[BioRuby] Remaining work to be done after BioHakathon

[Naohisa GOTO]

Dear Anthony,

On Mon, 16 Jun 2008 16:00:52 +0100
Anthony Underwood <email2ants at gmail.com> wrote:

> Dear Toshiaki and other biorubyists,
> 
> I had a look at the new REST interface implemented at TogoWS. It looks  
> really nice (and it's fast). You mention that there is work to be done  
> to convert GenBank, EMBL, UniProt, BioSQL in to the new Bio::Sequence  
> model.
> 
> What is the current status of this?

Current status is:

* Conversion of GenBank and EMBL from/to Bio::Sequence usually
  works fine, though some fields are not yet supported (for
  example, PROJECT, CONSRTM, SEGMENT, CONTIG in GenBank).
* Codes to support BioSQL from/to Bio::Sequence have been added,
  but not well tested.
* UniProt from/to Bio::Sequence is not supported. 
* A few documents and unit tests about the Bio::Sequence model
  and related codes.

> Is the work/progress made at the BioHackathon publicly visible?

It is stored in the CVS BRANCH-biohackathon2008 branch.
You can get via anonymous CVS or CVSWeb. Please see
http://www.open-bio.org/wiki/SourceCode . Unfortunately,
just now, I couldn't access the anonymous CVS, and this
suggests trouble in the code.open-bio.org.
(Note that CVS repository for developers is OK.)

> I would love to contribute and help - how can I help - perhaps the  
> most recent changes can be added to the repository now on github?

Now, CVS is still used for development. In the future, we
will move to svn and/or git (or Mercurial?).

Currently, I don't know whether changes made in the CVS are
pushed into the github repository.

Thanks,
-- 
Naohisa Goto
ng at bioruby.org / ngoto at gen-info.osaka-u.ac.jp