life123 1.0rc4

Dynamical Modeling of Biological Systems - Quantitative Reactomics

Life123

Dynamical Modeling of Biological Systems in 1, 2 and 3D (as well as single-compartment reactions)

Includes diffusion, reactions, diffusion/reaction, membranes and compartments.

Fundamental Goals

1. Detailed, quantitative biological simulations, including whole prokaryotic cells (bacteria), and later eukaryotic cells
2. Deeper quantitative insight into human tissue/organ/system physiology, for the advancement of medicine
3. A very integrative approach that is ultimate conducive to body-wide insights, with an eye to Longevity Science
4. Explore the minimalist essence of life-like dynamical systems
5. Investigate potential paths for the emergence of life on Earth and on Exoplanets
6. A community effort bringing together biologists, system biologists, programmers, machine-learning specialists, biochemists, power-computing engineers, doctors, data scientists, graphic designers, members of the public willing to share computing resources, etc.

Overview and Details

WEBSITE

Follow our blog/discussions

Try it Out Live on a hosted JupyterLab!

TRY IT OUT LIVE (no registration nor install!)
Click on

Then explore the notebooks under the experiments folder.

Note that several notebooks create HTML log files, by the same name as the notebook (eg, running the notebook called diffusion_1.ipynb will create a log file named diffusion_1.htm). These log files typically contain additional interactive graphics: currently, mostly interactive diagrams of the reaction networks.
(Most plots will show up inside the notebooks.)

"Binder", the host of the live demo, is akin to Google's Colab: short-term runs on a hosted JupyterLab environment.
It generally takes less than one minute to launch... and then you'll have your own private copy of all the notebooks, to run and/or change and re-run. (The notebooks are pre-existing; you may view them without having to run anything.)

Please remember that nothing gets saved long term on Binder; so, if you make changes you want to preserve, make sure to download the changed notebooks! For instruction on creating your own private local copy, read on...

(Note: if you want to simply VIEW the notebooks rather than run them, you may simply follow the
links in the Experiments Page )

Components

Experiments: See the Life123 List of Experiments

Libraries: See the Life123 Guide

Unit Testing (pytest):

• "tests" folder (top-level)

How to Use

See this short video

How to Run Locally

pip install life123

For details, see the Life123 Download/Install page