• DOWNLOAD Jupyter experiment notebooks directly from the GitHub repo
PLEASE NOTE:
if browsing the Jupyter notebooks on the repo, thru Github rendering,
be aware that the Plotly visualizations won't show on GitHub!
To see them, you can use the links that we provide on this page, which make use of a special converter to correctly render the plotly graphics inside the notebooks,
or you can run the notebooks on
your own computer or on a hosted environment.
Getting errors "max rate exceeded" when trying to view the notebooks? Try replacing http://155.248.202.124:8080 by https://nbviewer.org in your browser address bar!
Want to actually RUN the experiments below? Quick-start page
FILTER by available tags
(select one or multiple ones; click again to de-select. Experiments with the selected tags will appear circled in yellow 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 | |
| focus on large molecules | |
| focus on numerical analysis: approximations, errors, etc | |
| insight into the inner working of the software | |
| reactions in a single compartment, without any spatial modeling; in particular, no diffusion | |
| exploration of visualization modules | |
| not usable with recent versions; kept for instructional purposes or design insight |
Uniform (single) compartment Reactions
Reaction/Diffusion in 1D
In 2D
In 3D
Visualization modules
http://155.248.202.124:8080 by https://nbviewer.org in your browser address bar!
Want to actually RUN the experiments above? Quick-start page