Update citation section and links

README.rst

@@ -15,8 +15,8 @@ CADET
 
 - **Website (including documentation):** https://cadet.github.io
 - **Forum:** https://forum.cadet-web.de
-- **Source:** https://github.com/modsim/cadet
-- **Bug reports:** https://github.com/modsim/cadet/issues
+- **Source:** https://github.com/cadet/cadet-core
+- **Bug reports:** https://github.com/cadet/cadet-core/issues
 - **Demo:** https://www.cadet-web.de 
 - **Newsletter:** https://cadet-web.de/newsletter/
 
@@ -55,22 +55,10 @@ Therefore, we kindly ask that any publications or projects leveraging the capabi
 
 - Püttmann, A.; Schnittert, S.; Naumann, U.; von Lieres, E.: `Fast and accurate parameter sensitivities for the general rate model of column liquid chromatography <http://dx.doi.org/10.1016/j.compchemeng.2013.04.021>`_, Computers and Chemical Engineering **56** (2013), 46–57.
 
-**Selected applications:**
-
-- Heymann, W.; Glaser, J.; Schlegel, F.; Johnson, W.; Rolandi, P.; von Lieres, E.: `Advanced score system and automated search strategies for parameter estimation in mechanistic chromatography modeling <https://doi.org/10.1016/j.chroma.2021.462693>`_, Journal of Chromatography A **1661** (2022): 462693.
-
-- He, Q.-L.; Leweke, S.; von Lieres, E.: `Efficient numerical simulation of simulated moving bed chromatography with a single-column solver <http://doi.org/10.1016/j.compchemeng.2017.12.022>`_, Computers and Chemical Engineering **111** (2018), 183–198.
-
-- Freier, L.; von Lieres, E.: `Robust multi-objective global optimization of stochastic processes with a case study in gradient elution chromatography <http://doi.org/10.1002/biot.201700257>`_, Biotechnology Journal **13,1** (2018), 1700257.
-
-- Freier, L.; von Lieres, E.: [Multi-objective global optimization (MOGO): `Algorithm and case study in gradient elution chromatography <http://dx.doi.org/10.1002/biot.201600613>`_, Biotechnology Journal **12,7** (2017), 1600613.
-
-- Diedrich, J.; Heymann, W.; Leweke, S.; Kunert, C.; Johnson, W.; Hunt, S.; Todd, B.; von Lieres, E.: `Multi-state steric mass-action model and case study on complex high loading behavior of mAb on ion exchange tentacle resin <https://doi.org/10.1016/j.chroma.2017.09.039>`_, Journal of Chromatography A **1525** (2017), 60–70.
-
-- Püttmann, A.; Schnittert, S.; Leweke, S.; von Lieres, E.: `Utilizing algorithmic differentiation to efficiently compute chromatograms and parameter sensitivities <https://doi.org/10.1016/j.ces.2015.08.050>`_, Chemical Engineering Science, **139** (2016), 152–162.
-
 Additionally, to ensure reproducibility of your work, we recommend citing the zenodo doi corresponding to the specific CADET release that you used.
 
+Selected applications that demonstrate the capabilities and use-cases of CADET are highlighted in the `documentation <https://cadet.github.io>`_.
+
 Ongoing Development
 -------------------
 
@@ -79,7 +67,7 @@ We do our best to provide you with a stable API. However, CADET is actively deve
 Bugs
 ----
 
-Please report any bugs that you find `here <https://github.com/modsim/cadet/issues>`_. Or, even better, fork the repository on `GitHub <https://github.com/modsim/cadet>`_ and create a pull request (PR) with the fix. 
+Please report any bugs that you find `here <https://github.com/cadet/cadet-core/issues>`_. Or, even better, fork the repository on `GitHub <https://github.com/cadet/cadet-core>`_ and create a pull request (PR) with the fix. 
 
 Donations
 ---------
@@ -90,11 +78,11 @@ Donations
 License
 -------
 
-Released under GPL v3. License (see `LICENSE.txt <https://github.com/modsim/CADET/blob/master/LICENSE.txt>`_)::
+Released under GPL v3. License (see `LICENSE.txt <https://github.com/cadet/cadet-core/blob/master/LICENSE.txt>`_)::
 
 Acknowledgments
 ---------------
 
-Please refer to the `list of contributors <https://github.com/modsim/CADET/blob/master/CONTRIBUTORS.md>`_ who helped building and funding this project.
+Please refer to the `list of contributors <https://github.com/cadet/cadet-core/blob/master/CONTRIBUTORS.md>`_ who helped building and funding this project.
 
    Copyright (C) 2004-2024 CADET Authors

doc/index.rst

@@ -79,12 +79,30 @@ Donations
 Citing
 ------
 
-To cite CADET please use the following publication:
+Citing
+------------
+The development of CADET has been a collaborative effort, with multiple dedicated individuals contributing their expertise to create a powerful and versatile open-source software tool.
+Countless hours of hard work have been invested to provide the scientific community with a valuable resource.
+As an open-source project, CADET relies on the support and recognition from users and researchers to thrive.
+Therefore, we kindly ask that any publications or projects leveraging the capabilities of CADET acknowledge its creators and their contributions by citing an adequate selection of our publications.
+
+**General:**
+
+- Leweke, S.; von Lieres, E.: `Chromatography Analysis and Design Toolkit (CADET) <https://doi.org/10.1016/j.compchemeng.2018.02.025>`_, Computers and Chemical Engineering **113** (2018), 274–294.
+
+- von Lieres, E.; Andersson, J.: `A fast and accurate solver for the general rate model of column liquid chromatography <https://doi.org/10.1016/j.compchemeng.2010.03.008>`_, Computers and Chemical Engineering **34,8** (2010), 1180–1191.
+
+**Numerics:**
+
+- Breuer, J. M.; Leweke, S.; Schmölder, J.; Gassner, G.; von Lieres, E.: `Spatial discontinuous Galerkin spectral element method for a family of chromatography models in CADET <https://doi.org/10.1016/j.compchemeng.2023.108340>`_, Computers and Chemical Engineering **177** (2023), 108340.
+
+- Leweke, S.; von Lieres, E.: `Fast arbitrary order moments and arbitrary precision solution of the general rate model of column liquid chromatography with linear isotherm <http://dx.doi.org/10.1016/j.compchemeng.2015.09.009>`_, Computers and Chemical Engineering **84** (2016), 350–362.
+
+- Püttmann, A.; Schnittert, S.; Naumann, U.; von Lieres, E.: `Fast and accurate parameter sensitivities for the general rate model of column liquid chromatography <http://dx.doi.org/10.1016/j.compchemeng.2013.04.021>`_, Computers and Chemical Engineering **56** (2013), 46–57.
+
+Additionally, to ensure reproducibility of your work, we recommend citing the `zenodo doi <https://doi.org/10.5281/zenodo.8179015>`_ corresponding to the specific CADET release that you used.
 
-* Leweke, S.; von Lieres, E.: `Chromatography Analysis and Design Toolkit (CADET) <http://doi.org/10.1016/j.compchemeng.2018.02.025>`_, Computers and Chemical Engineering 113 (2018), 274–294.
-* Püttmann, A.; Schnittert, S.; Leweke, S.; von Lieres, E.: `Utilizing algorithmic differentiation to efficiently compute chromatograms and parameter sensitivities <http://doi.org/10.1016/j.ces.2015.08.050>`_, Chemical Engineering Science, 139 (2016), 152–162.
-* Püttmann, A.; Schnittert, S.; Naumann, U.; von Lieres, E.: `Fast and accurate parameter sensitivities for the general rate model of column liquid chromatography <http://doi.org/10.1016/j.compchemeng.2013.04.021>`_, Computers and Chemical Engineering 56,13 (2013), 46-57.
-* von Lieres, E.; Andersson, J.: `A fast and accurate solver for the general rate model of column liquid chromatography <http://doi.org/10.1016/j.compchemeng.2010.03.008>`_, Computers and Chemical Engineering 34,8 (2010), 1180–1191.
+Selected applications that demonstrate the capabilities and use-cases of CADET are highlighted `here <https://github.com/cadet/CADET-Core/tree/master/doc/publications.md>`_.
 
 Acknowledgments
 ---------------

doc/publications.md

@@ -0,0 +1,28 @@
+
+**General CADET-Core:**
+
+- Leweke, S.; von Lieres, E.: `Chromatography Analysis and Design Toolkit (CADET) <https://doi.org/10.1016/j.compchemeng.2018.02.025>`_, Computers and Chemical Engineering **113** (2018), 274–294.
+
+- von Lieres, E.; Andersson, J.: `A fast and accurate solver for the general rate model of column liquid chromatography <https://doi.org/10.1016/j.compchemeng.2010.03.008>`_, Computers and Chemical Engineering **34,8** (2010), 1180–1191.
+
+**CADET-Core numerics:**
+
+- Breuer, J. M.; Leweke, S.; Schmölder, J.; Gassner, G.; von Lieres, E.: `Spatial discontinuous Galerkin spectral element method for a family of chromatography models in CADET <https://doi.org/10.1016/j.compchemeng.2023.108340>`_, Computers and Chemical Engineering **177** (2023), 108340.
+
+- Leweke, S.; von Lieres, E.: `Fast arbitrary order moments and arbitrary precision solution of the general rate model of column liquid chromatography with linear isotherm <http://dx.doi.org/10.1016/j.compchemeng.2015.09.009>`_, Computers and Chemical Engineering **84** (2016), 350–362.
+
+- Püttmann, A.; Schnittert, S.; Naumann, U.; von Lieres, E.: `Fast and accurate parameter sensitivities for the general rate model of column liquid chromatography <http://dx.doi.org/10.1016/j.compchemeng.2013.04.021>`_, Computers and Chemical Engineering **56** (2013), 46–57.
+
+**Selected applications and use-cases of CADET-Core:**
+
+- Heymann, W.; Glaser, J.; Schlegel, F.; Johnson, W.; Rolandi, P.; von Lieres, E.: `Advanced score system and automated search strategies for parameter estimation in mechanistic chromatography modeling <https://doi.org/10.1016/j.chroma.2021.462693>`_, Journal of Chromatography A **1661** (2022): 462693.
+
+- He, Q.-L.; Leweke, S.; von Lieres, E.: `Efficient numerical simulation of simulated moving bed chromatography with a single-column solver <http://doi.org/10.1016/j.compchemeng.2017.12.022>`_, Computers and Chemical Engineering **111** (2018), 183–198.
+
+- Freier, L.; von Lieres, E.: `Robust multi-objective global optimization of stochastic processes with a case study in gradient elution chromatography <http://doi.org/10.1002/biot.201700257>`_, Biotechnology Journal **13,1** (2018), 1700257.
+
+- Freier, L.; von Lieres, E.: [Multi-objective global optimization (MOGO): `Algorithm and case study in gradient elution chromatography <http://dx.doi.org/10.1002/biot.201600613>`_, Biotechnology Journal **12,7** (2017), 1600613.
+
+- Diedrich, J.; Heymann, W.; Leweke, S.; Kunert, C.; Johnson, W.; Hunt, S.; Todd, B.; von Lieres, E.: `Multi-state steric mass-action model and case study on complex high loading behavior of mAb on ion exchange tentacle resin <https://doi.org/10.1016/j.chroma.2017.09.039>`_, Journal of Chromatography A **1525** (2017), 60–70.
+
+- Püttmann, A.; Schnittert, S.; Leweke, S.; von Lieres, E.: `Utilizing algorithmic differentiation to efficiently compute chromatograms and parameter sensitivities <https://doi.org/10.1016/j.ces.2015.08.050>`_, Chemical Engineering Science, **139** (2016), 152–162.