BioNetGen is software for rule-based modeling of biochemical systems. In the workshop you will learn how to construct, simulate, and analyze both nonspatial and compartmental models of biochemical systems. We will focus on the construction of simple models and then show how the same biochechemisty that we can represent in BioNetGen can also be simulated in MCell, where molecules and compartments have explicit spatial representation. We will compare results of the models to learn the role that space plays in cellular biochemistry.
If you are using your own laptop, install VS Code with BioNetGen extension.
Check the relevant folders for presentation materials, models, and notebooks and refresh regularly to make sure that you have the latest versions.
Reference
- BioNetGen website
- Quick reference guide for handy reference on BioNetGen syntax.
- BioNetGen primer for extended description and reference on BioNetGen modeling, including compartments.
- An extended GitHub-based tutorial on rule-based modeling with BioNetGen is here.