Added all of my GitLab repository, now I'm linking from there to this…

… place

extras/articles.md

@@ -1,3 +1,6 @@
 # Bioinformatics - Extra Resources
 
 # Articles
+1. [So you want to be a computational biologist?](http://www.nature.com/nbt/journal/v31/n11/full/nbt.2740.html) by Nick Loman and Mick Watson (2013).
+1. [A Quick Guide for Developing Effective Bioinformatics Programming Skills](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000589) by Joel Dudley and Atul Butte (2009).
+1. [Unix Philosophy](https://en.wikipedia.org/wiki/Unix_philosophy)

extras/free-books.md

@@ -1,3 +1,20 @@
 # Bioinformatics - Extra Resources
 
 # Free Books
+* [Molecular Biology of the Cell](https://www.ncbi.nlm.nih.gov/books/NBK21054/)
+* [An Introduction to Genetic Analysis](https://www.ncbi.nlm.nih.gov/books/NBK21766/)
+* [The GNU/Linux Command Line Interface (CLI)](http://linuxcommand.org/tlcl.php)
+* [Unix Grymoire](http://www.grymoire.com/)
+* [Algorithms and Data Structures](http://interactivepython.org/runestone/static/pythonds/index.html)
+* [Think like a Computer Scientist](http://interactivepython.org/runestone/static/thinkcspy/index.html)
+
+## Language Books
+* [Python](http://scipy.org/topical-software.html)
+  * [Interactive Py](http://interactivepython.org/runestone/static/pythonds/index.html)
+  * [Py For Biologists](http://pythonforbiologists.com/index.php/introduction-to-python-for-biologists/)
+* Perl
+  * [Perl 6](http://perl6intro.com/)
+  * [Unix and Perl for Biologists](http://korflab.ucdavis.edu/Unix_and_Perl/index.html)
+* [Haskell](http://learnyouahaskell.com/chapters)
+* [Julia](http://julialang.org/learning/) ([book](https://en.wikibooks.org/wiki/Introducing_Julia))
+* [Make](http://www.oreilly.com/openbook/make3/book/index.csp) pipelines

extras/free-courses.md

@@ -15,3 +15,53 @@ PH525.5x: Introduction to Bioconductor: annotation and analysis of genomes and g
 PH525.6x: High-performance computing for reproducible genomics
 
 PH525.7x: Case studies in functional genomics
+
+## Workshops and tutorials mostly:
+* [Data Carpentry](http://www.datacarpentry.org/lessons/)
+* [OpenHelix](http://www.openhelix.com/freeTutorials.cgi)
+* [BioStars](https://www.biostars.org/t/Tutorials/)
+* [GenomeSpace Recipes](http://recipes.genomespace.org/home)
+* [EMBL-EBI](https://www.ebi.ac.uk/training/online/course-list)
+* [UC SantaCruz Training](https://genome.ucsc.edu/training/index.html)
+* [UC Davis Workshops](http://bioinformatics.ucdavis.edu/training/documentation/)
+* [InsideDNA Tutorials](https://insidedna.me/tutorials)
+* [Stephen Turner's list](http://stephenturner.us/edu.html)
+* [Griffith's RNA-seq](https://github.com/griffithlab/rnaseq_tutorial/wiki)
+* [NCBI Tutorials](http://www.ncbi.nlm.nih.gov/home/learn.shtml)
+* [Homolog.us Tutorials](http://homolog.us/Tutorials/)
+
+  Try searching keywords like bioinformatics, biology, genomic, genetic, data analysis, data science, computer science, life science... in these websites:
+* [Coursera](https://www.coursera.org/)
+* [edX](https://www.edx.org/)
+* [MIT](http://ocw.mit.edu/courses)
+* [eBiomics](http://ebiomics.sdcinfo.com/)
+* [Khan Academy](http://www.khanacademy.org/)
+* [Udemy](http://www.udemy.com/)
+
+
+## Coding Courses and Tutorials
+* [Code Academy](https://www.codecademy.com/#!/exercises/0)
+* [Software Carpentry](http://software-carpentry.org/lessons/)
+* [Code Snipcademy](http://code.snipcademy.com)
+* [Udacity](https://www.udacity.com/)
+* [FreeCodeCamp](https://www.freecodecamp.com/)
+* Python
+  * [Matplotlib](http://www.loria.fr/~rougier/teaching/matplotlib/) - Plotting
+  * [Seaborn](https://web.stanford.edu/~mwaskom/software/seaborn/tutorial.html) - Plotting
+  * [Pandas](http://pandas.pydata.org/pandas-docs/stable/) - Data Analysis
+  * [Machine Learning](http://scikit-learn.org/stable/documentation.html) - Library
+  * [HTSeq](http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html) - Library
+* R
+  * [Quick-R](http://www.statmethods.net/)
+  * [Swirl](http://swirlstats.com/students.html)
+  * [ggplot2](http://ggplot2.org/)
+  * [R & NGS](http://manuals.bioinformatics.ucr.edu/home/ht-seq#TOC-SOAP)
+  * [Bioconductor Lib](http://bioconductor.org/help/workflows/)
+  * [RSeek Lib Search](http://www.rseek.org/)
+* Data Analysis Pipelines
+  * GNU Make
+    * [Dave Tang](http://davetang.org/muse/2015/05/31/learning-about-makefiles/)
+    * [Stat545](http://stat545.com/automation04_make-activity.html)
+    * [ZMJones](http://zmjones.com/make/)
+  * [NextFlow](http://www.nextflow.io/docs/latest/index.html)
+  * [SnakeMake](http://snakemake.bitbucket.org/snakemake-tutorial.html)

extras/other-resources.md

@@ -0,0 +1,53 @@
+# Handy Stuff
+* [UCSC FAQ](https://genome.ucsc.edu/FAQ/)
+* Rosalind [Glossary](http://rosalind.info/glossary/)
+* [Cheatsheets](http://overapi.com/)
+* [File Format Specifications](https://github.com/samtools/hts-specs)
+* [GATK](http://gatkforums.broadinstitute.org/gatk/categories)
+* [Genome Space](https://www.broadinstitute.org/scientific-community/science/projects/genomespace/genomespace)
+* [Writing your first academic paper](https://github.com/jtleek/firstpaper)
+* [Statistics for Biologists](http://www.nature.com/collections/qghhqm)
+
+# Forums Q&A
+* [BioStars](https://www.biostars.org/)
+* [SEQAnswers](http://seqanswers.com/)
+* [SEQanswers - Bioinformatics](http://seqanswers.com/forums/external.php?type=RSS2&forumids=18)
+* [Bioinformatics subreddit](https://www.reddit.com/r/bioinformatics/)
+* [Bio Databases subreddit](http://www.reddit.com/r/BioDatasets)
+* [Genomic subreddit](http://www.reddit.com/r/genomics)
+* [Biology Q&A](https://biology.stackexchange.com/)
+* [Unix and GNU/Linux Q&A](https://unix.stackexchange.com/)
+* [Code Q&A](http://stackoverflow.com/)
+* [Ion Community](http://ioncommunity.lifetechnologies.com/community/)
+* [LinuxQuestions](http://www.linuxquestions.org/questions/)
+
+# Wikis
+* [SEQAnswers](http://seqanswers.com/wiki/SEQanswers)
+* [GNU/Linux (Arch)Wiki](https://wiki.archlinux.org/)
+
+# Puzzles and Code Golf
+* [Code Golf](https://codegolf.stackexchange.com/)
+* [Project Euler](https://projecteuler.net/)
+* [Rosalind](http://rosalind.info/)
+* [Hacker Rank](https://www.hackerrank.com/domains/algorithms/warmup)
+
+# Other lists
+* [Bioinformatics Jobs](http://www.indeed.com/q-Bioinformatics-jobs.html)
+* [Biological Databases](https://en.wikipedia.org/wiki/List_of_biological_databases) (can't be up-to-date)
+* [Genomics Papers](https://github.com/jtleek/genomicspapers) by Leek Group
+* [Bioinformatics.org Educational Services](http://www.bioinformatics.org/wiki/Educational_services)
+* [ISCB courses](http://www.iscb.org/iscb-degree-certificate-programs)
+* Learning Programming Languages [[1]](http://hackr.io/) [[2]](https://github.com/vhf/free-programming-books)
+* Software
+  * [bio-tools.org](https://bio-tools.org/)
+  * [CCB at JHU](http://ccb.jhu.edu/software.shtml)
+  * [Galaxy Toolshed](https://toolshed.g2.bx.psu.edu/)
+  * [OMICtools](http://omictools.com/about)
+  * [Sanger's Isntitute list](http://www.sanger.ac.uk/science/tools)
+
+# Illegal resources [you should avoid](http://www.sciencemag.org/news/2016/04/whos-downloading-pirated-papers-everyone)
+* Sci-Hub
+* LibGen
+* Bookfi
+
+**And always, enjoy [open culture](http://www.openculture.com/)**

extras/paid-books.md

@@ -1,3 +1,7 @@
 # Bioinformatics - Extra Resources
 
 # Paid Books
+* Biological Sequence Analysis (R. Durbin et al)
+* Bioinformatics and Functional Genomics (J. Pevsner)
+* BioInfoBook [Figures](http://bioinfbook.org/php/powerpoints)
+* [Bioinformatic Algorithms](http://bioinformaticsalgorithms.com/)

extras/softwares.md

@@ -0,0 +1,55 @@
+# Bioinformatics - Extra Resources
+
+# Software Documentation
+* [Circos](http://circos.ca/documentation/course/)
+* [OpenGene Libraries](https://github.com/OpenGene)
+* [GATK Tools](https://www.broadinstitute.org/gatk/guide/tooldocs/index)
+* [ADAM](http://bdgenomics.org/) Big-Data Genomics
+* [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
+* samtools 1:[BioBits'](http://biobits.org/samtools_primer.html) 2:[DaveTang's](https://github.com/davetang/learning_bam_file) 3:[YanhuiFan's](https://felixfan.github.io/bam-sam/) 4:[BinaryFlags](https://broadinstitute.github.io/picard/explain-flags.html)
+* [bcftools](https://samtools.github.io/bcftools/howtos/variant-calling.html) 1:[GATK](http://gatkforums.broadinstitute.org/gatk/discussion/1268/what-is-a-vcf-and-how-should-i-interpret-it) 2:[DaveTang's](https://github.com/davetang/learning_vcf_file) 3:[Paper](https://www.researchgate.net/publication/230658044_A_beginners_guide_to_SNP_calling_from_high-Throughput_DNA-sequencing_data)
+* bedtools 1:[Quinlan](http://quinlanlab.org/tutorials/bedtools/bedtools.html) 2:[YanhuiFan's](https://felixfan.github.io/bedtools/)
+* BWA
+* bowtie2
+* [Tuxedo Suite](http://cole-trapnell-lab.github.io/cufflinks/) 1:[YanhuiFan's](http://felixfan.github.io/tophat-cufflinks/)
+* [bedops](https://bedops.readthedocs.org/en/latest/content/usage-examples.html)
+* [picard](http://broadinstitute.github.io/picard/)
+* [jvarkit](https://github.com/lindenb/jvarkit)
+* [Exomiser](http://www.sanger.ac.uk/science/tools/exomiser) disease causing variants
+* [PopSV](https://github.com/jmonlong/PopSV) structural variants
+* [Silva](http://compbio.cs.toronto.edu/silva/) silent mutations
+* [Variant Effect Predictor](http://www.ensembl.org/info/docs/tools/vep/index.html)
+* [ANNOVAR](http://annovar.openbioinformatics.org/en/latest/)
+* [BioGPS](http://biogps.org/help/)
+* [ABySS](http://sjackman.ca/abyss-activity/)
+* [GEMINI](https://gemini.readthedocs.io/en/latest/) annotation db
+* Graphical User Interface (GUI) apps
+  * [Integrative Genomics Viewer (IGV)](https://www.broadinstitute.org/software/igv/)
+  * [NCBI Genome Workbench](https://www.ncbi.nlm.nih.gov/tools/gbench/)
+  * [Savant](http://genomesavant.com/p/savant/index)
+  * [JBrowse](http://jbrowse.org/)
+
+# Other Non-specific Tools
+* [Atom](http://atom.io/) modern text editor
+* [Reference Manager](https://en.wikipedia.org/wiki/Comparison_of_reference_management_software)
+* [Git](https://git-scm.com/) Version Control
+  * [HowTo Guide](https://githowto.com/)
+  * [Try Online](https://try.github.io/)
+  * [Pro Book](https://progit.org/)
+  * [Short Videos](https://git-scm.com/videos)
+  * [Start Contributing Guide](https://about.gitlab.com/2016/06/16/fearless-contribution-a-guide-for-first-timers/)
+* [LaTeX](https://latex-project.org/intro.html)
+  * [Overleaf](http://www.overleaf.com/) write collaboratively
+* [Markdown](http://daringfireball.net/projects/markdown/)
+  * [Here](http://markdown-here.com/)
+* RegEx [Generator](http://www.regexr.com/)
+* [Plotly](https://plot.ly/)
+* [Small (bioinformatic) Tools Manifesto](https://github.com/pjotrp/bioinformatics)
+* [Terminal Multiplexer](https://robots.thoughtbot.com/a-tmux-crash-course)
+* [ZSH](http://ohmyz.sh/)
+* [ShellCheck your scripts](http://www.shellcheck.net/)
+* Writing
+    * [Correct your Grammar](https://www.grammarly.com/)
+    * [Look-up word by its meaning](http://www.onelook.com/reverse-dictionary.shtml)
+    * google translate, obviusly.
+* [Introduction to HTML](https://developer.mozilla.org/en-US/docs/Web/Guide/HTML/Introduction)