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

Toshiaki Katayama ktym at hgc.jp
Thu Apr 5 15:07:05 UTC 2007


On 2007/04/04, at 17:08, RJP wrote:

> Il giorno mer, 04/04/2007 alle 05.38 +0900, Toshiaki Katayama ha
> scritto:
>> 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, this list server seems to eliminate the attachments.
Could you put it on the web site or send it to me so that I can put somewhere.

>> 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 ?

Nakao-san is preparing a repository for rails related projects at rubyforge
(mainly for rails plugins utilizing bioruby library), so your code is also
welcomed to be there.

I proposed 'bioruby-annex' as the project name as the 'bioruby-rails-plugins'
is too long (rubyforge's limit is 15 chars).  Nakao-san, is your project
already granted?

We need to consider how to incorporate rails dependent codes in bioruby
in the near future.


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