Life123 : Dynamical Modeling of Biological Systems
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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.

JupyterLab is the next-generation user interface for Project Jupyter offering all the familiar building blocks of the classic Jupyter Notebook in a flexible and powerful user interface.
JupyterLab will eventually replace the classic 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.)

Life123 can be TRIED LIVE at Binder, with 1 click!
Akin to Google's Colab: short-term runs on a hosted JupyterLab environment
(say Cancel when asked to include "jupyterlab-dash" in the build!)

Single-compartment Reactions

These are reactions without any spatial modeling (in particular, no multiple bins, and no diffusion)

Experiments:



3D

coming soon...

2D

Reactions with Diffusion:

coming soon...

Diffusion (no reactions):



Reactions (without diffusion):



1D

Reactions with Diffusion:



Diffusion (no reactions):



Reactions (without diffusion):





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.