SBML Model Visualization

This notebook provides an example of using "visualizeSBMLModel" to visualize an SBML model.

<<mathsbml.m

MathSBML Version 2.6.0.6 (28-Oct-2006) using Mathematica Version 5.2 for Mac OS X x86 (32-bit) (February 24, 2006) reloaded 28-October-2006 17:39:03.248018

visualize the model

v = visualizeSBMLModel["test.xml", context→ None, visualizationFontSize→ 10, visualizationFontFamily→ Arial] ;

[Graphics:HTMLFiles/index_4.gif]

resize the graphics

Show[v, ImageSize→ 800, Background→ Pink]

[Graphics:HTMLFiles/index_6.gif]

-Graphics -

Display the contents of the model

SBMLRead["test.xml", verbose→ True, context→ None] ;

createModel[]

File Name:test.xml<br />SBML Level 2 Version 2

Model name: SBMLModel<br />Model id: SBMLModel<br />Model metaid: —SBMLModel

Function Definitions

----- None -----

Unit Definitions (Excluding Built-in Units)

----- None -----

CompartmentTypes

----- None -----

SpeciesTypes

----- None -----

Compartments

ID MetaID Name CompartmentType Dimension Size Units Derived Units Outside Constant
cell ··· cell ··· 3 1 volume litre ··· True

Species

ID Name SpeciesType Compartment initialType Value Units of the Species Derived Units of the Species B.C Constant Charge
En En ··· cell initialAmount 1 substance/volume mole/litre False False ···
S S ··· cell initialAmount 100 substance/volume mole/litre False False ···
SEn SEn ··· cell initialAmount 0 substance/volume mole/litre False False ···
P P ··· cell initialAmount 0 substance/volume mole/litre False False ···

Global Parameters

ID MetaID SBOTerm Name Value Units Derived Units Constant
k1 ··· ··· k1 0.5 ··· ··· True
k2 ··· ··· k2 0.1 ··· ··· True
k3 ··· ··· k3 1 ··· ··· True
kf ··· ··· kf 1 ··· ··· True
kr ··· ··· kr 1 ··· ··· True
k ··· ··· k 0.1 ··· ··· True
kd ··· ··· kd 0.1 ··· ··· True

Initial Assignments

----- None -----

Rules

----- None -----

Constraints

----- None -----

Reactions, contexts suppressed

ID MetaID SBOTerm Name Fast Reaction Reactants
ID MetaID SBOTerm		 Products
ID MetaID SBOTerm		 Modifiers
ID MetaID SBOTerm		 Parameters
ID=val MetaID SBOTerm		 Formula
SBOTerm
reaction1 ··· ··· reaction1 False Ø ⇔ En ···
En ··· ···
··· ···
0.5 - 0.1*En[t]
···
reaction2 ··· ··· reaction2 False En + S ⇔ SEn
S ··· ···
En ··· ···
SEn ··· ···
··· ···
En[t]*S[t] - SEn[t]
···
reaction3 ··· ··· reaction3 False SEn →  En + P
SEn ··· ···
En ··· ···
P ··· ···
··· ···
-0.1*En[t]*P[t] + 0.1*SEn[t]
···

Differential Equations, contexts suppressed

Variable ODEs
En En'[t]==(0.5 - 0.1*En[t] - 0.1*En[t]*P[t] - En[t]*S[t] + 1.1*SEn[t])/cell
P P'[t]==(-0.1*En[t]*P[t] + 0.1*SEn[t])/cell
S S'[t]==(-(En[t]*S[t]) + SEn[t])/cell
SEn SEn'[t]==(0.1*En[t]*P[t] + En[t]*S[t] - 1.1*SEn[t])/cell

Events

----- None -----

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