[BioRuby] A new plugin: BioRuby UCSC API

[Pjotr Prins]

Great stuff :)

On Fri, Apr 22, 2011 at 11:22:49AM +0900, 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
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