[BioRuby] Remaining work to be done after BioHakathon
Naohisa GOTO
ngoto at gen-info.osaka-u.ac.jp
Wed Jun 18 11:34:10 UTC 2008
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
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