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helpful-resources.txt
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helpful-resources.txt
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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
===========
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!