[BioRuby] combination bioruby and rails
ktym at hgc.jp
Tue May 9 19:38:45 UTC 2006
There will be many possibilities if BioRuby is used with Rails (especially with ActiveRecord).
The GFF database (which is used as a backend of GBrowse) loaded by the bp_load_gff.pl command in BioPerl is also a candidate in addition to the BioSQL.
There are some related efforts have been made, as far as I know.
* Nakao-san developed a Ensembl (Vega?) accessing module with ActiveRecord
* Nikaido-san posted a short Japanese tutorial to build a gene expression database viewer with Rails in his weblog.
* Ichinose-san created AJAX interface for BioRuby (and BioRuby shell)
The point would be, what kind of integration (or how tightly) is ideal, if we integrate Rails *in* BioRuby.
As for the Rails module in bio/shell, it is not finished but can be used in the following way for now:
1. start the bioruby shell in terminal1 and issue 'web' command
terminal1% bioruby foo
Copying web server files ... done
DRb::DRbConnError: druby://localhost:81064 - #<Errno::ECONNREFUSED: Connection refused - connect(2)
(my intention is to make this command will take care of following steps automatically, however,)
you may see the DRb::DRbConnError message here, then quit.
2. open another terminal and start the server
terminal2% cd foo
terminal2% ruby script/server
=> Booting WEBrick...
=> Rails application started on http://0.0.0.0:3000
=> Ctrl-C to shutdown server; call with --help for options
the rails (webrick httpd) server will start.
3. Switch back to terminal1 and restart bioruby session.
terminal1% bioruby foo
Connected to server druby://localhost:81064
4. open http://localhost:3000/shell/ in your web browser
the BioRuby logo and the message "Connected!" will be displayed.
5. then create some objects in the bioruby shell.
bioruby> x = 123
bioruby> na = seq("atgcatgcatgc")
bioruby> aa = na.translate
then reload your browser and variables will be listed.
By click on the variable, you may see the contents of the variable in Rails.
This feature is a experimental implementation and I'm not clear what the goal would be.
Do you want to call methods of the object in web interface?
All objects should be stored by ActiveRecord?
What kind of visualization is desired?
On 2006/05/10, at 3:22, jan aerts (RI) wrote:
> Hi all,
> Has anyone tried to integrate bioruby with rails? I noticed that there's a rails module in bio/shell, but couldn't get it working.
> How straightforward would it be to implement a BioSQL-based database with a rails interface? A feature of the web-interface could then be that sequences would be displayed graphically (with features annotated; using SVG?), and that the user could run remote BLASTs right from within the sequence viewer... or something.
> Anyone know of any bioruby/rails implementations?
> BioRuby mailing list
> BioRuby at lists.open-bio.org
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