Open Bio* libraries

Miscellaneous work on Open Bioinformatics Libraries, including:

BioRuby

• BioRuby 1.5 release
  • Resolving issues and pull requests on https://github.com/bioruby/bioruby/
    • Pull Request #96 by Joachim is split into a new Biogem plugin bio-location-rdfize. http://rubygems.org/gems/bio-location-rdfize
    • Resolved https://github.com/bioruby/bioruby/pull/77 and https://github.com/bioruby/bioruby/issues/43
    • Resolved https://github.com/bioruby/bioruby/issues/75
  • Testing with Ruby 1.8.7, 1.9.3, 2.0.0, 2.1, trunk (2.2)
• Extra Biogem packages
  • bio-location-rdfize http://rubygems.org/gems/bio-location-rdfize
    • Bio::Location to RDF, based on Pull Request #96
  • bio-old-biofetch-emulator http://rubygems.org/gems/bio-old-biofetch-emulator
    • Emulates the behavior of Bio::Fetch with former BioRuby BioFetch server.
    • The BioRuby BioFetch server (http://bioruby.org/cgi-bin/biofetch.rb) have stopped for years and we have no hope to restart the server service.
    • With the bio-old-biofetch-emulator, when the URL is given to set up Bio::Fetch client object, the emulator intercepts all queries, and they are changed to fetch entries from TogoWS, KEGG REST API, NCBI E-Utilities, or GenomeNet (DBGET) depending on the database names in the queries.
    • Useful for migrating old codes
• BioRuby objects from/to RDF conversion
  • (planned, in progress) Bio::Sequence to RDF output based on https://github.com/dbcls/rdfsummit/tree/master/insdc2ttl

Biopython

• Issues resolved or pull requests merged:
  • GitHub issue tracker triage (e.g. closing already resolved issues)
  • Cope with UniProt format changes https://github.com/biopython/biopython/issues/369
  • CodonAlign updates https://github.com/biopython/biopython/pull/417
  • KEGG REST API https://github.com/biopython/biopython/pull/152
  • Fixed dead link https://github.com/biopython/biopython/issues/404
  • reStructuredText docstrings https://github.com/biopython/biopython/pull/376
  • PEP8 style conformance https://github.com/biopython/biopython/pull/414 https://github.com/biopython/biopython/pull/415 https://github.com/biopython/biopython/pull/417 https://github.com/biopython/biopython/pull/420 https://github.com/biopython/biopython/pull/422 https://github.com/biopython/biopython/pull/423 https://github.com/biopython/biopython/pull/427 (etc?)
  • BLAST+ wrapper update https://github.com/biopython/biopython/pull/328
  • BioSQL fix for mysql-connector-python v2 https://github.com/biopython/biopython/issues/370
  • Relative paths in sequence indexes https://github.com/biopython/biopython/pull/381
  • Split LaTeX file for Tutorial https://github.com/biopython/biopython/pull/419
  • MedLine parser fix for MESH terms https://github.com/biopython/biopython/issues/286
  • URL problem with hevea documentation https://github.com/biopython/biopython/pull/426
• Reviewed but not resolved:
  • Restriction Enzyme rewrite https://github.com/biopython/biopython/pull/268
  • NCBI Entrez elink https://github.com/biopython/biopython/issues/361
  • Python 3 fix for phyloXML output https://github.com/biopython/biopython/issues/368
  • Melting Temperatures https://github.com/biopython/biopython/pull/192
• In progress or planned:
  • FALDO RDF from locations https://github.com/biopython/biopython/pull/346
  • Merging pure Python SAM/BAM branch https://github.com/peterjc/biopython/tree/SamBam2014a

G-Links: ID conversion service

• http://link.g-language.org
  • Example: http://link.g-language.org/BRCA1_HUMAN
• Manuscript submitted! http://f1000research.com/articles/3-285/v1

G-language Genome Analysis Environment

• Version 1.9.0 relased! (14.Nov.14th) http://www.g-language.org/wiki/changelog
  • 2.5 yr since the previous release … (v.1.8.13, 11.Apr.29)
  • so many features, but rich statistical analysis features added especially during this hackathon
  • Key Feature: Summary function http://rest.g-language.org/help/summary
    • Produces statistical overview for given data or data set
    • For a single array or array reference:
      • Data is nominal: Shows boxplot of categories https://dl.dropboxusercontent.com/u/429864/uni-n.png
      • Data is numerical: Shows histogram of distribution https://dl.dropboxusercontent.com/u/429864/uni-c.png
    • For two arrays references:
      • Both is nominal: Shows cross table with Cramer's V https://dl.dropboxusercontent.com/u/429864/nvn.png
      • Either is nominal: Shows boxplot of categories and ANOVA https://dl.dropboxusercontent.com/u/429864/nvc.png
      • Both is numerical: Shows correlation matrix https://dl.dropboxusercontent.com/u/429864/multi-c.png
    • For more array references:
      • All data is numerical: Shows correlation matrix https://dl.dropboxusercontent.com/u/429864/multi-c.png