Best website i have come across in Bioinformatics / Computational Biology / Genomics / Transcriptomics / Proteomics

Proteogenomics Labs : Ruggles Lab

Bestie Proteomics blog from Ben Orsburn

If you are interested in learning and working on Bioinformatics technology and need a tutorial then this will be a great place to explore yourself: Bioinformatics Review  

Plotting in R for Biologists is a beginner course in data analysis and plotting with R, designed for biologists as a starting point for plotting your own data.Interested in Plotting figures for Publications, Presentations, etc : Plotting in R for Biologist & Blog

Writing for Journals, What makes a great journal paper? : Elsevier interactive course and lecture

Expression Atlas update—an integrated database of gene and protein expression in humans, animals and plants: Article & Database webpage

The IsoFunc is a tool for assigning function to the Human Protein-Coding Splice Variants (PCSVs). Database webpage

Discovery @ Bioware: This server contains several tools for short linear motif (SLiM) discovery, peptide characterisation and related analyses of proteomics data.

Newbie its for you : Introduction to Computational Molecular Biology complete material avialable.

Mass spectrometry based proteomics search engine (Free for academic users)
Comet,
PatternLab software suite
X!Tandem search engine
MaxQuant software suite
ProteinProspector search tools
Sashimi TPP project
ProteoWizard library & tools
OpenMS library & tools
Crux project
LabKey project
MSToolkit data parsing library
UW Proteomics Resource
ReAdW Thermo mzXML converter


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