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 | |
|