diff --git a/README.md b/README.md index b447cf9..7433947 100644 --- a/README.md +++ b/README.md @@ -4,39 +4,4 @@ Synthesis of Most Permissive Boolean Networks from network architecture and dyna This software is distributed under the [CeCILL v2.1](http://www.cecill.info/index.en.html) free software license (GNU GPL compatible). -## Main related publications - -### Synthesis/Inference - -* **Synthesis of Boolean Networks from Biological Dynamical Constraints using Answer-Set Programming** (S Chevalier, C Froidevaux, L Paulevé, A Zinovyev). *In 2019 IEEE 31st International Conference on Tools with Artificial Intelligence (ICTAI), 34–41. Portland, Oregon, United States, 2019. IEEE.* [doi:10.1109/ICTAI.2019.00014](https://doi.org/10.1109/ICTAI.2019.00014) -* **Synthesis and Simulation of Ensembles of Boolean Networks for Cell Fate Decision** (S Chevalier, V Noël, L Calzone, A Zinovyev, L Paulevé) *In 18th International Conference on Computational Methods in Systems Biology (CMSB). Online, Germany, 2020.* Preprint at https://hal.archives-ouvertes.fr/hal-02898849/file/cmsb2020.pdf - -### Control/Reprogramming - -* **Tackling universal properties of minimal trap spaces of Boolean networks** - (S Riva, J-M Lagniez, G Magaña López, L Paulevé), *CMSB*, 2023 [doi:10.1007/978-3-031-42697-1_11](https://doi.org/10.1007/978-3-031-42697-1_11) [arXiv:2305.02442](http://arxiv.org/abs/2305.02442) -* **Marker and source-marker reprogramming of Most Permissive Boolean networks and ensembles with BoNesis** (L Paulevé), *Peer Community Journal*, 2023 -[doi:10.24072/pcjournal.255](https://doi.org/10.24072/pcjournal.255) - -## Installation - -### Using pip -``` -pip install bonesis -``` - -### Using conda -``` -conda install -c potassco -c colomoto bonesis -``` - -## Usage - -### Python API - -- [Tutorial](https://nbviewer.org/github/bnediction/bonesis/blob/master/examples/Tutorial.ipynb) - -### Command line tools - -* `bonesis-reprogramming`: marker reprogramming of minimal trap spaces (attractors of most permissive dynamics) -* `bonesis-attractors`: listing of minimal trap spaces (MP attractors) from ensembles of BNs +For installation instructions and usage, see [documentation](https://bnediction.github.io/bonesis).