https://github.com/pauleve/updating-modes-notebooks
Notebooks demonstrating colomoto.minibn for computing dynamics of Boolean networks with various update modes
https://github.com/pauleve/updating-modes-notebooks
boolean-networks notebooks
Last synced: 12 months ago
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Notebooks demonstrating colomoto.minibn for computing dynamics of Boolean networks with various update modes
- Host: GitHub
- URL: https://github.com/pauleve/updating-modes-notebooks
- Owner: pauleve
- Created: 2021-06-22T10:11:46.000Z (about 5 years ago)
- Default Branch: main
- Last Pushed: 2022-08-05T11:28:27.000Z (almost 4 years ago)
- Last Synced: 2024-05-01T22:14:36.663Z (about 2 years ago)
- Topics: boolean-networks, notebooks
- Language: Jupyter Notebook
- Homepage:
- Size: 181 KB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
Supplementary material to the chapter 6 "**Boolean networks and their dynamics: the impact of updates**" by [Loïc Paulevé](https://loicpauleve.name) and [Sylvain Sené](https://pageperso.lis-lab.fr/~sylvain.sene/) of the book "*Systems Biology Modelling and Analysis: Formal Bioinformatics Methods and Tools*" (First Edition), edited by Elisabetta De Maria (Wiley, 2023).
These notebooks demonstate how to use the Python module
[`colomoto.minibn`](https://github.com/colomoto/colomoto-jupyter) for computing
dynamics of Boolean networks with various updating modes.
They can be visualized online at https://nbviewer.jupyter.org/github/pauleve/updating-modes-notebooks/
They can be executed and modified online at https://mybinder.org/v2/gh/pauleve/updating-modes-notebooks/main
## Local installation
The module can be installed with a recent Python (≥3.7) distribution, using
`pip` or `conda`.
### Using pip (Python)
In a terminal/powershell
```sh
pip install -U colomoto-jupyter
```
### Using conda
```sh
conda install -c conda-forge -c colomoto colomoto-jupyter
```
### Using the CoLoMoTo Docker image
These notebooks can be executed within the [CoLoMoTo Docker distribution](https://colomoto.org/notebook) version `2022-07-01`:
1. download the notebooks from https://github.com/pauleve/updating-modes-notebooks/archive/main.zip and extract the zip file
2. execute the following commands, where ``notebooks`` is the folder in which you extracted the notebooks
```sh
sudo pip install -U colomoto-docker # you may have to use pip3 instead of pip
colomoto-docker -V 2022-07-01 --bind notebooks
```
## Related documentation
Other tutorials regarding the `minibn` module can be found at
https://nbviewer.jupyter.org/github/colomoto/colomoto-docker/tree/master/tutorials/minibn/
as well as other tools related to boolean networks at
https://nbviewer.jupyter.org/github/colomoto/colomoto-docker/tree/master/tutorials/
See http://colomoto.org/notebook for more information.