# Life123
Open-Source Engine for Quantitative Reactomics.
Dynamical Modeling of Biological Systems in 1, 2 and 3D (as well as single-compartment reactions)
Includes diffusion, reactions, diffusion/reaction, membranes and compartments.
[WEBSITE](https://life123.science/)
## 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](https://life123.science/)
[Follow our blog/discussions](https://github.com/BrainAnnex/life123/discussions)
## Try it Out Live on a hosted JupyterLab!
**TRY IT OUT LIVE** (no registration nor install!)
Click on
[](https://mybinder.org/v2/gh/BrainAnnex/life123/main)
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](https://life123.science/experiments) )
## Components
*Experiments:*
See the [Life123 List of Experiments](https://life123.science/experiments)
*Libraries:*
See the [Life123 Guide](https://life123.science/guide)
*Unit Testing (pytest):*
* "tests" folder (top-level)
## How to Use
See this [short video](https://www.youtube.com/watch?v=FOhQgPZaEsA)
## How to Run Locally
`pip install life123`
For details, see the [Life123 Download/Install page](https://life123.science/install)
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