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.)

Uniform (single) compartment Reactions Reaction/Diffusion in 1D In 2D In 3D

Available tags (use your browser to search for them) :

• quick-start (a good place to start for first-time users)
• basic (recommented for new users)
• chemistry (focus on some aspects of chemistry, such as thermodynamics, kinetics, etc)
• under-the-hood (insight into the inner working of the software)
• numerical (focus on numerical analysis: approximations, errors, etc)
• uniform compartment (reactions in a single compartment, without any spatial modeling; in particular, no diffusion)
• diffusion 1D
• reactions 1D
• diffusion 2D
• reactions 2D
• archived (not usable with new versions; kept for instructional purposes or design insight)

Note: experiment notebooks may also be browsed directly thru Github rendering, but be aware that none of the visualizations show up there. We recommend that you use the links provided by us, above; they make use of nbviewer.org , and correctly display the plotly graphics inside the notebooks.