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replaced whitepaper with paper DOI in README #167

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replaced whitepaper with paper DOI in README
orbeckst Sep 12, 2024
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Update README.rst
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44 changes: 30 additions & 14 deletions README.rst
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Expand Up @@ -8,34 +8,36 @@
Contents
========

This repository contains the source code for the MDAKits registry.
The registry hosts a list of MDAKits which it then both documents
and continually validate.
This repository contains the source code for the `MDAKits registry`_.

For more details about the MDAKit registry, see Section 4 of the
`MDAKit Whitepaper`_.
The registry hosts a list of MDAKits which it then both documents and
continually validates. For more details about the MDAKit registry, please see
the `MDAKit paper`_ in the section *The MDAKit registry*.

For detailed documentation and tutorials about MDAKits see the MDAKits site
https://mdakits.mdanalysis.org/


Creating a new MDAKit
=====================

The minimum specification for an MDAKit is defined under Section 3 of the
`MDAKit Whitepaper`_. To developers in creating best practices adhering
projects, a `cookiecutter`_ has been made available.
The minimum specification for an MDAKit is defined in the `MDAKit
paper`_ under *The MDAKit framework*. To developers in creating best
practices adhering projects, a `cookiecutter`_ has been made
available.


Adding a new MDAKit
===================

The registry is currently in development, the way by which new MDAKits
are added is likely to change significantly over time. If you have any
concerns or questions about the process, please reach out by raising an
issue!

Adding a new MDAKit involves making a PR against
this repository and adding a new `metadata`_ file within it's own
respective directory under `mdakits`.

*The registry is currently in development, the way by which new MDAKits are
added may change over time. If you have any concerns or questions about the
process, please reach out by raising an issue!*


License
=======
Expand All @@ -48,9 +50,23 @@ Acknowledgements

The development of this repository is supported by a grant from the Chan Zuckerberg Initiative under an EOSS4 award.

References
==========

1. Irfan Alibay, Lily Wang, Fiona Naughton, Ian Kenney, Jonathan Barnoud,
Richard J Gowers, and Oliver Beckstein. **MDAKits: A framework for
FAIR-compliant molecular simulation analysis.** In Meghann Agarwal, Chris
Calloway, and Dillon Niederhut, editors, *Proceedings of the 22nd Python in
Science Conference (SCIPY 2023)*, pages 76-84, Austin, TX, 2023. doi:
`10.25080/gerudo-f2bc6f59-00a`_.

.. _`MDAKits registry`: https://mdakits.mdanalysis.org/mdakits.html

.. _`metadata`: mdakits/template/metadata.yaml

.. _`MDAKit Whitepaper`: paper/whitepaper/MDAKits_whitepaper.pdf
.. _`MDAKit paper`: https://doi.org/10.25080/gerudo-f2bc6f59-00a

.. _`10.25080/gerudo-f2bc6f59-00a`: https://doi.org/10.25080/gerudo-f2bc6f59-00a

.. _`cookiecutter`: https://github.com/MDAnalysis/cookiecutter-mdakit

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