This little PDF is not a bad overview of assemblers and genome assembly for short-read technologies.
myExperiment makes it easy to find, use and share scientific workflows and other Research Objects, and to build communities.
Taverna is an open source and domain-independent Workflow Management System – a suite of tools used to design and execute scientific workflows and aid in silico experimentation.
This link is a great PDF of slides from a talk by Mark DePristo from the Broad.
Here are some nice lecture notes from a course about bioinformatics of high-throughput sequencing.
This is an interesting alternative to mathematica and matlab, implemented in python (+others). Graphing and math abilities look pretty advanced.
This is an interesting page showing world installations of next-gen sequencers on google maps.
This tool looks pretty nice for doing backups without much fuss.