Comments on: BioRuby and Ruby on Rails: Active BioRecords http://www.bioinformaticszen.com/2008/03/bioruby-and-ruby-on-rails/ Fri, 25 Jul 2008 10:29:32 +0000 http://wordpress.org/?v=2.6 By: Animesh Sharma http://www.bioinformaticszen.com/2008/03/bioruby-and-ruby-on-rails/#comment-18552 Animesh Sharma Sun, 01 Jun 2008 13:57:16 +0000 http://www.bioinformaticszen.com/2008/03/bioruby-and-ruby-on-rails/#comment-18552 Wow Ruby looks cool! BTW 1.87 is out there via svn, http://svn.ruby-lang.org/repos/ruby/tags/v1_8_7/NEWS . Wow Ruby looks cool! BTW 1.87 is out there via svn, http://svn.ruby-lang.org/repos/ruby/tags/v1_8_7/NEWS .

]]> By: jan. http://www.bioinformaticszen.com/2008/03/bioruby-and-ruby-on-rails/#comment-12685 jan. Tue, 11 Mar 2008 10:04:57 +0000 http://www.bioinformaticszen.com/2008/03/bioruby-and-ruby-on-rails/#comment-12685 Congratulations Mike. This post apparently made it onto the "Latest Ruby Links" section of RubyInside. Nice work. I'll have to keep this in mind as I'm interfacing a lot with external databases. As a matter of fact, I'll have to think about this to incorporate in the Ensembl API: make it possible to use a local sqlite3 store or something. BTW: We're at the moment rewriting part of bioruby so that Bio::EMBL, Bio::GenBank and colleagues actually create Bio::Sequence objects (which makes sense, because EMBL and GenBank are nothing more than sequence _formats_). That's all still in an SVN branch though and has not been merged into trunk. Congratulations Mike. This post apparently made it onto the “Latest Ruby Links” section of RubyInside.

Nice work. I’ll have to keep this in mind as I’m interfacing a lot with external databases. As a matter of fact, I’ll have to think about this to incorporate in the Ensembl API: make it possible to use a local sqlite3 store or something.

BTW: We’re at the moment rewriting part of bioruby so that Bio::EMBL, Bio::GenBank and colleagues actually create Bio::Sequence objects (which makes sense, because EMBL and GenBank are nothing more than sequence _formats_). That’s all still in an SVN branch though and has not been merged into trunk.

]]> By: BioBlogs 19: Bioengineering « O’Really? at Duncan.Hull.name http://www.bioinformaticszen.com/2008/03/bioruby-and-ruby-on-rails/#comment-12398 BioBlogs 19: Bioengineering « O’Really? at Duncan.Hull.name Fri, 07 Mar 2008 12:18:34 +0000 http://www.bioinformaticszen.com/2008/03/bioruby-and-ruby-on-rails/#comment-12398 [...] while pondering the merist of workflows. Michael Barton also outlined some of the challenges of re-using code in software engineering and bioinformatics. Data integration is always a massive engineering challenge in bioinformatics projects, Rod Page [...] [...] while pondering the merist of workflows. Michael Barton also outlined some of the challenges of re-using code in software engineering and bioinformatics. Data integration is always a massive engineering challenge in bioinformatics projects, Rod Page [...]

]]> By: Neil http://www.bioinformaticszen.com/2008/03/bioruby-and-ruby-on-rails/#comment-12333 Neil Thu, 06 Mar 2008 23:51:30 +0000 http://www.bioinformaticszen.com/2008/03/bioruby-and-ruby-on-rails/#comment-12333 Nice. I've used something vaguely similar <a href="http://nsaunders.wordpress.com/2006/04/06/bioperl-tip-for-the-day/" rel="nofollow">in the past</a> with BioPerl, to suck sequences from a URL into a sequence object. The ugly Perl one-line syntax would go something like: my $seqio = Bio::SeqIO->new('-fh' => IO::String->new(get($url)), '-format' => 'fasta'); One thing to watch out for: raw/plain text from URLs is sometimes wrapped in HTML 'pre' tags. Nice. I’ve used something vaguely similar in the past with BioPerl, to suck sequences from a URL into a sequence object. The ugly Perl one-line syntax would go something like:

my $seqio = Bio::SeqIO->new(’-fh’ => IO::String->new(get($url)), ‘-format’ => ‘fasta’);

One thing to watch out for: raw/plain text from URLs is sometimes wrapped in HTML ‘pre’ tags.

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