[BioRuby] A new plugin: BioRuby UCSC API
MISHIMA, Hiroyuki
missy at be.to
Fri Apr 22 02:22:49 UTC 2011
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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