Fierer Lab

Exploring the structure and function of microbial communities

Expected Errors

#A poem for any biologist who has ventured into the world of scripting.

By: Anne A. Madden

>>>file = open(“Expected_Errors.txt”, ‘r’)

>>>print

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”

 

>>>file.close()

~~~~~~~~~Poem Dictionary~~~~~~~~~

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

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