references.rst

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 <citations-using-duecredit>` 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 using Duecredit

Citations can be automatically generated using duecredit, depending on the packages used. Duecredit is easy to install via pip. Simply type:

pip install duecredit

duecredit will remain an optional dependency, i.e. any code using MDAnalysis will work correctly even without duecredit installed.

A list of citations for yourscript.py can be obtained using simple commands.

cd /path/to/yourmodule
python -m duecredit yourscript.py

or set the environment variable :envvar:`DUECREDIT_ENABLE`

DUECREDIT-ENABLE=yes python yourscript.py

Once the citations have been extracted (to a hidden file in the current directory), you can use the :program:`duecredit` program to export them to different formats. For example, one can display them in BibTeX format, using:

duecredit summary --format=bibtex

Please cite your use of MDAnalysis and the packages and algorithms that it uses. Thanks!

.. bibliography:: references.bib