UTGB (University of Tokyo Genome Browser) Toolkit is an open-source software for developing personalized genome browsers that work in web browsers.
Thanks for the list of good genome browsers. But if someone is looking to do some sort of coding/programming stuff and implement/add in any pipeline then GBrowse is there for the rescue. GBrowse is a combination of database and interactive web pages for manipulating and displaying annotations on genomes.
Find more at GBrowse wiki page http://gmod.org/wiki/GBrowse
Molecular biology for computer scientists
The Institute of Arable Crop Research Beginner's Guide to Molecular Biology http://www.rothamsted.ac.uk/notebook/index.php
The newbie bioinformatician can learn the basics at http://www.bioinformatics.nl/webportal/background/techniques.html
Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003326