Simulations

Species
Initial Condition
Diffusion Constant
R 0.0 0.0 [um2/s]
S t 0.0 [um2/s]

Specifications (Reaction) - Linear go to Simulations

Name
Enabled?
R_degradation included
R_synthesis included

Simulations - Linear go to Specifications

Name
End Time
Output Options
Simulation0 3.0

KeepEvery 1

KeepAtMost 1000

Linear Universal ID's

Linear Text Annotations

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

Format
File
VCML VCML File
BNGL
MatLab
SBML
Formatted XML
SEDML