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Life123 : Open-Source Engine for Quantitative Reactomics
Dynamical Modeling of Biological Systems   ♦   In-Silico Experiments
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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.

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
recommented for new users
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

Uniform (single) compartment Reactions

These are reactions in a single compartment, without any spatial modeling (in particular, no diffusion)

Experiments:



1D

Reactions with Diffusion:



Diffusion (no reactions):



Reactions (without diffusion):



2D

Reactions with Diffusion:

coming soon...

Diffusion (no reactions):



Reactions (without diffusion):



3D

coming soon...



Note: experiment notebooks may also be browsed directly from the repo, 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 to correctly render the plotly graphics inside the notebooks.

Want to actually RUN the experiments above? Quick-start page