operation system: google Bio-liunx you will find it and you can install it for free. If you use mac, you may consider to have a dual booting system or use a virtual machine. http://nebc.nerc.ac.uk/tools/bio-linux/bio-linux-7-info
websites:
GUI informatics tools:(non-programmers)
Galaxy http://galaxyproject.org/
ChIP-seq tools based on Galaxy developed by shirley Liu in harvard Cisgenome http://cistrome.dfci.harvard.edu/Cistrome/Cistrome_Project.html
Genome space http://www.genomespace.org/ if you really do not want to learn how to program, use it.
SeqMonk http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/ it is a great tool to analysis ChIP-seq, RNA-seq, Hi-C data
and can generate beautiful graphs. sometimes I am just too lazy to program by myself :) why not use the existing tools?
you can use it as a local Genome browser, or you can try IGV for an alternative http://www.broadinstitute.org/igv/
resources:
NCBI GEO datasets: http://www.ncbi.nlm.nih.gov/
Cancer Genome project http://www.sanger.ac.uk/genetics/CGP/
Cancer mutations http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/
cBio Cancer Genomics Portal http://www.cbioportal.org/public-portal/
Roadmap epigenetics http://roadmapepigenomics.org/
1000 genome http://www.1000genomes.org/
David pathway analysis http://david.abcc.ncifcrf.gov/
KEGG pathway analysis http://www.genome.jp/kegg/
free online courses https://www.coursera.org/ I took several python classes there, great!
I recommend the following courses for you, take them in order. You may have missed the class, but you can still log in and
watch the videos.
Learn to Program: The Fundamentals
Learn to Program: Crafting Quality Code
Introduction to Systematic Program Design
google python course: https://developers.google.com/edu/python/
If you use R http://www.r-project.org/ ,Bioconductor is based on R http://www.bioconductor.org/, there are many packages there also, just take time to learn.
check materials here http://www.bioconductor.org/help/course-materials/
SeqAnswer http://seqanswers.com/ good place to ask questions and get update of the current sequencing trend.
linux command line based for sequencing data manipulation (try to switch to linux, I am sure you will love it:) :
Samtools: http://samtools.sourceforge.net/
Bedtools :http://bedtools.readthedocs.org/en/latest/
Genometools: http://genometools.org/index.html
simple bioinformatics script http://code.google.com/p/bpbio/
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