#A poem for any biologist who has ventured into the world of scripting.
By: Anne A. Madden
>>>file = open(“Expected_Errors.txt”, ‘r’)
May I be so BOLD as to take a minute and discuss my current plight?
In my new job as a bioinformaticist, I can’t seem to get any code right.
Though I search for PERLs of wisdom from friends around the clock,
I still end every day wishing I could BASH my head in with a rock.
As much as I try and MUSCLE my way through every script and shell,
These MOTHUR F#@cking codes, files, and programs are straight out of hell.
Now people like MEGAN, my friend, tell me not to worry so,
But rather to enjoy scripting row upon row upon row.
But don’t start QIIMEing in with quips about the benefits found,
When USEARCH hard for the truth, and finally find something profound.
I’m not looking for a PRIMER on what joys I might miss,
Seriously, R you really willing to fight with me on this?
To take a step back, I do know I am not a GENEIOUS when it comes to computers,
In this area of my GALAXY, I was much better at finding male suitors.
I could find an ADONIS quicker than I can parse a dataset,
Though dating websites would suggest my older goals were harder met.
Yes, remember when my life involved PYTHONs and characters from a sitcom cast?
Back in the days when I played outside with nature, and science was a BLAST…
But speed up the time FASTA and FASTA to my position here,
And here I am ending my days feeling super AWK about my programming fear.
Now do you C what I mean, that my current status is sad?
My only solace is that one more cup of JAVA will make it seem not so bad.
Hopefully one day I will understand this world of developing a sequence processing pipeline,
But until then I shall just have to repeat the echo of the phrase: “It will all be just fine”
BOLD: Bar Code of Life Database
PERL: Programming language
MOTHUR: Clustering and alignment algorithm
QIIME: Pronounced “Chime” – pipeline for sequence processing
PRIMER: Primer checking/development software
BASH: Programming shell
BLAST: Search algorithm for sequence matching
FASTA: File format for sequences
PYTHON: Programming Language
R: Environment for data analysis
AWK: Programming language
GALAXY: Platform for sequence analysis
GENEIOUS: Platform for sequence analysis
ADONIS: Statistical test for community comparisons
JAVA: Programming language
C: Programming language
MEGAN: Metagenome Analyzer
USEARCH: Sequence analysis tool
MUSCLE: Multiple alignment tool