[BioRuby] "Read an ASN.1 file" and "Using a BioSQL database" !!!

[Toshiaki Katayama]

On 2007/03/27, at 14:48, Toshiaki Katayama wrote:

> On 2007/03/13, at 14:23, Moses M. Hohman wrote:
>> but AFAIK BioRuby does not support BioSQL,
>
> Currently it might be broken, but BioRuby supported BioSQL from the beginning of
> the BioSQL project which is developed during three BioHackathon meetings (2002, 2003).
>
> I wrote basic BioSQL module which support Cape Town schema (2002), but I was lazy
> to update it.
>
> However, AFAIK, RJP is working on ActiveRecord + BioSQL integration (2006, December)
> to replace my old one.  Raoul, could you post your recent status on it?

Sorry, I forgot but RJP also worked on fixing bio/io/sql.rb module in 2006,
so the current version should not be broken.

I don't follow the recent changes on BioSQL schema but during the last
Phyloinformatics Hackathon (2006 Dec http://hackathon.nescent.org/),
which we (Goto-san and me) had attended, Hilmar was working on
the integration of tree into the database.

https://www.nescent.org/wg/phyloinformatics/index.php?title=Supporting_NEXUS

  BioSQL The BioSQL group created a new set of tables, optional within BioSQL,
  for the purposes of storing phylogenetic trees, both sequence or species.
  A script was added to the package that allows one to read NEXUS files and
  write any trees found in the files to the database.

Toshiaki