Merge pull request #85 from loucerac/develop

Develop

README.md

@@ -1,9 +1,46 @@
-[![DOI](https://zenodo.org/badge/362395439.svg)](https://zenodo.org/badge/latestdoi/362395439) [![PyPI version](https://badge.fury.io/py/drexml.svg)](https://badge.fury.io/py/drexml) [![pdm-managed](https://img.shields.io/badge/pdm-managed-blueviolet)](https://pdm.fming.dev)
+[![DOI](https://img.shields.io/badge/DOI-10.1016/j.csbj.2024.02.027-FAB70C?logo=doi)](https://doi.org/10.1016/j.csbj.2024.02.027)
+[![DOI](https://zenodo.org/badge/362395439.svg)](https://zenodo.org/badge/latestdoi/362395439) 
+[![PyPI version](https://badge.fury.io/py/drexml.svg)](https://badge.fury.io/py/drexml)
+[![pdm-managed](https://img.shields.io/badge/pdm-managed-blueviolet)](https://pdm.fming.dev)
 
 # Drug REpurposing using eXplainable Machine Learning and Mechanistic Models of signal transduction
 
 Repository for the `drexml` python package: (DRExM³L) Drug REpurposing using eXplainable Machine Learning and Mechanistic Models of signal transduction
 
+## Citation
+
+Find the associated publication [here](https://doi.org/10.1016/j.csbj.2024.02.027):
+
+```
+Esteban-Medina M, de la Oliva Roque VM, Herráiz-Gil S, Peña-Chilet M, Dopazo J, Loucera C. drexml: A command line tool and Python package for drug repurposing. Computational and Structural Biotechnology Journal 2024;23:1129–43. https://doi.org/10.1016/j.csbj.2024.02.027.
+```
+
+Part of the [Intelligent Biology and Medicine](https://www.sciencedirect.com/science/journal/20010370/vsi/10XRHM1G1LS) special issue:
+
+https://www.sciencedirect.com/journal/computational-and-structural-biotechnology-journal/special-issue/10XRHM1G1LS
+
+
+And the `BIB` file:
+
+```
+@article{ESTEBANMEDINA20241129,
+title = {drexml: A command line tool and Python package for drug repurposing},
+journal = {Computational and Structural Biotechnology Journal},
+volume = {23},
+pages = {1129-1143},
+year = {2024},
+issn = {2001-0370},
+doi = {https://doi.org/10.1016/j.csbj.2024.02.027},
+url = {https://www.sciencedirect.com/science/article/pii/S2001037024000515}
+}
+```
+
+The article was written using `drexml` version `v1.1.0`. Install it using:
+```
+pip install drexml==1.1.0
+```
+Version `v1.1.1` improves the documentation and `README` by including a reference to the published article for easier access.
+
 ## Setup
 
 To install the `drexml` package use the following:

docs/source/index.rst

@@ -9,6 +9,33 @@ and signaling circuits.
 
    Holistic Drug REpurposing Model
 
+Citation
+========
+
+Find `here <https://doi.org/10.1016/j.csbj.2024.02.027>`_ the published article in Computational and Structural Biotechnology Journal's special issue on `Intelligent Biology and Medicine <https://www.sciencedirect.com/science/journal/20010370/vsi/10XRHM1G1LS>`_:
+
+.. code:: text
+
+   Esteban-Medina M, de la Oliva Roque VM, Herráiz-Gil S, Peña-Chilet M, Dopazo J, Loucera C. drexml: A command line tool and Python package for drug repurposing. Computational and Structural Biotechnology Journal 2024;23:1129–43. https://doi.org/10.1016/j.csbj.2024.02.027.
+
+And the ``BIB`` file:
+
+.. code:: text
+
+   @article{ESTEBANMEDINA20241129,
+   title = {drexml: A command line tool and Python package for drug repurposing},
+   journal = {Computational and Structural Biotechnology Journal},
+   volume = {23},
+   pages = {1129-1143},
+   year = {2024},
+   issn = {2001-0370},
+   doi = {https://doi.org/10.1016/j.csbj.2024.02.027},
+   url = {https://www.sciencedirect.com/science/article/pii/S2001037024000515}
+   }
+
+
+The article was written using ``drexml`` version ``v1.1.0``.
+
 Installation
 =============
 

pyproject.toml

@@ -21,7 +21,7 @@ dependencies = [
     "pystow>=0.5.0",
 ]
 name = "drexml"
-version = "1.1.0"
+version = "1.1.1"
 description = "(DRExM³L) Drug REpurposing using and eXplainable Machine Learning and Mechanistic Models of signal transduction\""
 readme = "README.md"