replaced whitepaper with paper DOI in README (#167)

* replaced whitepaper with paper DOI in README
   - fix #87
   - some more README clean-up

---------

Co-authored-by: Fiona Naughton <fiona@mdanalysis.org>

Author: orbeckst

README.rst

@@ -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
 =======
@@ -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