This tutorial deals with the creation and simulation of biochemical networks using bond graphs. In this tutorial, we will use the BondGraphTools package to:
- create and simulate bond graph models of biochemistry
- use chemical reaction networks to generate bond graph models
- extract efforts and flows from a bond graph to calculate reaction fluxes and affinities
- use bond graphs to represent an existing model of a transporter
Notebook | nbviewer | Binder |
---|---|---|
1 - Constructing simple examples with bond graphs | ||
2 - Reaction Builder | ||
3 - Energetic Analysis | ||
4 - Generating a model of SERCA | ||
5 - Enzymatic rate laws |