From d37f87b9db93881c925848a19b6db7c63fb9e6f2 Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Mon, 8 Oct 2018 17:13:09 -0700 Subject: [PATCH] fixed Gowers2016 reference (#2094) - fix #2092 - also added explanation why we ask for both citations - references page is again in sync with https://www.mdanalysis.org/pages/citations/ - added note/link at the top to the duecredit section --- .../source/documentation_pages/references.rst | 24 +++++++++++++++++-- 1 file changed, 22 insertions(+), 2 deletions(-) diff --git a/package/doc/sphinx/source/documentation_pages/references.rst b/package/doc/sphinx/source/documentation_pages/references.rst index c80c8a794b3..aa6f0cc484c 100644 --- a/package/doc/sphinx/source/documentation_pages/references.rst +++ b/package/doc/sphinx/source/documentation_pages/references.rst @@ -12,6 +12,16 @@ References ************ +MDAnalysis and the included algorithms are scientific software that +are described in academic publications. **Please cite these papers when you use +MDAnalysis in published work.** + +It is possible to :ref:`automatically generate a list of references +` for any program that uses +MDAnalysis. This list (in common reference manager formats) contains +the citations associated with the specific algorithms and libraries +that were used in the program. + Citations for the whole MDAnalysis library ========================================== @@ -19,6 +29,14 @@ Citations for the whole MDAnalysis library When using MDAnalysis in published work, please cite [Michaud-Agrawal2011]_ and [Gowers2016]_. +(We are currently asking you to cite *both* papers if at all possible +because the 2016 paper describes many updates to the original 2011 +paper and neither paper on its own provides a comprehensive +description of the library. We will publish a complete self-contained +paper with the upcoming 1.0 release of MDAnalysis, which will then +supersede these two citations.) + + .. [Michaud-Agrawal2011] N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. *J. Comput. Chem.* **32** (2011), @@ -28,7 +46,7 @@ When using MDAnalysis in published work, please cite Melo, S. L. Seyler, D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. `MDAnalysis: A Python package for the rapid analysis of molecular dynamics simulations`_. In S. Benthall and S. Rostrup, editors, - *Proceedings of the 15th Python in Science Conference*, pages 102 – 109, + *Proceedings of the 15th Python in Science Conference*, pages 98-105, Austin, TX, 2016. SciPy. .. _`10.1002/jcc.21787`: http://dx.doi.org/10.1002/jcc.21787 @@ -36,7 +54,7 @@ When using MDAnalysis in published work, please cite .. _`MDAnalysis: A Python package for the rapid analysis of molecular dynamics simulations`: http://conference.scipy.org/proceedings/scipy2016/oliver_beckstein.html - + .. _references-components: @@ -112,6 +130,8 @@ If you use the streamline visualization in .. _`10.1039/c3fd00145h`: https://doi.org/10.1039/c3fd00145h +.. _citations-using-duecredit: + Citations using Duecredit =========================