Sabin Katila

Bioinformatician, Computational Biologist, Programmer (and amateur wood worker) /linkedin/

List of pages I find useful

Programming/Database/Linux

• Database
  • Neo4j
  • Cypher Query Language
  • sqlite documentation
• Linux
  • kernel doc
  • memory management
  • more memory
  • [biolinux] (http://environmentalomics.org/bio-linux/)
  • [biolinux packages] (http://environmentalomics.org/bio-linux-software-list/)
• Python
  • docs
  • C API
• C
  • GNU C Reference Manual
  • glibc manual
  • glibc wiki
  • glib - gnome dev refrence manual
  • setjmp.h/wikipedia
  • setjmp.h/gnu.org
• References/Tutorials
  • Markdowns
  • samtools reference
• Tools
  • ipython-sql
  • jupyter-c

  • jupyter_contrib_nbextensions

    This requires a bit of extra work in order to get a nice extension table in the notebook itself.

      pip install jupyter_contrib_nbextensions
    		
      jupyter contrib nbextension install --user
    		
      pip install jupyter_nbextensions_configurator
    		
      jupyter nbextensions_configurator enable
    

• Wood Working
  • Wood Working for Mere Mortals Writing code is fun but, carving a bookshelf by yourself can be just as fun (when it works out).

Bioinformatics

• Graph
  • Cytoscape
  • reactome
  • UCSC Gene interaction pathways from curated database and text-mining
  • UCSC Gene Pathways interaction graph user guide
• Genome
  • UCSC Genome Browser
  • NCBI Genome
  • 100 Genome
• Online Tools
  • NCBI BLAST
  • UCSC BLAT
  • UCSC Table Browser
  • Galaxy
  • EBI Tools
  • Gene games
• Downloadable Tools
  • Clustal
  • MrBayes
  • samtools/htslib
  • samtools/github
  • Mega
  • Muscle
• Bulk Data

  • 1000 Genome

    ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/pilot_data

Extras

• git book
• The C Programming Language - K&R wikipedia page

Everything else

For more details see www.sabink.org