Thoughts on biology, genomics, and the ongoing threat to humanity from the bogus use of bioinformatics acronyms, by Keith Bradnam
These slides are adapted from a talk I gave at a Galaxy training workshop this week. This workshop is organized and taught by the UC Davis Bioinformatics Core. More details about this workshop are available online. If you want to know what Galaxy is…well that's one of the 13 questions!
I have an extra copy of the fantastic Bioinformatics Data Skills book by Vince Buffalo (who you should all be following on twitter at @vsbuffalo). I've come up with a fun little competition to let someone have a chance of winning this signed copy.
All you have to do is write a tweet that includes the #ACGT hashtag (so I can track all of the answers), which provides the following information:
Name a useful bioinformatics data skill
The winner will be chosen randomly — hopefully by a powerful scripted solution that Vince will help me with — in two weeks time. I will post details of any interesting (or funny) suggestions that you come up with on this site. The full details are below.
I came across this disturbing image on the web today. Warning, may cause offense:
Click to enlarge
Even more disturbing was the text that accompanied the image, text that appears on Microsoft Research's flickr account (emphasis mine):
The Microsoft Biology Initiative includes several Microsoft biology tools that enable biology and bioinformatics researchers to be more productive in making scientific discoveries. One such tool, the Microsoft Research Biology Extension for Excel, displays the contents of a FASTA file containing an Influenza A virus sequence. By importing FASTA data into Excel, researchers are better able to visualize and analyze information.
The point at which you want to import FASTA files into Excel is the point at which you should probably think about quitting bioinformatics.
A new article in The Scientist magazine by Jeffrey M. Perkel shares some coding advice from Cole Trapnell, C. Titus Brown, and Vince Buffalo (I interviewed Vince in my last blog post). It is a great article, and worth a look. I particularly enjoyed this piece of advice (something that is not mentioned enough):
Treat data as "read-only"
Use an abundance of caution when working with your hard-won data, Buffalo says. For instance, “treat data as read-only.” In other words, don’t work with original copies of the data, make working copies instead. “If you have the data in an Excel spreadsheet and you make a change, that original data is gone forever,” he says.
I have seen too many students double click on FASTA, GFF, and other large bioinformatics text files and end up 'viewing' them in some inappropriate program (including Microsoft Word). If you want to view text data, use a text viewer (such as less).