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

RJP raoul.bonnal at itb.cnr.it
Wed Apr 4 08:08:21 UTC 2007

Il giorno mer, 04/04/2007 alle 05.38 +0900, Toshiaki Katayama ha
> 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?
Ok I'm currently using it and seems to work quite well. The file is in
attachment, the code is a little bit dirty, sorry for that.

> 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 hope.

> 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.
Now I'm a littel bit busy for adding the ne schema and update
ActiveRecord implementation.

Now I did a schema for blast and described it by Active Record too,
could be of interest for you ?

Cheers form Italy.

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