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Getting Genetics Done

Getting Things Done in Genetics & Bioinformatics Research
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At the moment, the world is obsessed with “Big Data” yet it sometimes seems that people who use this phrase don’t have a good grasp of its meaning.  Like most good buzz-words, “Big Data” sparks the idea of something grand and complicated, while sounding ordinary enough that listeners feel like they have an intuitive understanding of the concept.

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Author Stephen Turner

This is one of those things I picked up years ago while in graduate school that I just assumed everyone else already knew about. GNU screen is a great utility built-in to most Linux installations for remote session management. Typing 'screen' at the command line enters a new screen session.

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Author Stephen Turner

Jeff Leek, biostats professor at Johns Hopkins and instructor of the Coursera Data Analysis course, recently posted on Simly Statistics this list of awesome things other people accomplished in 2013 in genomics, statistics, and data science. At risk of sounding too meta , I'll say that this list itself is one of the awesome things that was put together in 2013.

Published
Author Stephen Turner

Boston-based startup Curoverse has announced $1.5 million in funding to develop and support the open-source Arvados platform for cloud-based bioinformatics & genomics data analysis. The Arvados platform was developed in George Church's lab by scientists and engineers led by Alexander Wait Zaranek, now scientific director at Curoverse.

Published
Author Stephen Turner

Obi Griffith over at Biostar put together this excellent cheat sheet for dealing with one-based and zero-based genomic coordinate systems. The cheat sheet visually explains the difference between zero and one-based coordinate systems, as well as how to indicate a position, SNP, range, or indel using both coordinate systems.

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Author Unknown

One of the most powerful tools you can learn to use in genomics research is a relational database system, such as MySQL.  These systems are fairly easy to setup and use, and provide users the ability to organize and manipulate data and statistical results with simple commands.  As a graduate student (during the height of GWAS), this single skill quickly turned me into an “expert”.

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Author Unknown

Manhattan plots have become the standard way to visualize results for genetic association studies, allowing the viewer to instantly see significant results in the rough context of their genomic position.  Manhattan plots are typically shown on a linear X-axis (although the circos package can be used for radial plots), and this is consistent with the linear representation of the genome in online genome browsers.