From 0529fe5273d432e6e1d18604e96deba5b3ff7eaf Mon Sep 17 00:00:00 2001
From: Paul Jonas Jost <70631928+PaulJonasJost@users.noreply.github.com>
Date: Tue, 10 Oct 2023 11:07:26 -0400
Subject: [PATCH] Added How to Cite (#1125)

* Added How to Cite to readme.

* Added how_to_cite to read_the_docs

* added how_to_cite to index.rst
---
 README.md           | 27 ++++++++++++++++++++++++---
 doc/how_to_cite.rst | 28 ++++++++++++++++++++++++++++
 doc/index.rst       |  1 +
 doc/references.rst  |  4 ++--
 4 files changed, 55 insertions(+), 5 deletions(-)
 create mode 100644 doc/how_to_cite.rst

diff --git a/README.md b/README.md
index 58ef9ca52..e6f00ba30 100644
--- a/README.md
+++ b/README.md
@@ -59,8 +59,29 @@ We are happy about any contributions. For more information on how to contribute
 to pyPESTO check out
 <https://pypesto.readthedocs.io/en/latest/contribute.html>
 
+## Publications
+
+**Citeable DOI for the latest pyPESTO release:**
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2553546.svg)](https://doi.org/10.5281/zenodo.2553546)
+
+There is a list of [publications using pyPESTO](https://pypesto.readthedocs.io/en/latest/references.html).
+If you used pyPESTO in your work, we are happy to include
+your project, please let us know via a GitHub issue.
+
+When using pyPESTO in your project, please cite
+* Schälte, Y., Fröhlich, F., Jost, P. J., Vanhoefer, J., Pathirana, D., Stapor, P.,
+  Lakrisenko, P., Wang, D., Raimúndez, E., Merkt, S., Schmiester, L., Städter, P.,
+  Grein, S., Dudkin, E., Doresic, D., Weindl, D., & Hasenauer, J. (2023). pyPESTO: A
+  modular and scalable tool for parameter estimation for dynamic models [(arXiv:2305.01821)](https://doi.org/10.48550/arXiv.2305.01821).
+
+When presenting work that employs pyPESTO, feel free to use one of the icons in
+[doc/logo/](https://github.com/ICB-DCM/pyPESTO/tree/main/doc/logo):
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/ICB-DCM/pyPESTO/master/doc/logo/logo.png" height="75" alt="AMICI Logo">
+</p>
+
 ## References
 
-[**PESTO**](https://github.com/ICB-DCM/PESTO/):
-Parameter estimation toolbox for MATLAB. Development is discontinued, but PESTO
-comes with additional features waiting to be ported to pyPESTO.
+pyPESTO supersedes [**PESTO**](https://github.com/ICB-DCM/PESTO/) a parameter estimation
+toolbox for MATLAB, whose development is discontinued.
diff --git a/doc/how_to_cite.rst b/doc/how_to_cite.rst
new file mode 100644
index 000000000..53054abd8
--- /dev/null
+++ b/doc/how_to_cite.rst
@@ -0,0 +1,28 @@
+How to cite pyPESTO
+===================
+
+**Citeable DOI for the latest pyPESTO release:**
+
+.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.2553546.svg
+   :target: https://doi.org/10.5281/zenodo.2553546
+   :alt: pyPESTO release DOI
+
+
+There is a list of `publications using pyPESTO <https://pypesto.readthedocs.io/en/latest/references.html>`_.
+If you used pyPESTO in your work, we are happy to include
+your project, please let us know via a GitHub issue.
+
+When using pyPESTO in your project, please cite
+
+- Schälte, Y., Fröhlich, F., Jost, P. J., Vanhoefer, J., Pathirana, D., Stapor, P.,
+  Lakrisenko, P., Wang, D., Raimúndez, E., Merkt, S., Schmiester, L., Städter, P.,
+  Grein, S., Dudkin, E., Doresic, D., Weindl, D., & Hasenauer, J. (2023). pyPESTO: A
+  modular and scalable tool for parameter estimation for dynamic models `arXiv:2305.01821 <https://doi.org/10.48550/arXiv.2305.01821>`_.
+
+When presenting work that employs pyPESTO, feel free to use one of the icons in
+`doc/logo/ <https://github.com/ICB-DCM/pyPESTO/tree/main/doc/logo>`_:
+
+.. image:: https://raw.githubusercontent.com/ICB-DCM/pyPESTO/master/doc/logo/logo.png
+   :target: https://raw.githubusercontent.com/ICB-DCM/pyPESTO/master/doc/logo/logo.png
+   :height: 75
+   :alt: pyPESTO LOGO
diff --git a/doc/index.rst b/doc/index.rst
index 062f4c034..5035172d0 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -45,6 +45,7 @@ pyPESTO - Parameter EStimation TOolbox for python
    references
    contact
    license
+   how_to_cite
    logo
 
 
diff --git a/doc/references.rst b/doc/references.rst
index 79742222b..c8cb861c0 100644
--- a/doc/references.rst
+++ b/doc/references.rst
@@ -1,7 +1,7 @@
-Publications using pypesto
+Publications using pyPESTO
 ==========================
 
-pypesto was used in the following publications:
+pyPESTO was used in the following publications:
 
 .. bibliography:: using_pypesto.bib
    :list: enumerated