Bioinformatics resources

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/

http://www.netgestalt.org/#2

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

MIT open course: http://ocw.mit.edu/courses/electrical-engineering-and-computer-science/6-00-introduction-to-computer-science-and-programming-fall-2008/video-lectures/lecture-11/

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/

mysql