Madelaine Gogol

I am a Programmer Analyst II in the Computational Biology group at Stowers Institute. I work on a variety of projects in collaboration with people at the institute, including analyzing high-throughput sequencing data (mostly RNA-seq, ChIP-seq) and occasional microarray data.

Tips

Here's some good tips on being a computational biologist. I put my approaches in parentheses.

My favorite tips:

• Save everything in text files
• Learn the art of naming files & directories (sensible, short, no spaces or other weird characters)
• Learn a scripting language (perl)
• Learn a programmable stats package (R)
• Learn to use command-line plotting (R)
• Learn a real text editor (vi)
• Automate (mostly) everything
• Beware of hacking off the shelf software

I would also add

• Develop your searching skills (Google desktop, grep, windows grep, find, scopus)
• Learn useful key commands
• Leave notes for yourself and others in code and in directories
• Don't fear learning curves (too much)
• Graph paper is your friend when thinking in genomic space
• Check your assumptions

Links

UCSC Genome Browser
Galaxy
ask metafilter
Scopus
cl1p.net
BARF
Venny
vi graphical cheat sheet
Bioconductor
R graph gallery
Flickr photos
Shell-fu
Bio star
seqanswers
stackoverflow
google+
LinkedIn

Scripts & Tips

Here's some tips and scripts. Warning, I am a fan of sharing my ugly code.
github (I am sort of new to this...)
R plot layout cheat sheet
RMySQL and other R database connections (modified from a local wiki page)
Venn diagrams in and out of R (modified from a local wiki page)

mcm at stowers dot org