Credits
-------

Genepidgin was written by Clint Howarth and Matthew Pearson, with recent updates made by Janet Gainer-Dewar. Many people have contributed to the project:

cleaner
=======

The design of ``genepidgin cleaner`` grew out of years of suggestions from many people, including annotators who have worked in Genome Annotation in the Microbial Sequencing Platform at the Broad Institute. It was implemented by Clint Howarth and Matthew Pearson.

Many people have contributed to the name cleaning logic, including: Lucia Alvarado-Balderrama¹, Sinead Chapman¹, Zehua Chen¹, Jonathan Goldberg¹, Sharvari Gujja¹, Clint Howarth¹, Chinnappa Kodira², Teena Mehta¹, Matthew Pearson¹, Narmada Shenoy¹, Tom Walk¹, Chandri Yandava¹, Qiandong Zeng¹, and the Autoannotate development team³.

¹ `Broad Institute <http://www.broadinstitute.org>`_
² `454 Life Sciences <http://www.454.com/>`_
³ `J. Craig Venter Institute <http://www.jcvi.org/>`_


compare
=======

``genepidgin compare`` was designed and implemented by Matthew Pearson.

It includes an open-source implementation of the `Damerau-Levenshtein distance`_ written by `Michael Homer`_.

.. _`Damerau-Levenshtein distance`: http://en.wikipedia.org/wiki/Damerau-Levenshtein_distance
.. _`Michael Homer`: http://mwh.geek.nz/2009/04/26/python-damerau-levenshtein-distance/

select
======

``genepidgin select`` was designed by Sharvari Gujja, Brian Haas, Clint Howarth, Matthew Pearson, and Qiandong Zeng. Clint Howarth implemented it, and Janet Gainer-Dewar has added features.

Special Thanks
==============

Finally, thanks to the `Autoannotate`_ development team at `JCVI`_, who were kind enough to share the source code of their naming utility with us.  Seeing how hard their institute worked to reformat names motivated us to release and document our own naming logic.

.. _`JCVI`: http//:www.jcvi.org
.. _`Autoannotate`: http://sourceforge.net/projects/prokfunautoanno/

Project Name History
====================

This project began life as BioName. It turns out that there already is a project named `Bioname`_. Though this BioName addresses a completely different problem, our goal is to help reduce name-related confusion. Thus we decided to change the name of our software toolkit to Pidgin. We retain the term BioName as an internal class name for source compatibility. We are aware that there is an IM chat client called `Pidgin`_, and even though it's completely unrelated to gene naming, some people found this confusing. This project is now ``Genepidgin``, and that's that.

We would like to take this opportunity to point out that naming is a challenging problem, on many levels. We apologize for any confusion.

.. _`Pidgin`: http://www.pidgin.im/
.. _`Bioname`: http://bioname.org