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37 changes: 10 additions & 27 deletions pages/citations.md
Original file line number Diff line number Diff line change
Expand Up @@ -15,18 +15,9 @@ manager formats) contains the citations associated with the specific
algorithms and libraries that were used in the program.



## MDAnalysis library ##

When using MDAnalysis in published work, please cite the following two
papers.

(We are 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.)
To properly credit MDAnalysis, please cite both of the following papers. The 2016 paper details significant updates to the 2011 paper, and together they provide a comprehensive description of the library.

* <a name="Gowers2016"></a>R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy,
M. N. Melo, S. L. Seyler, D. L. Dotson, J. Domanski, S. Buchoux,
Expand All @@ -53,7 +44,7 @@ two citations.)
## Powered by MDAnalysis
[![Powered by MDAnalysis](https://img.shields.io/badge/powered%20by-MDAnalysis-orange.svg?logoWidth=16&logo=data:image/x-icon;base64,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)](https://www.mdanalysis.org)

We appreciate it if you display our badge in your projects that use MDAnalysis. You can use the embed code below that suits your markup:
If you use MDAnalysis in your projects, **we encourage you to display our badge**. You can use the embed code below that suits your markup:

<details>
<summary>Markdown</summary>
Expand Down Expand Up @@ -87,22 +78,14 @@ We appreciate it if you display our badge in your projects that use MDAnalysis.

## <a name="IncludedAlgorithms"></a>Included algorithms ##

The full list of [references for included
algorithms]({{site.pypi.docs}}/documentation_pages/references.html#citations-for-included-algorithms-and-modules)
is maintained and kept up-to-date as part of the documentation.
The full list of citations for [included algorithms]({{site.pypi.docs}}/documentation_pages/references.html#citations-for-included-algorithms-and-modules) is maintained in our documentation and updated regularly.

## Acknowledgements

MDAnalysis was originally inspired by the Schulten Group's
[MDTools](http://www.ks.uiuc.edu/Development/MDTools/) for Python, and the DCD
reading code is derived from VMD's
[catdcd](http://www.ks.uiuc.edu/Development/MDTools/catdcd/). MDAnalysis is GPL
licensed, except for some 3rd party code that is included under GPL-compatible
licenses; for instance the dcd reading code is under the [UIUC Open Source
Licence](http://www.ks.uiuc.edu/Development/MDTools/catdcd/license.html). See
the files AUTHORS and LICENSE in the distribution for details.

The **MDAnalysis 'Atom' Logo** was designed by [**Christian
Beckstein**](https://www.linkedin.com/in/beckstein/) and is licensed
under a [Creative Commons Attribution-NoDerivs 3.0 Unported
License](http://creativecommons.org/licenses/by-nd/3.0/).
MDAnalysis was inspired by the Schulten Group’s [MDTools](http://www.ks.uiuc.edu/Development/MDTools/) for Python.

The DCD reading code originates from VMD’s [catdcd](http://www.ks.uiuc.edu/Development/MDTools/catdcd/).

MDAnalysis is released under the [LGPL](https://www.gnu.org/licenses/lgpl-3.0.html) license, with some third-party code under LGPL-compatible licenses. For instance, the DCD reading code is licensed under the [UIUC Open Source Licence](http://www.ks.uiuc.edu/Development/MDTools/catdcd/license.html). See the files [AUTHORS](https://github.com/MDAnalysis/mdanalysis/blob/develop/package/AUTHORS) and [LICENSE](https://github.com/MDAnalysis/mdanalysis/blob/develop/package/LICENSE) in the distribution for details.

The **MDAnalysis 'Atom' Logo** was designed by [Christian Beckstein](https://www.linkedin.com/in/beckstein/). NumFOCUS as the fiscal sponsor of MDAnalysis holds all rights on the logo (see [branding/logos/LICENSE](https://github.com/MDAnalysis/branding/blob/main/logos/LICENSE)).
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