Update citation infomation (#267)

As we have added a lot of functionality since I first released BioMASS,
I encourage users to cite the following paper when using this software:
- Arakane, K., Imoto, H., Ormersbach, F. & Okada, M. Extending BioMASS
to construct mathematical models from external knowledge.
*Bioinformatics Advances*, vbae042 (2024).
https://doi.org/10.1093/bioadv/vbae042

CITATION.cff

@@ -3,20 +3,21 @@ message: "If you use this software in your work, we suggest citing the following
 preferred-citation:
   type: article
   authors:
+  - family-names: "Arakane"
+    given-names: "Kiwamu"
   - family-names: "Imoto"
     given-names: "Hiroaki"
     orcid: "https://orcid.org/0000-0002-6817-642X"
-  - family-names: "Zhang"
-    given-names: "Suxiang"
+  - family-names: "Ormersbach"
+    given-names: "Fabian"
+    orcid: "https://orcid.org/0000-0003-1838-5976"
   - family-names: "Okada"
     given-names: "Mariko"
     orcid: "https://orcid.org/0000-0002-6210-8223"
   doi: "10.3390/cancers12102878"
   journal: "Cancers"
-  title: "A Computational Framework for Prediction and Analysis of Cancer Signaling Dynamics from RNA Sequencing Data—Application to the ErbB Receptor Signaling Pathway"
-  issue: 10
-  volume: 12
-  start: 2878
-  end: 2878
-  year: 2020
-  url: "https://www.mdpi.com/2072-6694/12/10/2878"
+  title: "Extending BioMASS to construct mathematical models from external knowledge"
+  start: vbae042
+  end: vbae042
+  year: 2024
+  url: "https://doi.org/10.1093/bioadv/vbae042"

README.md

@@ -14,7 +14,7 @@
 [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/biomass-dev/biomass/master.svg)](https://results.pre-commit.ci/latest/github/biomass-dev/biomass/master)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 [![Imports: isort](https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336)](https://pycqa.github.io/isort/)
-[![Cancers Paper](https://img.shields.io/badge/DOI-10.3390%2Fcancers12102878-blue)](https://doi.org/10.3390/cancers12102878)
+[![Paper](https://img.shields.io/badge/DOI-10.1093%2Fbioadv%2Fvbae042-blue)](https://doi.org/10.1093/bioadv/vbae042)
 
 _BioMASS_ is a computational framework for modeling and analysis of biological signaling systems in Python.
 
@@ -41,6 +41,8 @@ BioMASS supports Python 3.8 or newer.
 
 - Imoto, H., Yamashiro, S. & Okada, M. A text-based computational framework for patient -specific modeling for classification of cancers. _iScience_ **25**, 103944 (2022). https://doi.org/10.1016/j.isci.2022.103944
 
+- Arakane, K., Imoto, H., Ormersbach, F. & Okada, M. Extending BioMASS to construct mathematical models from external knowledge. *Bioinformatics Advances*, vbae042 (2024). https://doi.org/10.1093/bioadv/vbae042
+
 ## Author
 
 [Hiroaki Imoto](https://github.com/himoto)

biomass/version.py

@@ -1,2 +1,3 @@
 """BioMASS library version"""
-__version__ = "0.12.0"
+
+__version__ = "0.13.0"

docs/citing.rst

@@ -3,23 +3,23 @@ Citing BioMASS
 
 If you use BioMASS in your research, please cite the following paper:
 
-* Imoto, H., Zhang, S. & Okada, M. A Computational Framework for Prediction and Analysis of Cancer Signaling Dynamics from RNA Sequencing Data—Application to the ErbB Receptor Signaling Pathway. *Cancers* **12**, 2878 (2020). https://doi.org/10.3390/cancers12102878
+* Arakane, K., Imoto, H., Ormersbach, F. & Okada, M. Extending BioMASS to construct mathematical models from external knowledge. *Bioinformatics Advances*, vbae042 (2024). https://doi.org/10.1093/bioadv/vbae042
 
 *In BibTeX format:*
 
 .. code-block:: bibtex
 
-    @article{cancers12102878,
-      author         = {Imoto, Hiroaki and Zhang, Suxiang and Okada, Mariko},
-      title          = {A Computational Framework for Prediction and Analysis of Cancer Signaling Dynamics from RNA Sequencing Data—Application to the ErbB Receptor Signaling Pathway},
-      journal        = {Cancers},
-      volume         = {12},
-      year           = {2020},
-      number         = {10},
-      article-number = {2878},
-      url            = {https://www.mdpi.com/2072-6694/12/10/2878},
-      issn           = {2072-6694},
-      doi            = {10.3390/cancers12102878}
+    @article{10.1093/bioadv/vbae042,
+      author  = {Arakane, Kiwamu and Imoto, Hiroaki and Ormersbach, Fabian and Okada, Mariko},
+      title   = "{Extending BioMASS to construct mathematical models from external knowledge}",
+      journal = {Bioinformatics Advances},
+      pages   = {vbae042},
+      year    = {2024},
+      month   = {04},
+      issn    = {2635-0041},
+      doi     = {10.1093/bioadv/vbae042},
+      url     = {https://doi.org/10.1093/bioadv/vbae042},
+      eprint  = {https://academic.oup.com/bioinformaticsadvances/advance-article-pdf/doi/10.1093/bioadv/vbae042/57163215/vbae042.pdf},
     }
 
 If you construct a mathematical model using :class:`biomass.construction.text2model.Text2Model`, please also cite the `Pasmopy <https://github.com/pasmopy/pasmopy>`_ paper:
@@ -47,4 +47,4 @@ When presenting work that uses BioMASS, feel free to use the logo.
 
 .. image:: _static/img/biomass-logo.png
    :width: 500px
-   :align: center
+   :align: center

docs/index.rst

@@ -9,7 +9,7 @@ BioMASS documentation
 .. toctree::
    :maxdepth: 1
    :caption: Contents:
-   
+
    about
    installation
    tutorial/index
@@ -54,6 +54,6 @@ BioMASS documentation
    :target: https://pycqa.github.io/isort/
    :alt: Imports: isort
 
-.. |Cancers Paper| image:: https://img.shields.io/badge/DOI-10.3390%2Fcancers12102878-blue
-   :target: https://doi.org/10.3390/cancers12102878
+.. |Paper| image:: https://img.shields.io/badge/DOI-10.1093%2Fbioadv%2Fvbae042-blue
+   :target: https://doi.org/10.1093/bioadv/vbae042
    :alt: DOI