[GSoC] [BioRuby] Final GSoC report

[Pjotr Prins]

Yes, linking to D from an interpreted language is not hard, basically
it is the same calling convention as that of C. So a D shared library
looks the same as a C shared library to the calling code - all
existing foreign function interfaces (FFI) work. That is the good
news.

The bad news, as Artem points out, is that there is a problem in the
D garbage collector. Items get collected, which should not. This will
be fixed sooner or later. The commitment is there, and it is moving
up the priority list.

For us it did not matter, as the parsers and tools happily run on
their own using a command line interface, without much overhead.
One advantage, from my perspective, is that we are not tied to Ruby,
at this point, and the tools can be hosted in Galaxy. Another
advantage, perhaps, is that we have not been side-tracked in
providing rich library interfaces. That appeals to my purist side.

Writing FFI bindings later is not a problem.

Pj.

On Wed, Aug 22, 2012 at 10:42:12AM +0400, Artem Tarasov wrote:
> Hi,
> 
> Unfortunately, the problem is on the side of D. PyD wiki (
> https://bitbucket.org/ariovistus/pyd/wiki/Home) says that "extension
> libraries are nominally working with LDC (FE 2.060 or later); however,
> druntime currently limits what can be done here".
> 
> However, this issue has become quite popular in last months, see e.g. this
> thread:
> http://forum.dlang.org/thread/mailman.1330.1345434177.31962.digitalmars-d@puremagic.com
> ?
> so maybe this'll get fixed soon.
> 
> --
> Artem
> 
> On Wed, Aug 22, 2012 at 4:55 AM, Mic <mictadlo at gmail.com> wrote:
> 
> > Hi,
> > Python is able to connect to D with help of http://pyd.dsource.org/ .
> >
> > Maybe it would be something for Biopython
> >
> > Cheers,
> > Mic
> >
> > On Wed, Aug 22, 2012 at 5:11 AM, Marjan Povolni <marian.povolny at gmail.com
> > >wrote:
> >
> > > http://blog.mpthecoder.com/post/29910330225/final-gsoc-report
> > >
> > > *Summary*
> > >
> > > Yesterday I tagged the 0.4 release of gff3-pltools, and that marks the
> > end
> > > of the summer. At least in GSoC terms. Should I say end of the project? I
> > > don?t think so. The tools can still be improved, and the Ruby bindings
> > > should follow.
> > >
> > > The major changes since the last release include the following:
> > >
> > >    - filtering functionality has been moved to a separate utility:
> > >    gff3-filter, along with a new language for specifying filtering
> > > expressions,
> > >    - conversion to table format of selected fields has been moved to a
> > >    separate utility: gff3-select. However, the ?select option is still
> > > part of
> > >    gff3-filter,
> > >    - gff3-ffetch is now fetching FASTA sequences from GFF3 and FASTA
> > files
> > >    for CDS and mRNA records and features,
> > >    - man pages for utilities.
> > >
> > > **
> > > The original idea was to create a GFF3/GTF parser in D and Ruby bindings.
> > > The Ruby bindings part didn?t work out because there is still no support
> > > for D shared libraries in Linux, but instead there are now a few useful
> > > command-line tools for processing GFF3 which can be used without
> > > programming knowledge.
> > >
> > > To me, the summer was fun, challenging, and a great experience. I even
> > got
> > > to meet my mentor in person, and other community members too, and to make
> > > my first steps in bioinformatics. I even gave a small presentation at the
> > > EU-codefest. What a summer it was!
> > >
> > > Thanks to everybody who made it possible: Google, Open Bioinformatics
> > > Foundation and my mentor Pjotr Prins.
> > >
> > > --
> > > Marjan
> > >
> > > _______________________________________________
> > > BioRuby Project - http://www.bioruby.org/
> > > BioRuby mailing list
> > > BioRuby at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioruby
> > >
> >
> > _______________________________________________
> > GSoC mailing list
> > GSoC at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/gsoc
> >
> 
> _______________________________________________
> GSoC mailing list
> GSoC at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/gsoc