Annotated experiments can be found in the "experiments" folder in the repository, as Jupyter Notebooks – ready to be used with JupyterLab (which we highly recommend) or the older Jupyter Notebook.
If you browse on GitHub, please note that GitHub automatically renders the Jupyter Notebooks files into the form they would appear if they were being used (in other words, an HTML snapshot of their active state.) HOWEVER, the Plotly visualizations won't show on GitHub! To see them, you can use the "nbviewer" links we provide on this page, or actually run the notebooks – either on your own computer or on a hosted environment, such as Binder (see below.)
Want to actually RUN the experiments below? Quick-start page
Uniform (single) compartment Reactions Reaction/Diffusion in 1D In 2D In 3D
Available tags
(select one or multiple ones; click again to de-select. Experiments with the selected tags will appear highlighted below) :
Selected: [[highlighted]]
| a good place to start for first-time users. Also consider the 'basic' filter | |
| recommended for new users; get familiarized with available features, demonstrated on simple systems. See also the 'quick-start' filter | |
| focus on some aspects of chemistry, such as thermodynamics, kinetics, etc | |
| focus on enzymes | |
| insight into the inner working of the software | |
| focus on numerical analysis: approximations, errors, etc | |
| reactions in a single compartment, without any spatial modeling; in particular, no diffusion | |
| not usable with recent versions; kept for instructional purposes or design insight |
Want to actually RUN the experiments above? Quick-start page