[BioRuby] A new plugin: BioRuby UCSC API

[Raoul Bonnal]

this is a great plugin.

Well done Hiro.
We need to update the wiki to make a list of active plugins new etc...


On 22/apr/2011, at 04.22, MISHIMA, Hiroyuki wrote:

> Hi all,
> 
> I uploaded a new BioRuby plugin 'bio-ucsc-api' to RubyGems.org.
> 
> RubyGem:
> https://rubygems.org/gems/bio-ucsc-api
> 
> GitHub:
> https://github.com/misshie/bioruby-ucsc-api
> 
> GitHub-Issues:
> http://github.com/misshie/bioruby-ucsc-api/issues
> 
> BioRuby UCSC API is a API for the UCSC genome browser database. The
> design is based on Ruby-Ensembl-API and Ruby-UCSC-API by Francesco
> Strozzi and Jan Aerts.
> 
> Features of Bioruby UCSC API is the followings:
> * Designed as a BioRuby plugin
> * Using ActiveRecord as an O/R mapping framework
> * Using the Bin index system to improve query performance
> * Automatic conversion of "1-based full-closed intervals" to internal
> "0-based half-closed intervals" (see also bioruby-genomic-interval)
> * Supporting non-official MySql hosts (e.g. local servers)
> * Using Rspec for the testing framework
> * Trying to support whole hg19 and hg18 databases.
> 
> Current version is still experimental. I have implemented only tables
> that I need to use now. Comments, suggestions, and requests are welcome.
> 
> Sincerely yours,
> Hiro.
> -- 
> MISHIMA, Hiroyuki, DDS, Ph.D.
> COE Research Fellow
> Department of Human Genetics
> Nagasaki University Graduate School of Biomedical Sciences
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby

Raoul Jean Pierre Bonnal
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