Simple implementation of Most Permissive Boolean networks
Project description
The mpbn Python module offers a simple implementation of reachability and attractor analysis (minimal trap spaces) in Most Permissive Boolean Networks (doi:10.1038/s41467-020-18112-5). The mpbn Python module also offers a Most Permissive simulator, which provides trajectory sampling and computes attractor propensities (see paper Variable-Depth Simulation of Most Permissive Boolean Networks for more details).
It is built on the minibn module from colomoto-jupyter which allows importation of Boolean networks in many formats. See http://colomoto.org/notebook.
Installation
CoLoMoTo Notebook environment
mpbn is distributed in the CoLoMoTo docker.
Using pip
pip install mpbn
Using conda
conda install -c colomoto -c potassco mpbn
Usage
Command line
- Enumeration of fixed points and attractors:
mpbn -h
- Simulation:
mpbn-sim -h
Python interface
Documentation is available at https://mpbn.readthedocs.io.
Example notebooks:
- https://nbviewer.org/github/bnediction/mpbn/tree/master/examples/
- http://doi.org/10.5281/zenodo.3719097
For the simulation:
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
File details
Details for the file mpbn-3.8.tar.gz.
File metadata
- Download URL: mpbn-3.8.tar.gz
- Upload date:
- Size: 16.2 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/5.1.1 CPython/3.12.5
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 0ec869578bf210756f1dda42427780c9ad1133ec33efad8971124fc4f72136ea |
|
| MD5 | b628decbfc2a2f68beabec1cca96e02d |
|
| BLAKE2b-256 | 62163796afbdedd99a5c8a7f47bbbeacd6d9f0aa8c403e9e85274ce3724d6e2c |
File details
Details for the file mpbn-3.8-py3-none-any.whl.
File metadata
- Download URL: mpbn-3.8-py3-none-any.whl
- Upload date:
- Size: 19.9 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/5.1.1 CPython/3.12.5
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | f2c7d697f6733def5972344c9238299f1aba94ad195a98a73e665f52dfef0cec |
|
| MD5 | 6ec00132a961fda2fd9e392f626278b1 |
|
| BLAKE2b-256 | 4d77a06e97d34eaf014c32c08b34d32ca63d2e59dab0dc1010c81aea96d8a85c |
