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Life123 : Open-Source Engine for Quantitative Reactomics
Dynamical Modeling of Biological Systems   ♦   In-Silico Experiments
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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 "nbviewer" links that we provide on this page, which correctly render the plotly graphics inside the notebooks, or you can run the notebooks on your own computer or on a hosted environment.


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 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
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