Madelaine Gogol

I am a Programmer Analyst II in the microarray group at Stowers Institute. I work on a variety of projects, including microarray design, web infrastructure, and data analysis for in-house spotted arrays, Agilent, and Affymetrix microarray platforms.

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

Links

Some of my favorite links:
UCSC Genome Browser
Galaxy
del.icio.us
ask metafilter
Google Desktop
php.net
Scopus
cl1p.net
BARF
Venny
vi graphical cheat sheet
Bioconductor
R graph gallery
Solexa google group
Flickr photos
Shell-fu

My Firefox Setup

My essential add-ons:
del.icio.us
ScrapBook
Tab Mix Plus
Web Developer

My essential Search Engines:
Google (duh) and Google desktop
delicious
MySQL
NCBI Global
NCBI Pubmed
Scopus
Wikipedia
php manual
Ask Metafilter
SGD

These two are by me:
GeneDB S. pombe
UCSC genome browser (yeast)
more search plugins

Scripts & Tips

Here's some R/linux/unix/programming-related tips and (not very well documented) scripts that I find handy.
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)
tips.tar.gz
scripts.tar.gz
Juice excel training worksheets

mcm at stowers dash institute dot org