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Helpful resources
=================

Learning Python
---------------

* Python for Biologists: http://pythonforbiologists.com/

* `Practical Computing for Biologists <http://practicalcomputing.org/>`__

  This is a highly recommended book for people looking for a systematic
  presentation on shell scripting, programming, UNIX, etc.

Shell tutorials and references
------------------------------

https://github.com/JorySchossau/shell

http://explainshell.com/

* `Biostar <http://biostars.org>`__

  A high quality question & answer Web site.

* `SEQanswers <http://seqanswers.com/>`__

  A discussion and information site for next-generation sequencing.

* `Software Carpentry lessons <http://software-carpentry.org/4_0/index.html>`__

  A large number of open and reusable tutorials on the shell, programming,
  version control, etc.

Additional Web sites
--------------------

The NGS course tutorials: http://ged.msu.edu/angus/tutorials-2013/

UW Seattle "zero entry" workshop: http://2013-uw-zero-entry.readthedocs.org/

Recommended books and other resources
-------------------------------------

* `Practical Computing for Biologists <http://practicalcomputing.org/>`__

  This is a highly recommended book for people looking for a systematic
  presentation on shell scripting, programming, UNIX, etc.

Computing and Data
------------------

* `A Quick Guide to Organizing Computational Biology Projects <http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000424>`__, Noble, PLoS Comp Biology, 2009.

* `Willingness to Share Research Data Is Related to the Strength of the Evidence and the Quality of Reporting of Statistical Results <http://software-carpentry.org/blog/2012/05/the-most-important-scientific-result-published-in-the-last-year.html>`__, Wicherts et al., PLoS One, 2011.

* `Got replicability? <http://econjwatch.org/articles/got-replicability-the-journal-of-money-credit-and-banking-archive>`__, McCullough, Economics in Practice, 2007.

Also see this great pair of blog posts on `organizing projects <http://nicercode.github.io/blog/2013-04-05-projects/>`__ and `research workflow <http://carlboettiger.info/2012/05/06/research-workflow.html>`__.

Other Links
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Humor
-----

* `Data Sharing and Management Snafu in 3 Short Acts <http://www.youtube.com/watch?v=N2zK3sAtr-4&feature=youtu.be>`__

Blogs
-----

* http://www.genomesunzipped.org/

  Genomes Unzipped.

* http://ivory.idyll.org/blog/

  Titus's blog.

* http://bcbio.wordpress.com/

  Blue Collar Bioinformatics

* http://massgenomics.org/

  Mass Genomics

* http://blog.nextgenetics.net/

  Next Genetics

* http://gettinggeneticsdone.blogspot.com/

  Getting Genetics Done

* http://omicsomics.blogspot.com/

  Omics! Omics!