[BioRuby] BaseSpace Ruby SDK Official Release Announcement

[Pjotr Prins]

And in that vein, I suggest every Ruby developer to read Will's
RDFization of data sources:

  http://gsocsemantic.wordpress.com/2013/08/05/bio-publisci/

and Zuhao's wrapping of Vega visualisation:

  http://wanzuhao.com/posts/how-to-create-a-scale-using-plotrb/

For some, Alberto's Weka wrapper could be of interest too and Monica's gene
predictions. All listed on http://biogems.info/

We are having a very good Google Summer of Code!

Pj.

On Tue, Aug 06, 2013 at 03:13:58PM +0900, Toshiaki Katayama wrote:
> Hi all,
> 
> As described by Joachim and in his blog at http://joachimbaran.wordpress.com/2013/08/05/basespace-ruby-sdk/ this SDK enables Ruby developers to create and publish your app for the BaseSpace.
> 
> My original motivation to push this project was not a vender lock-in, of course. For preparation of my BOSC presentation on BioRuby update this year http://www.open-bio.org/bosc2013/day1/BOSC2013_BioRuby_Update_-_Toshiaki_Katayama.pdf I started interviews with some Biogem developers (which will be published on the BioRuby web site in the near future, stay tuned ;).
> 
> Through those interviews, I learnt that many unique NGS packages are already available for BioRuby/Biogem users. However to gain many users for them is an another problem even though the functionality and quality of those packages are great. On the other hand, large part of current NGS data are produced by Illumina's instruments and users of them will need applications to analyze the data by one-click especially when sequencing will become commodity. Therefore, if Biogem developers also wrap their lib/app for the BaseSpace, it will raise mutual benefits.
> 
> Enjoy!
> 
> Joachim, congratulations and thank you for all your efforts to make this handover completed!
> 
> Cheers,
> Toshiaki Katayama
> 
> On 2013/08/06, at 9:08, Joachim Baran <joachim.baran at gmail.com> wrote:
> 
> > Hello BioRuby Community,
> > 
> >  We are proud to announce the first official release of BaseSpace Ruby SDK for Illumina?s BaseSpace genomics cloud computing platform.
> > 
> >  BaseSpace Ruby SDK can be used in the development of BaseSpace Apps as well as for creating next-gen sequencing data analysis workflows. The SDK is freely available under an open-source license as Ruby gem/Biogem that provides an easy-to-use Ruby environment for interacting with the BaseSpace cloud.
> > 
> >  We present hands-on examples of BaseSpace Ruby SDK that tackle authentication and working with privileges, browsing data, accessing files in the cloud, querying BAM- and VCF-files, and uploading analysis results into the BaseSpace cloud. An extensive reference documentation covers all of the SDK?s classes, their methods and parameters.
> > 
> >  BaseSpace Ruby SDK integrates seamlessly into BioRuby projects and works well with other Biogems. It is also compatible with the recently released Ruby 2.0.0, whose performance improvements make it an interesting development platform for the genomics and bioinformatics community.
> > 
> >  If you have questions or would like to provide feedback about the SDK, please do not hesitate to get in touch with us by replying to this email either on this list or in private. We also have an issue and feature request tracker, which can be used for contacting us too (see link below).
> > 
> > Useful links:
> > 
> >  *  Illumina BaseSpace Ruby SDK: https://developer.basespace.illumina.com/docs/content/documentation/sdk-samples/ruby-sdk-overview
> >  *  Illumina?s release announcement: https://groups.google.com/d/msg/basespace-developers/GW_hQ2OkCiQ/3aqnM2FdSeQJ
> >  *  Official Ruby gem: https://rubygems.org/gems/bio-basespace-sdk
> >  *  SDK documentation: http://rubydoc.info/gems/bio-basespace-sdk/0.1.6/frames
> >  *  Source-code repository: https://github.com/basespace/basespace-ruby-sdk
> >  *  Issue and feature request tracker: https://github.com/basespace/basespace-ruby-sdk/issues
> > 
> > Best wishes,
> > 
> > The BaseSpace Rubyists
> > 
> > 
> > _______________________________________________
> > BioRuby Project - http://www.bioruby.org/
> > BioRuby mailing list
> > BioRuby at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioruby
> 
> 
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