From bonnalraoul at ingm.it  Wed Sep  1 09:39:44 2010
From: bonnalraoul at ingm.it (Raoul Bonnal)
Date: Wed, 1 Sep 2010 15:39:44 +0200
Subject: [BioRuby] R:  Fwd: Re: BioSQL development
In-Reply-To: <op.vhuh3umxztul55@jn-themachine>
References: <AANLkTinnBXnxfQ=0G9qo2wqg7Mzcct0DBe=_tpYbvXZC@mail.gmail.com><op.vhtz5q0uztul55@jn-themachine><AANLkTi=vVH6e4ZXgR58Q=w4vtWonSqXtOAognTjz1J6X@mail.gmail.com><op.vht2g3osztul55@jn-themachine>
	<op.vht4sdiyztul55@jn-themachine><DBAEAA32-1EA1-4775-8D8A-5B95B06B842B@drycafe.net><AANLkTim_BdBoduYkng74CpUj9bW724KHvN539bfTy+zU@mail.gmail.com><AANLkTi=84YhHRtgbaooRXm4oHgoK31kf1zSZ8CaLY9DS@mail.gmail.com><A
	ANLkTinfSktFrdWXE9RFr-bUsw3fMQaro8b45bUm8t2Q@mail.gmail.com>
	<op.vhuh3umxztul55@jn-themachine>
Message-ID: <dec0288d-ccf9-4032-b5ad-66724feca914@ingm.it>

Hello,
I didn't start to map GFF3 to BioSQL in BioRuby, sorry for that.
Theoretically if the format is readable in BioRuby as a BioSequence object then is possible to start to map it to the BioSQL schema.
If you wrote some code please share it with git or gist http://gist.github.com/ pointing out which are the GFF3's "features", to start the GFF3 support in BioRuby/BioSQL.


About CHADO, I think that adding another schema is a good thing, supporting more schemas give us the flexibility to satisfy more users, is good.

The problem of loading huge datasets is a big problem in BioRuby/BioSQL too, creating the BioSequence object and then moving it to biosql low level is very cpu/memory consuming. Now my brain is still in vacation so any idea on how to speed up the process without relying on better implementation of the RubyVM is appreciated.

Now BioSQL is distributed with BioRuby one of the ideas is to move biosql to an optional plugin and I think that the CHADO implementation should follow the same path. BUT we have to discuss more deeply the plugin system in BioRuby.

About which ORM is better to use ? Actually, at the beginning I was very confortable with DataMapper because had some nice features like composite primary key or lazy loading, unfortunately the majority of the Rails applications use ActiveRecord and maintaining different ORM it's a messy and I had to choose the more supported/spread/known ORM. Now I'll not convert BioSQL to DataMapper (I have an original implementation) however I'm very open to discuss about alternative ORM, it is also very fascinating at least for me.


Day 1, the hell is knocking to my door.

--
Raoul J.P. Bonnal
Life Science Informatics
Integrative Biology Program
Fondazione INGM
Via F. Sforza 28
20122 Milano, IT
phone: +39 02 006 623  26
fax: +39 02 006 623 46
http://www.ingm.it


> -----Messaggio originale-----
> Da: bioruby-bounces at lists.open-bio.org [mailto:bioruby-
> bounces at lists.open-bio.org] Per conto di Julian Nordt
> Inviato: domenica 22 agosto 2010 17:18
> A: Hilmar Lapp; Rob Syme
> Cc: bioruby at lists.open-bio.org
> Oggetto: Re: [BioRuby] Fwd: Re: BioSQL development
> 
> One more thing in regard to the mapping between BioSQL and GFF3:
> 
> I tried to follow the mapping given by the biosql wiki and blue collar
> bioinformatics. The mapping is acceptable in the sense that you can
> store
> *most* or even all (?) of the features that GFF3 offers. The further I
> got
> though within the development the unclearer things got me, especially
> in
> terms of the "attribute" column.
> 
> If you compare the table at the biosql wiki (for the attribute column)
> with the one at blue collar bioinformatics, one will notice that the
> there
> are keywords that occour in one, but not at the other table. That not
> mentioning the todos on the wiki regarding the "standard" columns. I
> havn't looked in that detail though through blue collars code, maybe
> the
> answer is given there.
> 
> However I wrote a small library that managed to store most - but not
> all
> the given information of the GFF3-files - correctly to BioSQL. There
> were
> some points where the mapping has been unclear to me and where I stored
> the given information where I thought it would fit best.
> 
> Considering that I chose a standard db schema to avoid any ambiguously
> and
> the fact that I experienced performance issues with MYSQL+Rails (not
> related to BioSQL) at the project made it enough for me to switch to
> CHADO
> backed by POSTGRES.
> 
> The documentation regarding CHADO is in my opinion richer and most
> importantly one can follow gmod_bulk_load_gff3.pl for the mapping
> relatively easy, since it is well documented.
> 
> I would very much welcome other opinions on the topic, especially in
> combination with the use of web applications.
> 
> -- Julian
> 
> 
> 
> 
> 
> On Sun, 22 Aug 2010 16:17:45 +0200, Rob Syme <rob.syme at gmail.com>
> wrote:
> 
> > I've had a look around and a pretty solid mapping seems to be
> available:
> > http://www.biosql.org/wiki/Annotation_Mapping#GFF3
> >
> > Blue collar bioinformatics gave it a shot here:
> > http://bcbio.wordpress.com/2009/02/22/exploring-bioperl-genbank-to-
> gff-mapping/
> >
> > -r
> >
> > On 22 Aug 2010 22:02, "Hilmar Lapp" <hlapp at drycafe.net> wrote:
> > Is the issue with GFF3 in the Bioruby to BioSQL mapping, or is
> somehow in
> > the BioSQL schema?
> >
> > I recall there was a thread on GFF recently which I wasn't able to
> > follow,
> > so if the answer is in that thread and isn't easy to sum up here,
> just
> > point
> > me there.
> >
> >        -hilmar
> >
> >
> >
> > On Aug 22, 2010, at 6:30 AM, Julian Nordt wrote:
> >
> >> Hi Rob,
> >>
> >> I just wanted to point that there ...
> 
> 
> --
> Using Opera's revolutionary email client: http://www.opera.com/mail/
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby



From rob.syme at gmail.com  Wed Sep  1 10:31:54 2010
From: rob.syme at gmail.com (Rob Syme)
Date: Wed, 1 Sep 2010 22:31:54 +0800
Subject: [BioRuby] Fwd: Re: BioSQL development
In-Reply-To: <dec0288d-ccf9-4032-b5ad-66724feca914@ingm.it>
References: <AANLkTinnBXnxfQ=0G9qo2wqg7Mzcct0DBe=_tpYbvXZC@mail.gmail.com>
	<op.vhtz5q0uztul55@jn-themachine>
	<AANLkTi=vVH6e4ZXgR58Q=w4vtWonSqXtOAognTjz1J6X@mail.gmail.com>
	<op.vht2g3osztul55@jn-themachine> <op.vht4sdiyztul55@jn-themachine>
	<DBAEAA32-1EA1-4775-8D8A-5B95B06B842B@drycafe.net>
	<AANLkTim_BdBoduYkng74CpUj9bW724KHvN539bfTy+zU@mail.gmail.com>
	<AANLkTi=84YhHRtgbaooRXm4oHgoK31kf1zSZ8CaLY9DS@mail.gmail.com>
	<op.vhuh3umxztul55@jn-themachine>
	<dec0288d-ccf9-4032-b5ad-66724feca914@ingm.it>
Message-ID: <AANLkTi=NZQzGuxyYAkFZKiccqOk20VN8hvwpAL6KoQmV@mail.gmail.com>

I agree that db schemas and associated code should be implemented as
plugins. I haven't been keeping up-to-date with how the plugin system
works. From?Pjotr's gff3 post
(http://thebird.nl/bioruby/BioRuby_GFF3.html) and github repo
(http://github.com/pjotrp/bioruby-gff3-plugin) it looks like we just
put our plugin under the Bio module and add the plugin lib dir to the
search path. Is this correct?
-r

On Wed, Sep 1, 2010 at 9:39 PM, Raoul Bonnal <bonnalraoul at ingm.it> wrote:
>
> Hello,
> I didn't start to map GFF3 to BioSQL in BioRuby, sorry for that.
> Theoretically if the format is readable in BioRuby as a BioSequence object then is possible to start to map it to the BioSQL schema.


From pjotr.public14 at thebird.nl  Sat Sep  4 07:49:30 2010
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Sat, 4 Sep 2010 13:49:30 +0200
Subject: [BioRuby] Fwd: Re: BioSQL development
In-Reply-To: <AANLkTi=NZQzGuxyYAkFZKiccqOk20VN8hvwpAL6KoQmV@mail.gmail.com>
References: <op.vhtz5q0uztul55@jn-themachine>
	<AANLkTi=vVH6e4ZXgR58Q=w4vtWonSqXtOAognTjz1J6X@mail.gmail.com>
	<op.vht2g3osztul55@jn-themachine> <op.vht4sdiyztul55@jn-themachine>
	<DBAEAA32-1EA1-4775-8D8A-5B95B06B842B@drycafe.net>
	<AANLkTim_BdBoduYkng74CpUj9bW724KHvN539bfTy+zU@mail.gmail.com>
	<AANLkTi=84YhHRtgbaooRXm4oHgoK31kf1zSZ8CaLY9DS@mail.gmail.com>
	<op.vhuh3umxztul55@jn-themachine>
	<dec0288d-ccf9-4032-b5ad-66724feca914@ingm.it>
	<AANLkTi=NZQzGuxyYAkFZKiccqOk20VN8hvwpAL6KoQmV@mail.gmail.com>
Message-ID: <20100904114930.GA27474@thebird.nl>

On Wed, Sep 01, 2010 at 10:31:54PM +0800, Rob Syme wrote:
> (http://github.com/pjotrp/bioruby-gff3-plugin) it looks like we just
> put our plugin under the Bio module and add the plugin lib dir to the
> search path. Is this correct?

Yes. Raoul and Toshiaki wrote a prototype plugin handler, which will
come to be. E.g. 

  bioruby --install plugin-name

will fetch the plugin and add it to the search path automagically.

For now, merely adding the plugin lib dir to the search path is good
enough, as that will be compatible.

Pj.

From gmsaner at gmail.com  Mon Sep  6 20:31:07 2010
From: gmsaner at gmail.com (=?ISO-8859-2?Q?Maciej_=A3opatka?=)
Date: Tue, 7 Sep 2010 02:31:07 +0200
Subject: [BioRuby] BioRuby, EMBL file
Message-ID: <AANLkTi=Yqg1qJDvg8pj9Hk9veb=QxMhGiMfARNqa5ynw@mail.gmail.com>

Hello,

In my program I need complete genomes of bacterias. I download them from
Ensembl's FTP server (for example
ftp://ftp.ensemblgenomes.org/pub/bacteria/current/embl/bacillus_collection/B_amyloliquefaciens/
).
Those files have embl format.

The genomes in those files are in parts, so I need to iterate over them (I
use file.each_entry do {} ), however they are not in correct order so they
can't be simply concatenated. At the moment I use Regex to get entry's
position which is provided in entry's definition property. This is not very
clean way.

Is there a better way to get information about entry's position in genome?

Thanks,
Maciej Lopatka

From chmille4 at gmail.com  Tue Sep  7 23:01:09 2010
From: chmille4 at gmail.com (Chase Miller)
Date: Tue, 7 Sep 2010 23:01:09 -0400
Subject: [BioRuby] Bio::Assembly + Ace Parser
Message-ID: <AANLkTinG-vKb84vowTCkbZymO3pvnJJRZs831o4MEqH4@mail.gmail.com>

Hi All

I finally got around to doing this and have written a simple Bio::Assembly
class with a streaming ace parser.   As part of this, I have
Bio::Assembly::Contig and Bio::Assembly::Read classes.  The general flow
goes like this - a Bio::Assembly object relates to a single ace file and is
made up of Bio::Assembly::Contig objects, which are in turn made up of
Bio::Assembly::Read objects.

It probably needs a bit more work (see TODO below), but I thought I'd go
ahead and get some feedback. Take a look and let me know what you think.

http://github.com/chmille4/bioruby


TODO:

   - Currently, the ace parser is integrated into bio/assembly.rb, but I'd
   like to extract this out to make it easier to support more file formats.
    Any ideas on a good (bioruby) way to do this?
   - Flesh out the features.  Any requests?
   - Add more tests (8 so far in test/unit/bio/test_assembly.rb)
   - Make sure that manipulating Bio::Assembly objects ( i.e deleting
   contigs ) does not the cause the ace unparser to create illegal ace files.
   - Add more documentation


Cheers!
Chase

From gmsaner at gmail.com  Thu Sep  9 17:01:55 2010
From: gmsaner at gmail.com (=?ISO-8859-2?Q?Maciej_=A3opatka?=)
Date: Thu, 9 Sep 2010 23:01:55 +0200
Subject: [BioRuby] BioRuby, performance, cut_with_enzyme
Message-ID: <AANLkTi=e-xSJwxX_OhzCFztRe1cVnrJ=WCmdgmh1QZR4@mail.gmail.com>

Hello,

I've got a big problem with performance of BioRuby. I need to cut sequence
(about 5MB <  < 17MB) with restriction enzymes. It takes ages to cut it with
just one enzyme, it just doesn't stop, and I have no idea what is going on.
My friend for the same task used BioPython and it took just 2 minutes for 20
enzymes.

I know that Ruby is slower than Python, but it doesn't explain this. Has
anyone had similar problems?

I've tested this on Ubuntu 9.04 and Windows 7 with Ruby 1.8.7 on Linux, and
Ruby 1.9.2 on Windows.

Thanks,
Maciek Lopatka

From trevor at corevx.com  Thu Sep  9 17:29:44 2010
From: trevor at corevx.com (Trevor Wennblom)
Date: Thu, 9 Sep 2010 16:29:44 -0500
Subject: [BioRuby] BioRuby, performance, cut_with_enzyme
In-Reply-To: <AANLkTi=e-xSJwxX_OhzCFztRe1cVnrJ=WCmdgmh1QZR4@mail.gmail.com>
References: <AANLkTi=e-xSJwxX_OhzCFztRe1cVnrJ=WCmdgmh1QZR4@mail.gmail.com>
Message-ID: <E1E7F48A-C50D-48A1-A20B-72BB703677C0@corevx.com>

Also - which version of Ruby are you using? Performance should be significantly faster on 1.9.2 versus 1.8 due to improvements to the RegExp engine.

From trevor at corevx.com  Thu Sep  9 17:11:53 2010
From: trevor at corevx.com (Trevor Wennblom)
Date: Thu, 9 Sep 2010 16:11:53 -0500
Subject: [BioRuby] BioRuby, performance, cut_with_enzyme
In-Reply-To: <AANLkTi=e-xSJwxX_OhzCFztRe1cVnrJ=WCmdgmh1QZR4@mail.gmail.com>
References: <AANLkTi=e-xSJwxX_OhzCFztRe1cVnrJ=WCmdgmh1QZR4@mail.gmail.com>
Message-ID: <F2728011-A1CB-494A-A796-F564F2D07E9D@corevx.com>


On Sep 9, 2010, at 4:01 PM, Maciej ?opatka wrote:

> I've got a big problem with performance of BioRuby. I need to cut sequence
> (about 5MB <  < 17MB) with restriction enzymes. It takes ages to cut it with
> just one enzyme, it just doesn't stop, and I have no idea what is going on.
> My friend for the same task used BioPython and it took just 2 minutes for 20
> enzymes.



Hi Maciek,

I'm the author of that particular extension. One of the particular points of the design - several years ago - was to accommodate the particular cut patterns on both strands of the sequence. If I recall, other libraries concentrate on only one strand of the sequence.

This does take a considerable performance hit, interpreted language aside. I'm also relatively certain that I didn't implement the most efficient algorithm as it was my first crack at solving the issue back then.

If you'd like to email me with a link to the particular dataset you're using and what you're trying to do with it I'd be happy to take a look at it in the next few days. Another question is are you interested in the results of having both strands considered - which would give more accurate results - or just a single strand?

From georgkam at gmail.com  Fri Sep 17 03:25:35 2010
From: georgkam at gmail.com (George Githinji)
Date: Fri, 17 Sep 2010 10:25:35 +0300
Subject: [BioRuby] Biosprint bepipred implementation
Message-ID: <AANLkTikj-zUfLen_0xDg=FTN3cuk9s0Yw-bOwh45KwS-@mail.gmail.com>

Hi,
The Biosprint started here in Nairobi yesterday. Most of the
participants are new to Ruby and some to programming in general.
There are about 4 CS guys who are experts in other
languages(php,java,perl and python)
We are using git for version control and have forked GeorgeG bioruby
fork from github

Task 1 Description
BepiPred predicts the location of linear B-cell epitopes in proteins
using a combination of a hidden Markov  model and a propensity scale
method. The method is described in the following article:
#   Improved method for predicting linear B-cell epitopes.
#   Jens Erik Pontoppidan Larsen, Ole Lund and Morten Nielsen
#   Immunome Research 2:2, 2006.

We are implementing a wrapper class for bepipred linear B-cell epitope
prediction tool. Specifically we want to

1) be able to call it from within bioruby  as follows
  # === Examples
  #
  #   require 'bio'
  #   seq_file = 'test.fasta'
  #
  #   factory = Bio::Bepipred.new(seq_file)
  #   report = factory.query
  #   report.class # => Bio::Bepipred::Report

2) The report class should take the bepipred predictions and format them to GFF3

3) Document the tasks

4) Write unit tests for the methods.


We have divided ourselves into 4 groups to accomplish this task.

A couple of questions:
1) While developing, which is the best development lifecycle?
      - when testing the development version

2) what is the best way to call a command line program from within
bioruby. for example  I have this


require 'bio/command'
require 'shellwords'

module Bio

  # == Description
  #
  # A wrapper for Bepipred linear B-cell epitope prediction program.
  #
  # === Examples
  #
  #   require 'bio'
  #   seq_file = 'test.fasta'
  #
  #   factory = Bio::Bepipred.new(seq_file)
  #   report = factory.query
  #   report.class # => Bio::Bepipred::Report
  #
class Bepipred
  autoload :Report, 'bio/appl/bepipred/report'

  # Creates a new Bepipred execution wrapper object
  def initialize(program='bepipred',score_threshold=0.35,file_name='')
    @program = program
    @score_threshold = score_threshold
    @file_name = file_name
  end

  # name of the program ('bepipred' in UNIX/Linux)
  attr_accessor :program

  # options
  attr_accessor :score_threshold

  # return the names of the input sequences
  attr_reader :sequence_names

  def sequence_names(file)
    sequence_names = []
    Bio::FlatFile.auto(@file) do |f|
      f.each do |entry|
        sequence_names << entry.definition
      end
    end
    sequence_names
  end

  # TODO create a list of query sequences


  #TODO create a commandline as an array cmd
  def make_command
    cmd = [@program,"-t #{@score_threshold}", at file_name ]
  end

  #query the file
  def query(file_name)
    cmd = make_command
    exec_local(cmd)
  end

  # TODO create a parser class for the ouput
  # parse_results

 private
 #executes bepipred when called localy
 #The input is a file name or a path to the file containing protein
sequences in fasta format
 #This method does not work
 # There could be a bug in the way the cmd argument is created.
 def exec_local(cmd)
   Bio::Command.query_command(cmd)
 end

end
end

Seems not to work.
Please assist. Thanks.



-- 
---------------
Sincerely
George
KEMRI/Wellcome-Trust Research Program
Skype: george_g2
Blog: http://biorelated.wordpress.com/

From yannick.wurm at unil.ch  Thu Sep 23 02:35:45 2010
From: yannick.wurm at unil.ch (Yannick Wurm)
Date: Thu, 23 Sep 2010 13:35:45 +0700
Subject: [BioRuby] rails blast server
Message-ID: <1DF3B9FB-24B8-44AC-9791-61A2EBBF7BE0@unil.ch>

Hi all,

I'd like to set up a small server for people to run BLAST against some of my sequences & see the results. 
GMOD obviously comes to mind, but it seems like overkill. 
And perhaps there is an almost automagic way to do this with ruby on rails. Has anyone done this yet?

Thanks!

Yannick

--------------------------------------------
          yannick . wurm @ unil . ch
Ant Genomics, Ecology & Evolution @ Lausanne
   http://www.unil.ch/dee/page28685_fr.html



From biopython at maubp.freeserve.co.uk  Thu Sep 23 06:52:54 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 23 Sep 2010 11:52:54 +0100
Subject: [BioRuby] rails blast server
In-Reply-To: <1DF3B9FB-24B8-44AC-9791-61A2EBBF7BE0@unil.ch>
References: <1DF3B9FB-24B8-44AC-9791-61A2EBBF7BE0@unil.ch>
Message-ID: <AANLkTi=O+tWj2ptrWy7SC7QUT+mCUMVQHPkGyQ-iF1+H@mail.gmail.com>

On Thu, Sep 23, 2010 at 7:35 AM, Yannick Wurm <yannick.wurm at unil.ch> wrote:
>
> Hi all,
>
> I'd like to set up a small server for people to run BLAST against
> some of my sequences & see the results.
> GMOD obviously comes to mind, but it seems like overkill.
> And perhaps there is an almost automagic way to do this with
> ruby on rails. Has anyone done this yet?
>
> Thanks!
>
> Yannick

Hi,

We just use the NCBI's wwwblast, but it hasn't been updated
recently and is very basic compared to the NCBI website.

Peter

From yannick.wurm at unil.ch  Thu Sep 23 07:09:52 2010
From: yannick.wurm at unil.ch (Yannick Wurm)
Date: Thu, 23 Sep 2010 18:09:52 +0700
Subject: [BioRuby] rails blast server
In-Reply-To: <AANLkTi=O+tWj2ptrWy7SC7QUT+mCUMVQHPkGyQ-iF1+H@mail.gmail.com>
References: <1DF3B9FB-24B8-44AC-9791-61A2EBBF7BE0@unil.ch>
	<AANLkTi=O+tWj2ptrWy7SC7QUT+mCUMVQHPkGyQ-iF1+H@mail.gmail.com>
Message-ID: <516E5D15-25D5-433A-ABEA-4688FCA56C31@unil.ch>

Yeah thanks..... that's the impression I had :-/

On 23 Sep 2010, at 17:52, Peter wrote:

> On Thu, Sep 23, 2010 at 7:35 AM, Yannick Wurm <yannick.wurm at unil.ch> wrote:
>> 
>> Hi all,
>> 
>> I'd like to set up a small server for people to run BLAST against
>> some of my sequences & see the results.
>> GMOD obviously comes to mind, but it seems like overkill.
>> And perhaps there is an almost automagic way to do this with
>> ruby on rails. Has anyone done this yet?
>> 
>> Thanks!
>> 
>> Yannick
> 
> Hi,
> 
> We just use the NCBI's wwwblast, but it hasn't been updated
> recently and is very basic compared to the NCBI website.
> 
> Peter


From trevor at corevx.com  Thu Sep 23 07:20:51 2010
From: trevor at corevx.com (Trevor Wennblom)
Date: Thu, 23 Sep 2010 06:20:51 -0500
Subject: [BioRuby] rails blast server
In-Reply-To: <1DF3B9FB-24B8-44AC-9791-61A2EBBF7BE0@unil.ch>
References: <1DF3B9FB-24B8-44AC-9791-61A2EBBF7BE0@unil.ch>
Message-ID: <23ACF172-B4D1-4237-81A9-BDE1A70A508C@corevx.com>

Hi Yannick,

It's pretty straight-forward. Put your sequences into a blast database as usual with formatdb. Setup a page in Rails with a textarea or file upload submit form. Take the submitted text / sequence, use it to query against your blast database by saving the input to a file and running the commandline tool (such as blastn), and finally return the file containing results.

This is assuming your queries run quickly since the page render will be delayed until blast is complete. If you need to search against a large database there's a bit more work to it.


From yannick.wurm at unil.ch  Thu Sep 23 09:08:35 2010
From: yannick.wurm at unil.ch (Yannick Wurm)
Date: Thu, 23 Sep 2010 20:08:35 +0700
Subject: [BioRuby] rails blast server
In-Reply-To: <1285246169.29263.158.camel@deskpro15336.dynamic.sanger.ac.uk>
References: <1DF3B9FB-24B8-44AC-9791-61A2EBBF7BE0@unil.ch>
	<23ACF172-B4D1-4237-81A9-BDE1A70A508C@corevx.com>
	<1285246169.29263.158.camel@deskpro15336.dynamic.sanger.ac.uk>
Message-ID: <5D9604BB-313A-44B4-A91B-B868873D26C8@unil.ch>

Thanks for the feedback Frank and Trevor

While I do want something simple, something with a few extra fun features & that can be extended easily wouldn't hurt :)
Eg: 
  - autodetection of whether the use entered nucleotide or aminoacid sequence --> autolimited selection of what blast programs are appropriate
  ---> automatically populated list of available databases
  - links in the results that let you fetch the original sequences of the database hits (by providing links to hits, and batch download of the database sequences). 

I've never done any rails before, so its probably a good opportunity. 

all the best,
yannick

On 23 Sep 2010, at 19:49, Frank Schwach wrote:

> What Trever describes is how I do it too. If this is all you want then a
> Rails app is a bit overkill because this is a very simple cgi script
> that doesn't even connect to a database.
> Basically, you just need some validation of input and then issue a
> system command (blsatall ....).
> As Trever pointed out, for larger databses this may be impractical
> because there will be no feedback until the search has completed and if
> your site is popular then many BLAST searches on a single server may
> quickly become a problem. Two possible solutions:
> 1) automatically send the results by email and just display a page
> showing that the search has been submitted. I use Perl for sending such
> messages but it should be just as easy in Ruby
> 2) use a job queueing system and run jobs in the background. The
> simplest solution is to use the Linux "batch" queue
> (http://linux.about.com/library/cmd/blcmdl1_batch.htm). 
> You can just submit jobs to the queue and they are only run when system
> resources are available. Ensure that the results are written into a file
> with a unique job ID in the file name and display a results page with
> some AJAX which keeps querying for the BLAST result file (by its ID) and
> inserts it into the page as soon as it is available.
> 
> Hope this helps.
> 
> Frank
> 
> 
> On Thu, 2010-09-23 at 06:20 -0500, Trevor Wennblom wrote:
>> Hi Yannick,
>> 
>> It's pretty straight-forward. Put your sequences into a blast database as usual with formatdb. Setup a page in Rails with a textarea or file upload submit form. Take the submitted text / sequence, use it to query against your blast database by saving the input to a file and running the commandline tool (such as blastn), and finally return the file containing results.
>> 
>> This is assuming your queries run quickly since the page render will be delayed until blast is complete. If you need to search against a large database there's a bit more work to it.
>> 
>> _______________________________________________
>> BioRuby Project - http://www.bioruby.org/
>> BioRuby mailing list
>> BioRuby at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioruby
> 
> 
> 
> -- 
> The Wellcome Trust Sanger Institute is operated by Genome Research 
> Limited, a charity registered in England with number 1021457 and a 
> company registered in England with number 2742969, whose registered 
> office is 215 Euston Road, London, NW1 2BE. 



From fs5 at sanger.ac.uk  Thu Sep 23 08:49:29 2010
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Thu, 23 Sep 2010 13:49:29 +0100
Subject: [BioRuby] rails blast server
In-Reply-To: <23ACF172-B4D1-4237-81A9-BDE1A70A508C@corevx.com>
References: <1DF3B9FB-24B8-44AC-9791-61A2EBBF7BE0@unil.ch>
	<23ACF172-B4D1-4237-81A9-BDE1A70A508C@corevx.com>
Message-ID: <1285246169.29263.158.camel@deskpro15336.dynamic.sanger.ac.uk>

What Trever describes is how I do it too. If this is all you want then a
Rails app is a bit overkill because this is a very simple cgi script
that doesn't even connect to a database.
Basically, you just need some validation of input and then issue a
system command (blsatall ....).
As Trever pointed out, for larger databses this may be impractical
because there will be no feedback until the search has completed and if
your site is popular then many BLAST searches on a single server may
quickly become a problem. Two possible solutions:
1) automatically send the results by email and just display a page
showing that the search has been submitted. I use Perl for sending such
messages but it should be just as easy in Ruby
2) use a job queueing system and run jobs in the background. The
simplest solution is to use the Linux "batch" queue
(http://linux.about.com/library/cmd/blcmdl1_batch.htm). 
You can just submit jobs to the queue and they are only run when system
resources are available. Ensure that the results are written into a file
with a unique job ID in the file name and display a results page with
some AJAX which keeps querying for the BLAST result file (by its ID) and
inserts it into the page as soon as it is available.

Hope this helps.

Frank


On Thu, 2010-09-23 at 06:20 -0500, Trevor Wennblom wrote:
> Hi Yannick,
> 
> It's pretty straight-forward. Put your sequences into a blast database as usual with formatdb. Setup a page in Rails with a textarea or file upload submit form. Take the submitted text / sequence, use it to query against your blast database by saving the input to a file and running the commandline tool (such as blastn), and finally return the file containing results.
> 
> This is assuming your queries run quickly since the page render will be delayed until blast is complete. If you need to search against a large database there's a bit more work to it.
> 
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

From fs5 at sanger.ac.uk  Thu Sep 23 09:44:31 2010
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Thu, 23 Sep 2010 14:44:31 +0100
Subject: [BioRuby] rails blast server
In-Reply-To: <5D9604BB-313A-44B4-A91B-B868873D26C8@unil.ch>
References: <1DF3B9FB-24B8-44AC-9791-61A2EBBF7BE0@unil.ch>
	<23ACF172-B4D1-4237-81A9-BDE1A70A508C@corevx.com>
	<1285246169.29263.158.camel@deskpro15336.dynamic.sanger.ac.uk>
	<5D9604BB-313A-44B4-A91B-B868873D26C8@unil.ch>
Message-ID: <1285249471.29263.166.camel@deskpro15336.dynamic.sanger.ac.uk>

Hi Yannick,

Of course you can do this in Rails but even those additional
requirements won't really get you started actually using Rails' features
because you probably don't want a backend database just to hold a few
names of FASTA files that you can BLAST against (you can either fetch
them directly from a directory listing or a short config text file). The
(simple) autodetection is just one relatively simple regex and to fetch
the original sequences you will probably want to get them straight out
of the flat (FASTA) files using BioRuby methods, so again no database.
Anyway, I don't want to curb your enthusiasm for learning Rails, so good
luck! :-)

Frank


, so learning a new framework might reallz 

On Thu, 2010-09-23 at 20:08 +0700, Yannick Wurm wrote:
> Thanks for the feedback Frank and Trevor
> 
> While I do want something simple, something with a few extra fun features & that can be extended easily wouldn't hurt :)
> Eg: 
>   - autodetection of whether the use entered nucleotide or aminoacid sequence --> autolimited selection of what blast programs are appropriate
>   ---> automatically populated list of available databases
>   - links in the results that let you fetch the original sequences of the database hits (by providing links to hits, and batch download of the database sequences). 
> 
> I've never done any rails before, so its probably a good opportunity. 
> 
> all the best,
> yannick
> 
> On 23 Sep 2010, at 19:49, Frank Schwach wrote:
> 
> > What Trever describes is how I do it too. If this is all you want then a
> > Rails app is a bit overkill because this is a very simple cgi script
> > that doesn't even connect to a database.
> > Basically, you just need some validation of input and then issue a
> > system command (blsatall ....).
> > As Trever pointed out, for larger databses this may be impractical
> > because there will be no feedback until the search has completed and if
> > your site is popular then many BLAST searches on a single server may
> > quickly become a problem. Two possible solutions:
> > 1) automatically send the results by email and just display a page
> > showing that the search has been submitted. I use Perl for sending such
> > messages but it should be just as easy in Ruby
> > 2) use a job queueing system and run jobs in the background. The
> > simplest solution is to use the Linux "batch" queue
> > (http://linux.about.com/library/cmd/blcmdl1_batch.htm). 
> > You can just submit jobs to the queue and they are only run when system
> > resources are available. Ensure that the results are written into a file
> > with a unique job ID in the file name and display a results page with
> > some AJAX which keeps querying for the BLAST result file (by its ID) and
> > inserts it into the page as soon as it is available.
> > 
> > Hope this helps.
> > 
> > Frank
> > 
> > 
> > On Thu, 2010-09-23 at 06:20 -0500, Trevor Wennblom wrote:
> >> Hi Yannick,
> >> 
> >> It's pretty straight-forward. Put your sequences into a blast database as usual with formatdb. Setup a page in Rails with a textarea or file upload submit form. Take the submitted text / sequence, use it to query against your blast database by saving the input to a file and running the commandline tool (such as blastn), and finally return the file containing results.
> >> 
> >> This is assuming your queries run quickly since the page render will be delayed until blast is complete. If you need to search against a large database there's a bit more work to it.
> >> 
> >> _______________________________________________
> >> BioRuby Project - http://www.bioruby.org/
> >> BioRuby mailing list
> >> BioRuby at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioruby
> > 
> > 
> > 
> > -- 
> > The Wellcome Trust Sanger Institute is operated by Genome Research 
> > Limited, a charity registered in England with number 1021457 and a 
> > company registered in England with number 2742969, whose registered 
> > office is 215 Euston Road, London, NW1 2BE. 
> 



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

From yannick.wurm at unil.ch  Thu Sep 23 13:14:39 2010
From: yannick.wurm at unil.ch (Yannick Wurm)
Date: Fri, 24 Sep 2010 00:14:39 +0700
Subject: [BioRuby] rails blast server
In-Reply-To: <1285249471.29263.166.camel@deskpro15336.dynamic.sanger.ac.uk>
References: <1DF3B9FB-24B8-44AC-9791-61A2EBBF7BE0@unil.ch>
	<23ACF172-B4D1-4237-81A9-BDE1A70A508C@corevx.com>
	<1285246169.29263.158.camel@deskpro15336.dynamic.sanger.ac.uk>
	<5D9604BB-313A-44B4-A91B-B868873D26C8@unil.ch>
	<1285249471.29263.166.camel@deskpro15336.dynamic.sanger.ac.uk>
Message-ID: <90EA9391-3216-4634-BC69-0960C8D881DF@unil.ch>

Dang I thought Rails would make AJAX stuff easier too? Or is that only if I need a database backend?
Sorry for the noob questions, I haven't done any web dev in a long time...

On 23 Sep 2010, at 20:44, Frank Schwach wrote:

> Hi Yannick,
> 
> Of course you can do this in Rails but even those additional
> requirements won't really get you started actually using Rails' features
> because you probably don't want a backend database just to hold a few
> names of FASTA files that you can BLAST against (you can either fetch
> them directly from a directory listing or a short config text file). The
> (simple) autodetection is just one relatively simple regex and to fetch
> the original sequences you will probably want to get them straight out
> of the flat (FASTA) files using BioRuby methods, so again no database.
> Anyway, I don't want to curb your enthusiasm for learning Rails, so good
> luck! :-)
> 
> Frank
> 
> 
> , so learning a new framework might reallz 
> 
> On Thu, 2010-09-23 at 20:08 +0700, Yannick Wurm wrote:
>> Thanks for the feedback Frank and Trevor
>> 
>> While I do want something simple, something with a few extra fun features & that can be extended easily wouldn't hurt :)
>> Eg: 
>>  - autodetection of whether the use entered nucleotide or aminoacid sequence --> autolimited selection of what blast programs are appropriate
>>  ---> automatically populated list of available databases
>>  - links in the results that let you fetch the original sequences of the database hits (by providing links to hits, and batch download of the database sequences). 
>> 
>> I've never done any rails before, so its probably a good opportunity. 
>> 
>> all the best,
>> yannick
>> 
>> On 23 Sep 2010, at 19:49, Frank Schwach wrote:
>> 
>>> What Trever describes is how I do it too. If this is all you want then a
>>> Rails app is a bit overkill because this is a very simple cgi script
>>> that doesn't even connect to a database.
>>> Basically, you just need some validation of input and then issue a
>>> system command (blsatall ....).
>>> As Trever pointed out, for larger databses this may be impractical
>>> because there will be no feedback until the search has completed and if
>>> your site is popular then many BLAST searches on a single server may
>>> quickly become a problem. Two possible solutions:
>>> 1) automatically send the results by email and just display a page
>>> showing that the search has been submitted. I use Perl for sending such
>>> messages but it should be just as easy in Ruby
>>> 2) use a job queueing system and run jobs in the background. The
>>> simplest solution is to use the Linux "batch" queue
>>> (http://linux.about.com/library/cmd/blcmdl1_batch.htm). 
>>> You can just submit jobs to the queue and they are only run when system
>>> resources are available. Ensure that the results are written into a file
>>> with a unique job ID in the file name and display a results page with
>>> some AJAX which keeps querying for the BLAST result file (by its ID) and
>>> inserts it into the page as soon as it is available.
>>> 
>>> Hope this helps.
>>> 
>>> Frank
>>> 
>>> 
>>> On Thu, 2010-09-23 at 06:20 -0500, Trevor Wennblom wrote:
>>>> Hi Yannick,
>>>> 
>>>> It's pretty straight-forward. Put your sequences into a blast database as usual with formatdb. Setup a page in Rails with a textarea or file upload submit form. Take the submitted text / sequence, use it to query against your blast database by saving the input to a file and running the commandline tool (such as blastn), and finally return the file containing results.
>>>> 
>>>> This is assuming your queries run quickly since the page render will be delayed until blast is complete. If you need to search against a large database there's a bit more work to it.
>>>> 
>>>> _______________________________________________
>>>> BioRuby Project - http://www.bioruby.org/
>>>> BioRuby mailing list
>>>> BioRuby at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioruby
>>> 
>>> 
>>> 
>>> -- 
>>> The Wellcome Trust Sanger Institute is operated by Genome Research 
>>> Limited, a charity registered in England with number 1021457 and a 
>>> company registered in England with number 2742969, whose registered 
>>> office is 215 Euston Road, London, NW1 2BE. 
>> 
> 
> 
> 
> -- 
> The Wellcome Trust Sanger Institute is operated by Genome Research 
> Limited, a charity registered in England with number 1021457 and a 
> company registered in England with number 2742969, whose registered 
> office is 215 Euston Road, London, NW1 2BE. 



From anurag08priyam at gmail.com  Thu Sep 23 14:06:44 2010
From: anurag08priyam at gmail.com (Anurag Priyam)
Date: Thu, 23 Sep 2010 23:36:44 +0530
Subject: [BioRuby] rails blast server
In-Reply-To: <90EA9391-3216-4634-BC69-0960C8D881DF@unil.ch>
References: <1DF3B9FB-24B8-44AC-9791-61A2EBBF7BE0@unil.ch>
	<23ACF172-B4D1-4237-81A9-BDE1A70A508C@corevx.com>
	<1285246169.29263.158.camel@deskpro15336.dynamic.sanger.ac.uk>
	<5D9604BB-313A-44B4-A91B-B868873D26C8@unil.ch>
	<1285249471.29263.166.camel@deskpro15336.dynamic.sanger.ac.uk>
	<90EA9391-3216-4634-BC69-0960C8D881DF@unil.ch>
Message-ID: <AANLkTikWcP45fCERmLReBEgBb0fenHhRQOi1QHtpatrf@mail.gmail.com>

> Dang I thought Rails would make AJAX stuff easier too? Or is that only if I need a database backend?
> Sorry for the noob questions, I haven't done any web dev in a long time...

Yea Rails will help you with AJAX a bit. It will also help you with
the upload process - paperclip plugin.

But yea, as Frank said, for something as simple as this you do not
need something as heavy as Rails. You might just want to write a Ruby
CGI script or perhaps a Sinatra app. To make life simple with AJAX you
can just use jQuery library.

I have got some web development experience; feel free to contact me
off the list :).

-- 
Anurag Priyam,
3rd Year Undergraduate,
Department of Mechanical Engineering,
IIT Kharagpur.
+91-9775550642

From russell.whitaker at gmail.com  Fri Sep 24 03:34:06 2010
From: russell.whitaker at gmail.com (Russell Whitaker)
Date: Fri, 24 Sep 2010 03:34:06 -0400
Subject: [BioRuby] May I contribute a 23andMe flatfile parser?
Message-ID: <AANLkTikgQbSpwxZF4k=5oS4MsUK1v3xR45E3Bu7iaYrW@mail.gmail.com>

Hi all / ???????????????

[Please let me know if my Japanese is mojibake / ????]

I'm a former professional software engineer who left Google 3 years
ago to pursue a degree in biochemistry from Columbia University (which
I did in fact complete, 4 months ago). After having programmed other languages
over a nearly 20 year career - one in Japan, by the way - I switched from
Python to Ruby/Rails at Google, and have committed to continue with that
as primary platform (except for statistical applications, for which I'm doing R
when needed).

I've been researching best platforms for going general bioinformatics
work, and of course discovered BioRuby, which is why I'm here on this list.

A few hours of digging have convinced me that a 23andMe SNP/genotype
flatfile parser does not yet exist in BioRuby. However, I may be wrong, so I'll
ask: does one exist? No mention of "23andMe" exists in the list archives.

Would anyone object to my writing one? I've been familiarizing myself with
the development process for this group, e.g.:

http://lists.open-bio.org/pipermail/bioruby/2010-June/001319.html

I already have a GitHub account, of course.

Thanks in advance for your help, and I look forward to contributing to this
project.

?????????????
????

-- 
Russell Whitaker
http://twitter.com/OrthoNormalRuss

From fs5 at sanger.ac.uk  Fri Sep 24 04:04:19 2010
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Fri, 24 Sep 2010 09:04:19 +0100
Subject: [BioRuby] rails blast server
In-Reply-To: <AANLkTikWcP45fCERmLReBEgBb0fenHhRQOi1QHtpatrf@mail.gmail.com>
References: <1DF3B9FB-24B8-44AC-9791-61A2EBBF7BE0@unil.ch>
	<23ACF172-B4D1-4237-81A9-BDE1A70A508C@corevx.com>
	<1285246169.29263.158.camel@deskpro15336.dynamic.sanger.ac.uk>
	<5D9604BB-313A-44B4-A91B-B868873D26C8@unil.ch>
	<1285249471.29263.166.camel@deskpro15336.dynamic.sanger.ac.uk>
	<90EA9391-3216-4634-BC69-0960C8D881DF@unil.ch>
	<AANLkTikWcP45fCERmLReBEgBb0fenHhRQOi1QHtpatrf@mail.gmail.com>
Message-ID: <1285315459.29263.193.camel@deskpro15336.dynamic.sanger.ac.uk>

Yes, Rails will give you some sugar for the AJAX stuff but, to be
honeest, it isn't that hard to code that "by hand" and if you need to
learn Rails first then it really won't be worth it for this project.
This is a bit off-topic for a BioRuby list but maybe it helps, so
here is what I use on one of my websites to check for the status of a
job. In this case, there is a cgi script that checks the job status
because this is a slightly more complex system, but you could just check
for the existence of the BLAST result file (but see below). You just
populate the job ID in the javascript function below in your template as
you generate the page. 
When my job is finished, I redirect to a different page which displays
the results but you could just as easily simply insert a link to
download the BLAST resutl file on the same page. I use Prototype.

<script  type="text/javascript"
src="../your/path/to/prototype.js"></script>

<script type="text/javascript">
function statusChecker(){
  new Ajax.Updater( 
  { success: 'jobStatus'}, 
  '../cgi-bin/some_job_status_checker.cgi',
    {
      parameters: 'jobid=1234567',
      method    : 'get',
      onComplete : onJobCompleteRedirect
    }
  );
} ;
/* the job_status_checker returns 'complete' if job is ready to download   */
function onJobCompleteRedirect(response){
  var status = response.responseText;
  if( status == 'completed') {
     window.location.href='../cgi-bin/result_page.cgi?jobid=1234567';
  }
} ;

/* this actually runs the StatusChecker every 5 secs */
new PeriodicalExecuter(statusChecker, 5) ;
</script>


Somewhere on the page I have this:
<span id="jobStatus">queued...</span> 

That's the bit that gets updated with whatever
some_job_status_checker.cgi returns. If it returns 'completed' the
results page is loaded.

One thing to bear in mind if you just check for the existence of files
to indicate job status: the BLAST result file exists before the job is
complete. For that reason you need a sysmte command that first runs
BLAST and then does something to indicate the job is finished, something
like "blastall ....; indicate_completeness.sh". 
That could be either to copy the BLAST result into the public download
folder, so your job status checker doesn't see it before it is complete
or to simply "touch" a file in that folder with a name like this:
"JOBID_complete". Then you take the existence of that file as proof that
the job is finished.
Hope this help. Good luck!

Frank




On Thu, 2010-09-23 at 23:36 +0530, Anurag Priyam wrote:
> > Dang I thought Rails would make AJAX stuff easier too? Or is that only if I need a database backend?
> > Sorry for the noob questions, I haven't done any web dev in a long time...
> 
> Yea Rails will help you with AJAX a bit. It will also help you with
> the upload process - paperclip plugin.
> 
> But yea, as Frank said, for something as simple as this you do not
> need something as heavy as Rails. You might just want to write a Ruby
> CGI script or perhaps a Sinatra app. To make life simple with AJAX you
> can just use jQuery library.
> 
> I have got some web development experience; feel free to contact me
> off the list :).
> 



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

From yannick.wurm at unil.ch  Sat Sep 25 03:49:39 2010
From: yannick.wurm at unil.ch (Yannick Wurm)
Date: Sat, 25 Sep 2010 14:49:39 +0700
Subject: [BioRuby] rails blast server
In-Reply-To: <1285315459.29263.193.camel@deskpro15336.dynamic.sanger.ac.uk>
References: <1DF3B9FB-24B8-44AC-9791-61A2EBBF7BE0@unil.ch>
	<23ACF172-B4D1-4237-81A9-BDE1A70A508C@corevx.com>
	<1285246169.29263.158.camel@deskpro15336.dynamic.sanger.ac.uk>
	<5D9604BB-313A-44B4-A91B-B868873D26C8@unil.ch>
	<1285249471.29263.166.camel@deskpro15336.dynamic.sanger.ac.uk>
	<90EA9391-3216-4634-BC69-0960C8D881DF@unil.ch>
	<AANLkTikWcP45fCERmLReBEgBb0fenHhRQOi1QHtpatrf@mail.gmail.com>
	<1285315459.29263.193.camel@deskpro15336.dynamic.sanger.ac.uk>
Message-ID: <08DAFC33-6B56-4F3A-8BA7-510ECA2BCD6B@unil.ch>

Thanks guys for the code and advice!

I apologize for taking the list so far off track...

Thanks and regards,
Yannick


On 24 Sep 2010, at 15:04, Frank Schwach wrote:

> Yes, Rails will give you some sugar for the AJAX stuff but, to be
> honeest, it isn't that hard to code that "by hand" and if you need to
> learn Rails first then it really won't be worth it for this project.
> This is a bit off-topic for a BioRuby list but maybe it helps, so
> here is what I use on one of my websites to check for the status of a
> job. In this case, there is a cgi script that checks the job status
> because this is a slightly more complex system, but you could just check
> for the existence of the BLAST result file (but see below). You just
> populate the job ID in the javascript function below in your template as
> you generate the page. 
> When my job is finished, I redirect to a different page which displays
> the results but you could just as easily simply insert a link to
> download the BLAST resutl file on the same page. I use Prototype.
> 
> <script  type="text/javascript"
> src="../your/path/to/prototype.js"></script>
> 
> <script type="text/javascript">
> function statusChecker(){
>  new Ajax.Updater( 
>  { success: 'jobStatus'}, 
>  '../cgi-bin/some_job_status_checker.cgi',
>    {
>      parameters: 'jobid=1234567',
>      method    : 'get',
>      onComplete : onJobCompleteRedirect
>    }
>  );
> } ;
> /* the job_status_checker returns 'complete' if job is ready to download   */
> function onJobCompleteRedirect(response){
>  var status = response.responseText;
>  if( status == 'completed') {
>     window.location.href='../cgi-bin/result_page.cgi?jobid=1234567';
>  }
> } ;
> 
> /* this actually runs the StatusChecker every 5 secs */
> new PeriodicalExecuter(statusChecker, 5) ;
> </script>
> 
> 
> Somewhere on the page I have this:
> <span id="jobStatus">queued...</span> 
> 
> That's the bit that gets updated with whatever
> some_job_status_checker.cgi returns. If it returns 'completed' the
> results page is loaded.
> 
> One thing to bear in mind if you just check for the existence of files
> to indicate job status: the BLAST result file exists before the job is
> complete. For that reason you need a sysmte command that first runs
> BLAST and then does something to indicate the job is finished, something
> like "blastall ....; indicate_completeness.sh". 
> That could be either to copy the BLAST result into the public download
> folder, so your job status checker doesn't see it before it is complete
> or to simply "touch" a file in that folder with a name like this:
> "JOBID_complete". Then you take the existence of that file as proof that
> the job is finished.
> Hope this help. Good luck!
> 
> Frank
> 
> 
> 
> 
> On Thu, 2010-09-23 at 23:36 +0530, Anurag Priyam wrote:
>>> Dang I thought Rails would make AJAX stuff easier too? Or is that only if I need a database backend?
>>> Sorry for the noob questions, I haven't done any web dev in a long time...
>> 
>> Yea Rails will help you with AJAX a bit. It will also help you with
>> the upload process - paperclip plugin.
>> 
>> But yea, as Frank said, for something as simple as this you do not
>> need something as heavy as Rails. You might just want to write a Ruby
>> CGI script or perhaps a Sinatra app. To make life simple with AJAX you
>> can just use jQuery library.
>> 
>> I have got some web development experience; feel free to contact me
>> off the list :).
>> 
> 
> 
> 
> -- 
> The Wellcome Trust Sanger Institute is operated by Genome Research 
> Limited, a charity registered in England with number 1021457 and a 
> company registered in England with number 2742969, whose registered 
> office is 215 Euston Road, London, NW1 2BE. 



--------------------------------------------
          yannick . wurm @ unil . ch
Ant Genomics, Ecology & Evolution @ Lausanne
   http://www.unil.ch/dee/page28685_fr.html




From protasdeo at yahoo.com  Sat Sep 25 15:15:39 2010
From: protasdeo at yahoo.com (protasdeo at yahoo.com)
Date: Sat, 25 Sep 2010 19:15:39 +0000
Subject: [BioRuby] Bioruby mailing list
Message-ID: <490907.92596.qm@smtp106-mob.biz.mail.ird.yahoo.com>

Bioruby mailing lists subscribe.



From russell.whitaker at gmail.com  Sat Sep 25 15:47:52 2010
From: russell.whitaker at gmail.com (Russell Whitaker)
Date: Sat, 25 Sep 2010 15:47:52 -0400
Subject: [BioRuby] Bioruby mailing list
In-Reply-To: <490907.92596.qm@smtp106-mob.biz.mail.ird.yahoo.com>
References: <490907.92596.qm@smtp106-mob.biz.mail.ird.yahoo.com>
Message-ID: <0FA7D197-9154-4959-8AFA-90DACDC68E7A@gmail.com>

Wonder Twin powers activate!

Russell Whitaker
Sent from my iPhone

On Sep 25, 2010, at 3:15 PM, "protasdeo at yahoo.com" <protasdeo at yahoo.com> wrote:

> Bioruby mailing lists subscribe.
> 
> 
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby


From protasdeo at yahoo.com  Sun Sep 26 12:06:40 2010
From: protasdeo at yahoo.com (protasdeo at yahoo.com)
Date: Sun, 26 Sep 2010 16:06:40 +0000
Subject: [BioRuby] BioRuby mailing list submission
Message-ID: <686985.30438.qm@smtp106-mob.biz.mail.ird.yahoo.com>



 BioRuby mailing list submissions to
	

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When replying, please edit your Subject line so it is more specific
than "Re: Contents of BioRuby digest..."


Today's Topics:

   1. Bioruby mailing list (protasdeo at yahoo.com)
   2. Re: Bioruby mailing list (Russell Whitaker)


----------------------------------------------------------------------

Message: 1
Date: Sat, 25 Sep 2010 19:15:39 +0000
From: "protasdeo at yahoo.com" <protasdeo at yahoo.com>
Subject: [BioRuby] Bioruby mailing list
To: "bioruby at lists.open-bio.org" <bioruby at lists.open-bio.org>
Message-ID: <490907.92596.qm at smtp106-mob.biz.mail.ird.yahoo.com>
Content-Type: text/plain;	charset="utf-8"

Bioruby mailing lists subscribe.




------------------------------

Message: 2
Date: Sat, 25 Sep 2010 15:47:52 -0400
From: Russell Whitaker <russell.whitaker at gmail.com>
Subject: Re: [BioRuby] Bioruby mailing list
To: "protasdeo at yahoo.com" <protasdeo at yahoo.com>
Cc: "bioruby at lists.open-bio.org" <bioruby at lists.open-bio.org>
Message-ID: <0FA7D197-9154-4959-8AFA-90DACDC68E7A at gmail.com>
Content-Type: text/plain; charset=us-ascii

Wonder Twin powers activate!

Russell Whitaker
Sent from my iPhone

On Sep 25, 2010, at 3:15 PM, "protasdeo at yahoo.com" <protasdeo at yahoo.com> wrote:

> Bioruby mailing lists subscribe.
> 
> 
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby



------------------------------

_______________________________________________
BioRuby mailing list
BioRuby at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioruby


End of BioRuby Digest, Vol 60, Issue 10
***************************************



From bonnalraoul at ingm.it  Mon Sep 27 06:52:50 2010
From: bonnalraoul at ingm.it (Raoul Bonnal)
Date: Mon, 27 Sep 2010 12:52:50 +0200
Subject: [BioRuby] Ruby 1.9.2 and BioRuby
Message-ID: <69b8f26b-7ca6-402a-a559-cea06e5dd4bf@ingm.it>

Hello guys, 
Do you have any idea how to solve this error?
/home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-3.0.0/lib/active_support/dependencies.rb:479:in `load_missing_constant': Bio is not missing constant Sequence! (ArgumentError)
        from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-3.0.0/lib/active_support/dependencies.rb:183:in `block in const_missing'
        from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-3.0.0/lib/active_support/dependencies.rb:181:in `each'
        from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-3.0.0/lib/active_support/dependencies.rb:181:in `const_missing'
        from /home/ra/deve/bioruby/lib/bio/sequence/compat.rb:15:in `<module:Bio>'
        from /home/ra/deve/bioruby/lib/bio/sequence/compat.rb:13:in `<top (required)>'
        from <internal:lib/rubygems/custom_require>:29:in `require'
        from <internal:lib/rubygems/custom_require>:29:in `require'
        from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-3.0.0/lib/active_support/dependencies.rb:239:in `block in require'
        from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-3.0.0/lib/active_support/dependencies.rb:225:in `block in load_dependency'
        from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-3.0.0/lib/active_support/dependencies.rb:591:in `new_constants_in'
        from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-3.0.0/lib/active_support/dependencies.rb:225:in `load_dependency'
        from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-3.0.0/lib/active_support/dependencies.rb:239:in `require'
        from /home/ra/deve/bioruby/lib/bio/sequence.rb:15:in `<top (required)>'
        from /home/ra/deve/bioruby/lib/bio/shell/plugin/midi.rb:20:in `<top (required)>'
        from <internal:lib/rubygems/custom_require>:29:in `require'
        from <internal:lib/rubygems/custom_require>:29:in `require'
        from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-3.0.0/lib/active_support/dependencies.rb:239:in `block in require'
        from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-3.0.0/lib/active_support/dependencies.rb:225:in `block in load_dependency'
        from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-3.0.0/lib/active_support/dependencies.rb:591:in `new_constants_in'
        from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-3.0.0/lib/active_support/dependencies.rb:225:in `load_dependency'
        from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-3.0.0/lib/active_support/dependencies.rb:239:in `require'
        from /home/ra/deve/bioruby/lib/bio/shell.rb:29:in `<module:Shell>'
        from /home/ra/deve/bioruby/lib/bio/shell.rb:17:in `<top (required)>'
        from <internal:lib/rubygems/custom_require>:29:in `require'
        from <internal:lib/rubygems/custom_require>:29:in `require'
        from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-3.0.0/lib/active_support/dependencies.rb:239:in `block in require'
        from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-3.0.0/lib/active_support/dependencies.rb:225:in `block in load_dependency'
        from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-3.0.0/lib/active_support/dependencies.rb:591:in `new_constants_in'
        from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-3.0.0/lib/active_support/dependencies.rb:225:in `load_dependency'
        from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-3.0.0/lib/active_support/dependencies.rb:239:in `require'
        from /home/ra/deve/bioruby/bin/bioruby:18:in `<main>'

--
Raoul J.P. Bonnal
Life Science Informatics
Integrative Biology Program
Fondazione INGM
Via F. Sforza 28
20122 Milano, IT
phone: +39 02 006 623  26
fax: +39 02 006 623 46
http://www.ingm.it





From bonnalraoul at ingm.it  Mon Sep 27 09:10:56 2010
From: bonnalraoul at ingm.it (Raoul Bonnal)
Date: Mon, 27 Sep 2010 15:10:56 +0200
Subject: [BioRuby] R:  Ruby 1.9.2 and BioRuby
In-Reply-To: <69b8f26b-7ca6-402a-a559-cea06e5dd4bf@ingm.it>
References: <69b8f26b-7ca6-402a-a559-cea06e5dd4bf@ingm.it>
Message-ID: <89b0ec08-ad5d-4684-acf9-aa05403be430@ingm.it>

And ... it works on 1.8.7 and 1.9.1

--
Raoul J.P. Bonnal
Life Science Informatics
Integrative Biology Program
Fondazione INGM
Via F. Sforza 28
20122 Milano, IT
phone: +39 02 006 623  26
fax: +39 02 006 623 46
http://www.ingm.it


> -----Messaggio originale-----
> Da: bioruby-bounces at lists.open-bio.org [mailto:bioruby-
> bounces at lists.open-bio.org] Per conto di Raoul Bonnal
> Inviato: luned? 27 settembre 2010 12:53
> A: bioruby at lists.open-bio.org
> Oggetto: [BioRuby] Ruby 1.9.2 and BioRuby
> 
> Hello guys,
> Do you have any idea how to solve this error?
> /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> 3.0.0/lib/active_support/dependencies.rb:479:in
> `load_missing_constant': Bio is not missing constant Sequence!
> (ArgumentError)
>         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> 3.0.0/lib/active_support/dependencies.rb:183:in `block in
> const_missing'
>         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> 3.0.0/lib/active_support/dependencies.rb:181:in `each'
>         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> 3.0.0/lib/active_support/dependencies.rb:181:in `const_missing'
>         from /home/ra/deve/bioruby/lib/bio/sequence/compat.rb:15:in
> `<module:Bio>'
>         from /home/ra/deve/bioruby/lib/bio/sequence/compat.rb:13:in
> `<top (required)>'
>         from <internal:lib/rubygems/custom_require>:29:in `require'
>         from <internal:lib/rubygems/custom_require>:29:in `require'
>         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> 3.0.0/lib/active_support/dependencies.rb:239:in `block in require'
>         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> 3.0.0/lib/active_support/dependencies.rb:225:in `block in
> load_dependency'
>         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> 3.0.0/lib/active_support/dependencies.rb:591:in `new_constants_in'
>         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> 3.0.0/lib/active_support/dependencies.rb:225:in `load_dependency'
>         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> 3.0.0/lib/active_support/dependencies.rb:239:in `require'
>         from /home/ra/deve/bioruby/lib/bio/sequence.rb:15:in `<top
> (required)>'
>         from /home/ra/deve/bioruby/lib/bio/shell/plugin/midi.rb:20:in
> `<top (required)>'
>         from <internal:lib/rubygems/custom_require>:29:in `require'
>         from <internal:lib/rubygems/custom_require>:29:in `require'
>         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> 3.0.0/lib/active_support/dependencies.rb:239:in `block in require'
>         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> 3.0.0/lib/active_support/dependencies.rb:225:in `block in
> load_dependency'
>         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> 3.0.0/lib/active_support/dependencies.rb:591:in `new_constants_in'
>         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> 3.0.0/lib/active_support/dependencies.rb:225:in `load_dependency'
>         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> 3.0.0/lib/active_support/dependencies.rb:239:in `require'
>         from /home/ra/deve/bioruby/lib/bio/shell.rb:29:in
> `<module:Shell>'
>         from /home/ra/deve/bioruby/lib/bio/shell.rb:17:in `<top
> (required)>'
>         from <internal:lib/rubygems/custom_require>:29:in `require'
>         from <internal:lib/rubygems/custom_require>:29:in `require'
>         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> 3.0.0/lib/active_support/dependencies.rb:239:in `block in require'
>         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> 3.0.0/lib/active_support/dependencies.rb:225:in `block in
> load_dependency'
>         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> 3.0.0/lib/active_support/dependencies.rb:591:in `new_constants_in'
>         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> 3.0.0/lib/active_support/dependencies.rb:225:in `load_dependency'
>         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> 3.0.0/lib/active_support/dependencies.rb:239:in `require'
>         from /home/ra/deve/bioruby/bin/bioruby:18:in `<main>'
> 
> --
> Raoul J.P. Bonnal
> Life Science Informatics
> Integrative Biology Program
> Fondazione INGM
> Via F. Sforza 28
> 20122 Milano, IT
> phone: +39 02 006 623  26
> fax: +39 02 006 623 46
> http://www.ingm.it
> 
> 
> 
> 
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby



From bonnalraoul at ingm.it  Mon Sep 27 09:25:00 2010
From: bonnalraoul at ingm.it (Raoul Bonnal)
Date: Mon, 27 Sep 2010 15:25:00 +0200
Subject: [BioRuby] R:  Ruby 1.9.2 and BioRuby
In-Reply-To: <89b0ec08-ad5d-4684-acf9-aa05403be430@ingm.it>
References: <69b8f26b-7ca6-402a-a559-cea06e5dd4bf@ingm.it>
	<89b0ec08-ad5d-4684-acf9-aa05403be430@ingm.it>
Message-ID: <fbda1caf-be6c-4e0b-839c-ad708dfc23de@ingm.it>

It's a problem of loading path. In Ruby 1.9.2 the '.' is not loaded by default.
Adding the $:<<'.' Seems to patch the problem.
I did some test and probably 

In activerecord, for instance, they do in this way.


activesupport_path = File.expand_path('../../../activesupport/lib', __FILE__)
$:.unshift(activesupport_path) if File.directory?(activesupport_path) && !$:.include?(activesupport_path)

activemodel_path = File.expand_path('../../../activemodel/lib', __FILE__)
$:.unshift(activemodel_path) if File.directory?(activemodel_path) && !$:.include?(activemodel_path)

require 'active_support'
require 'active_support/i18n'
require 'active_model'
require 'arel'
--
Raoul J.P. Bonnal
Life Science Informatics
Integrative Biology Program
Fondazione INGM
Via F. Sforza 28
20122 Milano, IT
phone: +39 02 006 623  26
fax: +39 02 006 623 46
http://www.ingm.it


> -----Messaggio originale-----
> Da: Raoul Bonnal [mailto:bonnalraoul at ingm.it]
> Inviato: luned? 27 settembre 2010 15:11
> A: 'Raoul Bonnal'; bioruby at lists.open-bio.org
> Oggetto: R: [BioRuby] Ruby 1.9.2 and BioRuby
> 
> And ... it works on 1.8.7 and 1.9.1
> 
> --
> Raoul J.P. Bonnal
> Life Science Informatics
> Integrative Biology Program
> Fondazione INGM
> Via F. Sforza 28
> 20122 Milano, IT
> phone: +39 02 006 623  26
> fax: +39 02 006 623 46
> http://www.ingm.it
> 
> 
> > -----Messaggio originale-----
> > Da: bioruby-bounces at lists.open-bio.org [mailto:bioruby-
> > bounces at lists.open-bio.org] Per conto di Raoul Bonnal
> > Inviato: luned? 27 settembre 2010 12:53
> > A: bioruby at lists.open-bio.org
> > Oggetto: [BioRuby] Ruby 1.9.2 and BioRuby
> >
> > Hello guys,
> > Do you have any idea how to solve this error?
> > /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> > 3.0.0/lib/active_support/dependencies.rb:479:in
> > `load_missing_constant': Bio is not missing constant Sequence!
> > (ArgumentError)
> >         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> > 3.0.0/lib/active_support/dependencies.rb:183:in `block in
> > const_missing'
> >         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> > 3.0.0/lib/active_support/dependencies.rb:181:in `each'
> >         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> > 3.0.0/lib/active_support/dependencies.rb:181:in `const_missing'
> >         from /home/ra/deve/bioruby/lib/bio/sequence/compat.rb:15:in
> > `<module:Bio>'
> >         from /home/ra/deve/bioruby/lib/bio/sequence/compat.rb:13:in
> > `<top (required)>'
> >         from <internal:lib/rubygems/custom_require>:29:in `require'
> >         from <internal:lib/rubygems/custom_require>:29:in `require'
> >         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> > 3.0.0/lib/active_support/dependencies.rb:239:in `block in require'
> >         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> > 3.0.0/lib/active_support/dependencies.rb:225:in `block in
> > load_dependency'
> >         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> > 3.0.0/lib/active_support/dependencies.rb:591:in `new_constants_in'
> >         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> > 3.0.0/lib/active_support/dependencies.rb:225:in `load_dependency'
> >         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> > 3.0.0/lib/active_support/dependencies.rb:239:in `require'
> >         from /home/ra/deve/bioruby/lib/bio/sequence.rb:15:in `<top
> > (required)>'
> >         from /home/ra/deve/bioruby/lib/bio/shell/plugin/midi.rb:20:in
> > `<top (required)>'
> >         from <internal:lib/rubygems/custom_require>:29:in `require'
> >         from <internal:lib/rubygems/custom_require>:29:in `require'
> >         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> > 3.0.0/lib/active_support/dependencies.rb:239:in `block in require'
> >         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> > 3.0.0/lib/active_support/dependencies.rb:225:in `block in
> > load_dependency'
> >         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> > 3.0.0/lib/active_support/dependencies.rb:591:in `new_constants_in'
> >         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> > 3.0.0/lib/active_support/dependencies.rb:225:in `load_dependency'
> >         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> > 3.0.0/lib/active_support/dependencies.rb:239:in `require'
> >         from /home/ra/deve/bioruby/lib/bio/shell.rb:29:in
> > `<module:Shell>'
> >         from /home/ra/deve/bioruby/lib/bio/shell.rb:17:in `<top
> > (required)>'
> >         from <internal:lib/rubygems/custom_require>:29:in `require'
> >         from <internal:lib/rubygems/custom_require>:29:in `require'
> >         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> > 3.0.0/lib/active_support/dependencies.rb:239:in `block in require'
> >         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> > 3.0.0/lib/active_support/dependencies.rb:225:in `block in
> > load_dependency'
> >         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> > 3.0.0/lib/active_support/dependencies.rb:591:in `new_constants_in'
> >         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> > 3.0.0/lib/active_support/dependencies.rb:225:in `load_dependency'
> >         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> > 3.0.0/lib/active_support/dependencies.rb:239:in `require'
> >         from /home/ra/deve/bioruby/bin/bioruby:18:in `<main>'
> >
> > --
> > Raoul J.P. Bonnal
> > Life Science Informatics
> > Integrative Biology Program
> > Fondazione INGM
> > Via F. Sforza 28
> > 20122 Milano, IT
> > phone: +39 02 006 623  26
> > fax: +39 02 006 623 46
> > http://www.ingm.it
> >
> >
> >
> >
> > _______________________________________________
> > BioRuby Project - http://www.bioruby.org/
> > BioRuby mailing list
> > BioRuby at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioruby



From bonnalraoul at ingm.it  Wed Sep  1 13:39:44 2010
From: bonnalraoul at ingm.it (Raoul Bonnal)
Date: Wed, 1 Sep 2010 15:39:44 +0200
Subject: [BioRuby] R:  Fwd: Re: BioSQL development
In-Reply-To: <op.vhuh3umxztul55@jn-themachine>
References: <AANLkTinnBXnxfQ=0G9qo2wqg7Mzcct0DBe=_tpYbvXZC@mail.gmail.com><op.vhtz5q0uztul55@jn-themachine><AANLkTi=vVH6e4ZXgR58Q=w4vtWonSqXtOAognTjz1J6X@mail.gmail.com><op.vht2g3osztul55@jn-themachine>
	<op.vht4sdiyztul55@jn-themachine><DBAEAA32-1EA1-4775-8D8A-5B95B06B842B@drycafe.net><AANLkTim_BdBoduYkng74CpUj9bW724KHvN539bfTy+zU@mail.gmail.com><AANLkTi=84YhHRtgbaooRXm4oHgoK31kf1zSZ8CaLY9DS@mail.gmail.com><A
	ANLkTinfSktFrdWXE9RFr-bUsw3fMQaro8b45bUm8t2Q@mail.gmail.com>
	<op.vhuh3umxztul55@jn-themachine>
Message-ID: <dec0288d-ccf9-4032-b5ad-66724feca914@ingm.it>

Hello,
I didn't start to map GFF3 to BioSQL in BioRuby, sorry for that.
Theoretically if the format is readable in BioRuby as a BioSequence object then is possible to start to map it to the BioSQL schema.
If you wrote some code please share it with git or gist http://gist.github.com/ pointing out which are the GFF3's "features", to start the GFF3 support in BioRuby/BioSQL.


About CHADO, I think that adding another schema is a good thing, supporting more schemas give us the flexibility to satisfy more users, is good.

The problem of loading huge datasets is a big problem in BioRuby/BioSQL too, creating the BioSequence object and then moving it to biosql low level is very cpu/memory consuming. Now my brain is still in vacation so any idea on how to speed up the process without relying on better implementation of the RubyVM is appreciated.

Now BioSQL is distributed with BioRuby one of the ideas is to move biosql to an optional plugin and I think that the CHADO implementation should follow the same path. BUT we have to discuss more deeply the plugin system in BioRuby.

About which ORM is better to use ? Actually, at the beginning I was very confortable with DataMapper because had some nice features like composite primary key or lazy loading, unfortunately the majority of the Rails applications use ActiveRecord and maintaining different ORM it's a messy and I had to choose the more supported/spread/known ORM. Now I'll not convert BioSQL to DataMapper (I have an original implementation) however I'm very open to discuss about alternative ORM, it is also very fascinating at least for me.


Day 1, the hell is knocking to my door.

--
Raoul J.P. Bonnal
Life Science Informatics
Integrative Biology Program
Fondazione INGM
Via F. Sforza 28
20122 Milano, IT
phone: +39 02 006 623  26
fax: +39 02 006 623 46
http://www.ingm.it


> -----Messaggio originale-----
> Da: bioruby-bounces at lists.open-bio.org [mailto:bioruby-
> bounces at lists.open-bio.org] Per conto di Julian Nordt
> Inviato: domenica 22 agosto 2010 17:18
> A: Hilmar Lapp; Rob Syme
> Cc: bioruby at lists.open-bio.org
> Oggetto: Re: [BioRuby] Fwd: Re: BioSQL development
> 
> One more thing in regard to the mapping between BioSQL and GFF3:
> 
> I tried to follow the mapping given by the biosql wiki and blue collar
> bioinformatics. The mapping is acceptable in the sense that you can
> store
> *most* or even all (?) of the features that GFF3 offers. The further I
> got
> though within the development the unclearer things got me, especially
> in
> terms of the "attribute" column.
> 
> If you compare the table at the biosql wiki (for the attribute column)
> with the one at blue collar bioinformatics, one will notice that the
> there
> are keywords that occour in one, but not at the other table. That not
> mentioning the todos on the wiki regarding the "standard" columns. I
> havn't looked in that detail though through blue collars code, maybe
> the
> answer is given there.
> 
> However I wrote a small library that managed to store most - but not
> all
> the given information of the GFF3-files - correctly to BioSQL. There
> were
> some points where the mapping has been unclear to me and where I stored
> the given information where I thought it would fit best.
> 
> Considering that I chose a standard db schema to avoid any ambiguously
> and
> the fact that I experienced performance issues with MYSQL+Rails (not
> related to BioSQL) at the project made it enough for me to switch to
> CHADO
> backed by POSTGRES.
> 
> The documentation regarding CHADO is in my opinion richer and most
> importantly one can follow gmod_bulk_load_gff3.pl for the mapping
> relatively easy, since it is well documented.
> 
> I would very much welcome other opinions on the topic, especially in
> combination with the use of web applications.
> 
> -- Julian
> 
> 
> 
> 
> 
> On Sun, 22 Aug 2010 16:17:45 +0200, Rob Syme <rob.syme at gmail.com>
> wrote:
> 
> > I've had a look around and a pretty solid mapping seems to be
> available:
> > http://www.biosql.org/wiki/Annotation_Mapping#GFF3
> >
> > Blue collar bioinformatics gave it a shot here:
> > http://bcbio.wordpress.com/2009/02/22/exploring-bioperl-genbank-to-
> gff-mapping/
> >
> > -r
> >
> > On 22 Aug 2010 22:02, "Hilmar Lapp" <hlapp at drycafe.net> wrote:
> > Is the issue with GFF3 in the Bioruby to BioSQL mapping, or is
> somehow in
> > the BioSQL schema?
> >
> > I recall there was a thread on GFF recently which I wasn't able to
> > follow,
> > so if the answer is in that thread and isn't easy to sum up here,
> just
> > point
> > me there.
> >
> >        -hilmar
> >
> >
> >
> > On Aug 22, 2010, at 6:30 AM, Julian Nordt wrote:
> >
> >> Hi Rob,
> >>
> >> I just wanted to point that there ...
> 
> 
> --
> Using Opera's revolutionary email client: http://www.opera.com/mail/
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby




From rob.syme at gmail.com  Wed Sep  1 14:31:54 2010
From: rob.syme at gmail.com (Rob Syme)
Date: Wed, 1 Sep 2010 22:31:54 +0800
Subject: [BioRuby] Fwd: Re: BioSQL development
In-Reply-To: <dec0288d-ccf9-4032-b5ad-66724feca914@ingm.it>
References: <AANLkTinnBXnxfQ=0G9qo2wqg7Mzcct0DBe=_tpYbvXZC@mail.gmail.com>
	<op.vhtz5q0uztul55@jn-themachine>
	<AANLkTi=vVH6e4ZXgR58Q=w4vtWonSqXtOAognTjz1J6X@mail.gmail.com>
	<op.vht2g3osztul55@jn-themachine> <op.vht4sdiyztul55@jn-themachine>
	<DBAEAA32-1EA1-4775-8D8A-5B95B06B842B@drycafe.net>
	<AANLkTim_BdBoduYkng74CpUj9bW724KHvN539bfTy+zU@mail.gmail.com>
	<AANLkTi=84YhHRtgbaooRXm4oHgoK31kf1zSZ8CaLY9DS@mail.gmail.com>
	<op.vhuh3umxztul55@jn-themachine>
	<dec0288d-ccf9-4032-b5ad-66724feca914@ingm.it>
Message-ID: <AANLkTi=NZQzGuxyYAkFZKiccqOk20VN8hvwpAL6KoQmV@mail.gmail.com>

I agree that db schemas and associated code should be implemented as
plugins. I haven't been keeping up-to-date with how the plugin system
works. From?Pjotr's gff3 post
(http://thebird.nl/bioruby/BioRuby_GFF3.html) and github repo
(http://github.com/pjotrp/bioruby-gff3-plugin) it looks like we just
put our plugin under the Bio module and add the plugin lib dir to the
search path. Is this correct?
-r

On Wed, Sep 1, 2010 at 9:39 PM, Raoul Bonnal <bonnalraoul at ingm.it> wrote:
>
> Hello,
> I didn't start to map GFF3 to BioSQL in BioRuby, sorry for that.
> Theoretically if the format is readable in BioRuby as a BioSequence object then is possible to start to map it to the BioSQL schema.



From pjotr.public14 at thebird.nl  Sat Sep  4 11:49:30 2010
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Sat, 4 Sep 2010 13:49:30 +0200
Subject: [BioRuby] Fwd: Re: BioSQL development
In-Reply-To: <AANLkTi=NZQzGuxyYAkFZKiccqOk20VN8hvwpAL6KoQmV@mail.gmail.com>
References: <op.vhtz5q0uztul55@jn-themachine>
	<AANLkTi=vVH6e4ZXgR58Q=w4vtWonSqXtOAognTjz1J6X@mail.gmail.com>
	<op.vht2g3osztul55@jn-themachine> <op.vht4sdiyztul55@jn-themachine>
	<DBAEAA32-1EA1-4775-8D8A-5B95B06B842B@drycafe.net>
	<AANLkTim_BdBoduYkng74CpUj9bW724KHvN539bfTy+zU@mail.gmail.com>
	<AANLkTi=84YhHRtgbaooRXm4oHgoK31kf1zSZ8CaLY9DS@mail.gmail.com>
	<op.vhuh3umxztul55@jn-themachine>
	<dec0288d-ccf9-4032-b5ad-66724feca914@ingm.it>
	<AANLkTi=NZQzGuxyYAkFZKiccqOk20VN8hvwpAL6KoQmV@mail.gmail.com>
Message-ID: <20100904114930.GA27474@thebird.nl>

On Wed, Sep 01, 2010 at 10:31:54PM +0800, Rob Syme wrote:
> (http://github.com/pjotrp/bioruby-gff3-plugin) it looks like we just
> put our plugin under the Bio module and add the plugin lib dir to the
> search path. Is this correct?

Yes. Raoul and Toshiaki wrote a prototype plugin handler, which will
come to be. E.g. 

  bioruby --install plugin-name

will fetch the plugin and add it to the search path automagically.

For now, merely adding the plugin lib dir to the search path is good
enough, as that will be compatible.

Pj.


From gmsaner at gmail.com  Tue Sep  7 00:31:07 2010
From: gmsaner at gmail.com (=?ISO-8859-2?Q?Maciej_=A3opatka?=)
Date: Tue, 7 Sep 2010 02:31:07 +0200
Subject: [BioRuby] BioRuby, EMBL file
Message-ID: <AANLkTi=Yqg1qJDvg8pj9Hk9veb=QxMhGiMfARNqa5ynw@mail.gmail.com>

Hello,

In my program I need complete genomes of bacterias. I download them from
Ensembl's FTP server (for example
ftp://ftp.ensemblgenomes.org/pub/bacteria/current/embl/bacillus_collection/B_amyloliquefaciens/
).
Those files have embl format.

The genomes in those files are in parts, so I need to iterate over them (I
use file.each_entry do {} ), however they are not in correct order so they
can't be simply concatenated. At the moment I use Regex to get entry's
position which is provided in entry's definition property. This is not very
clean way.

Is there a better way to get information about entry's position in genome?

Thanks,
Maciej Lopatka


From chmille4 at gmail.com  Wed Sep  8 03:01:09 2010
From: chmille4 at gmail.com (Chase Miller)
Date: Tue, 7 Sep 2010 23:01:09 -0400
Subject: [BioRuby] Bio::Assembly + Ace Parser
Message-ID: <AANLkTinG-vKb84vowTCkbZymO3pvnJJRZs831o4MEqH4@mail.gmail.com>

Hi All

I finally got around to doing this and have written a simple Bio::Assembly
class with a streaming ace parser.   As part of this, I have
Bio::Assembly::Contig and Bio::Assembly::Read classes.  The general flow
goes like this - a Bio::Assembly object relates to a single ace file and is
made up of Bio::Assembly::Contig objects, which are in turn made up of
Bio::Assembly::Read objects.

It probably needs a bit more work (see TODO below), but I thought I'd go
ahead and get some feedback. Take a look and let me know what you think.

http://github.com/chmille4/bioruby


TODO:

   - Currently, the ace parser is integrated into bio/assembly.rb, but I'd
   like to extract this out to make it easier to support more file formats.
    Any ideas on a good (bioruby) way to do this?
   - Flesh out the features.  Any requests?
   - Add more tests (8 so far in test/unit/bio/test_assembly.rb)
   - Make sure that manipulating Bio::Assembly objects ( i.e deleting
   contigs ) does not the cause the ace unparser to create illegal ace files.
   - Add more documentation


Cheers!
Chase


From gmsaner at gmail.com  Thu Sep  9 21:01:55 2010
From: gmsaner at gmail.com (=?ISO-8859-2?Q?Maciej_=A3opatka?=)
Date: Thu, 9 Sep 2010 23:01:55 +0200
Subject: [BioRuby] BioRuby, performance, cut_with_enzyme
Message-ID: <AANLkTi=e-xSJwxX_OhzCFztRe1cVnrJ=WCmdgmh1QZR4@mail.gmail.com>

Hello,

I've got a big problem with performance of BioRuby. I need to cut sequence
(about 5MB <  < 17MB) with restriction enzymes. It takes ages to cut it with
just one enzyme, it just doesn't stop, and I have no idea what is going on.
My friend for the same task used BioPython and it took just 2 minutes for 20
enzymes.

I know that Ruby is slower than Python, but it doesn't explain this. Has
anyone had similar problems?

I've tested this on Ubuntu 9.04 and Windows 7 with Ruby 1.8.7 on Linux, and
Ruby 1.9.2 on Windows.

Thanks,
Maciek Lopatka


From trevor at corevx.com  Thu Sep  9 21:29:44 2010
From: trevor at corevx.com (Trevor Wennblom)
Date: Thu, 9 Sep 2010 16:29:44 -0500
Subject: [BioRuby] BioRuby, performance, cut_with_enzyme
In-Reply-To: <AANLkTi=e-xSJwxX_OhzCFztRe1cVnrJ=WCmdgmh1QZR4@mail.gmail.com>
References: <AANLkTi=e-xSJwxX_OhzCFztRe1cVnrJ=WCmdgmh1QZR4@mail.gmail.com>
Message-ID: <E1E7F48A-C50D-48A1-A20B-72BB703677C0@corevx.com>

Also - which version of Ruby are you using? Performance should be significantly faster on 1.9.2 versus 1.8 due to improvements to the RegExp engine.


From trevor at corevx.com  Thu Sep  9 21:11:53 2010
From: trevor at corevx.com (Trevor Wennblom)
Date: Thu, 9 Sep 2010 16:11:53 -0500
Subject: [BioRuby] BioRuby, performance, cut_with_enzyme
In-Reply-To: <AANLkTi=e-xSJwxX_OhzCFztRe1cVnrJ=WCmdgmh1QZR4@mail.gmail.com>
References: <AANLkTi=e-xSJwxX_OhzCFztRe1cVnrJ=WCmdgmh1QZR4@mail.gmail.com>
Message-ID: <F2728011-A1CB-494A-A796-F564F2D07E9D@corevx.com>


On Sep 9, 2010, at 4:01 PM, Maciej ?opatka wrote:

> I've got a big problem with performance of BioRuby. I need to cut sequence
> (about 5MB <  < 17MB) with restriction enzymes. It takes ages to cut it with
> just one enzyme, it just doesn't stop, and I have no idea what is going on.
> My friend for the same task used BioPython and it took just 2 minutes for 20
> enzymes.



Hi Maciek,

I'm the author of that particular extension. One of the particular points of the design - several years ago - was to accommodate the particular cut patterns on both strands of the sequence. If I recall, other libraries concentrate on only one strand of the sequence.

This does take a considerable performance hit, interpreted language aside. I'm also relatively certain that I didn't implement the most efficient algorithm as it was my first crack at solving the issue back then.

If you'd like to email me with a link to the particular dataset you're using and what you're trying to do with it I'd be happy to take a look at it in the next few days. Another question is are you interested in the results of having both strands considered - which would give more accurate results - or just a single strand?


From georgkam at gmail.com  Fri Sep 17 07:25:35 2010
From: georgkam at gmail.com (George Githinji)
Date: Fri, 17 Sep 2010 10:25:35 +0300
Subject: [BioRuby] Biosprint bepipred implementation
Message-ID: <AANLkTikj-zUfLen_0xDg=FTN3cuk9s0Yw-bOwh45KwS-@mail.gmail.com>

Hi,
The Biosprint started here in Nairobi yesterday. Most of the
participants are new to Ruby and some to programming in general.
There are about 4 CS guys who are experts in other
languages(php,java,perl and python)
We are using git for version control and have forked GeorgeG bioruby
fork from github

Task 1 Description
BepiPred predicts the location of linear B-cell epitopes in proteins
using a combination of a hidden Markov  model and a propensity scale
method. The method is described in the following article:
#   Improved method for predicting linear B-cell epitopes.
#   Jens Erik Pontoppidan Larsen, Ole Lund and Morten Nielsen
#   Immunome Research 2:2, 2006.

We are implementing a wrapper class for bepipred linear B-cell epitope
prediction tool. Specifically we want to

1) be able to call it from within bioruby  as follows
  # === Examples
  #
  #   require 'bio'
  #   seq_file = 'test.fasta'
  #
  #   factory = Bio::Bepipred.new(seq_file)
  #   report = factory.query
  #   report.class # => Bio::Bepipred::Report

2) The report class should take the bepipred predictions and format them to GFF3

3) Document the tasks

4) Write unit tests for the methods.


We have divided ourselves into 4 groups to accomplish this task.

A couple of questions:
1) While developing, which is the best development lifecycle?
      - when testing the development version

2) what is the best way to call a command line program from within
bioruby. for example  I have this


require 'bio/command'
require 'shellwords'

module Bio

  # == Description
  #
  # A wrapper for Bepipred linear B-cell epitope prediction program.
  #
  # === Examples
  #
  #   require 'bio'
  #   seq_file = 'test.fasta'
  #
  #   factory = Bio::Bepipred.new(seq_file)
  #   report = factory.query
  #   report.class # => Bio::Bepipred::Report
  #
class Bepipred
  autoload :Report, 'bio/appl/bepipred/report'

  # Creates a new Bepipred execution wrapper object
  def initialize(program='bepipred',score_threshold=0.35,file_name='')
    @program = program
    @score_threshold = score_threshold
    @file_name = file_name
  end

  # name of the program ('bepipred' in UNIX/Linux)
  attr_accessor :program

  # options
  attr_accessor :score_threshold

  # return the names of the input sequences
  attr_reader :sequence_names

  def sequence_names(file)
    sequence_names = []
    Bio::FlatFile.auto(@file) do |f|
      f.each do |entry|
        sequence_names << entry.definition
      end
    end
    sequence_names
  end

  # TODO create a list of query sequences


  #TODO create a commandline as an array cmd
  def make_command
    cmd = [@program,"-t #{@score_threshold}", at file_name ]
  end

  #query the file
  def query(file_name)
    cmd = make_command
    exec_local(cmd)
  end

  # TODO create a parser class for the ouput
  # parse_results

 private
 #executes bepipred when called localy
 #The input is a file name or a path to the file containing protein
sequences in fasta format
 #This method does not work
 # There could be a bug in the way the cmd argument is created.
 def exec_local(cmd)
   Bio::Command.query_command(cmd)
 end

end
end

Seems not to work.
Please assist. Thanks.



-- 
---------------
Sincerely
George
KEMRI/Wellcome-Trust Research Program
Skype: george_g2
Blog: http://biorelated.wordpress.com/


From yannick.wurm at unil.ch  Thu Sep 23 06:35:45 2010
From: yannick.wurm at unil.ch (Yannick Wurm)
Date: Thu, 23 Sep 2010 13:35:45 +0700
Subject: [BioRuby] rails blast server
Message-ID: <1DF3B9FB-24B8-44AC-9791-61A2EBBF7BE0@unil.ch>

Hi all,

I'd like to set up a small server for people to run BLAST against some of my sequences & see the results. 
GMOD obviously comes to mind, but it seems like overkill. 
And perhaps there is an almost automagic way to do this with ruby on rails. Has anyone done this yet?

Thanks!

Yannick

--------------------------------------------
          yannick . wurm @ unil . ch
Ant Genomics, Ecology & Evolution @ Lausanne
   http://www.unil.ch/dee/page28685_fr.html




From biopython at maubp.freeserve.co.uk  Thu Sep 23 10:52:54 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 23 Sep 2010 11:52:54 +0100
Subject: [BioRuby] rails blast server
In-Reply-To: <1DF3B9FB-24B8-44AC-9791-61A2EBBF7BE0@unil.ch>
References: <1DF3B9FB-24B8-44AC-9791-61A2EBBF7BE0@unil.ch>
Message-ID: <AANLkTi=O+tWj2ptrWy7SC7QUT+mCUMVQHPkGyQ-iF1+H@mail.gmail.com>

On Thu, Sep 23, 2010 at 7:35 AM, Yannick Wurm <yannick.wurm at unil.ch> wrote:
>
> Hi all,
>
> I'd like to set up a small server for people to run BLAST against
> some of my sequences & see the results.
> GMOD obviously comes to mind, but it seems like overkill.
> And perhaps there is an almost automagic way to do this with
> ruby on rails. Has anyone done this yet?
>
> Thanks!
>
> Yannick

Hi,

We just use the NCBI's wwwblast, but it hasn't been updated
recently and is very basic compared to the NCBI website.

Peter


From yannick.wurm at unil.ch  Thu Sep 23 11:09:52 2010
From: yannick.wurm at unil.ch (Yannick Wurm)
Date: Thu, 23 Sep 2010 18:09:52 +0700
Subject: [BioRuby] rails blast server
In-Reply-To: <AANLkTi=O+tWj2ptrWy7SC7QUT+mCUMVQHPkGyQ-iF1+H@mail.gmail.com>
References: <1DF3B9FB-24B8-44AC-9791-61A2EBBF7BE0@unil.ch>
	<AANLkTi=O+tWj2ptrWy7SC7QUT+mCUMVQHPkGyQ-iF1+H@mail.gmail.com>
Message-ID: <516E5D15-25D5-433A-ABEA-4688FCA56C31@unil.ch>

Yeah thanks..... that's the impression I had :-/

On 23 Sep 2010, at 17:52, Peter wrote:

> On Thu, Sep 23, 2010 at 7:35 AM, Yannick Wurm <yannick.wurm at unil.ch> wrote:
>> 
>> Hi all,
>> 
>> I'd like to set up a small server for people to run BLAST against
>> some of my sequences & see the results.
>> GMOD obviously comes to mind, but it seems like overkill.
>> And perhaps there is an almost automagic way to do this with
>> ruby on rails. Has anyone done this yet?
>> 
>> Thanks!
>> 
>> Yannick
> 
> Hi,
> 
> We just use the NCBI's wwwblast, but it hasn't been updated
> recently and is very basic compared to the NCBI website.
> 
> Peter



From trevor at corevx.com  Thu Sep 23 11:20:51 2010
From: trevor at corevx.com (Trevor Wennblom)
Date: Thu, 23 Sep 2010 06:20:51 -0500
Subject: [BioRuby] rails blast server
In-Reply-To: <1DF3B9FB-24B8-44AC-9791-61A2EBBF7BE0@unil.ch>
References: <1DF3B9FB-24B8-44AC-9791-61A2EBBF7BE0@unil.ch>
Message-ID: <23ACF172-B4D1-4237-81A9-BDE1A70A508C@corevx.com>

Hi Yannick,

It's pretty straight-forward. Put your sequences into a blast database as usual with formatdb. Setup a page in Rails with a textarea or file upload submit form. Take the submitted text / sequence, use it to query against your blast database by saving the input to a file and running the commandline tool (such as blastn), and finally return the file containing results.

This is assuming your queries run quickly since the page render will be delayed until blast is complete. If you need to search against a large database there's a bit more work to it.



From yannick.wurm at unil.ch  Thu Sep 23 13:08:35 2010
From: yannick.wurm at unil.ch (Yannick Wurm)
Date: Thu, 23 Sep 2010 20:08:35 +0700
Subject: [BioRuby] rails blast server
In-Reply-To: <1285246169.29263.158.camel@deskpro15336.dynamic.sanger.ac.uk>
References: <1DF3B9FB-24B8-44AC-9791-61A2EBBF7BE0@unil.ch>
	<23ACF172-B4D1-4237-81A9-BDE1A70A508C@corevx.com>
	<1285246169.29263.158.camel@deskpro15336.dynamic.sanger.ac.uk>
Message-ID: <5D9604BB-313A-44B4-A91B-B868873D26C8@unil.ch>

Thanks for the feedback Frank and Trevor

While I do want something simple, something with a few extra fun features & that can be extended easily wouldn't hurt :)
Eg: 
  - autodetection of whether the use entered nucleotide or aminoacid sequence --> autolimited selection of what blast programs are appropriate
  ---> automatically populated list of available databases
  - links in the results that let you fetch the original sequences of the database hits (by providing links to hits, and batch download of the database sequences). 

I've never done any rails before, so its probably a good opportunity. 

all the best,
yannick

On 23 Sep 2010, at 19:49, Frank Schwach wrote:

> What Trever describes is how I do it too. If this is all you want then a
> Rails app is a bit overkill because this is a very simple cgi script
> that doesn't even connect to a database.
> Basically, you just need some validation of input and then issue a
> system command (blsatall ....).
> As Trever pointed out, for larger databses this may be impractical
> because there will be no feedback until the search has completed and if
> your site is popular then many BLAST searches on a single server may
> quickly become a problem. Two possible solutions:
> 1) automatically send the results by email and just display a page
> showing that the search has been submitted. I use Perl for sending such
> messages but it should be just as easy in Ruby
> 2) use a job queueing system and run jobs in the background. The
> simplest solution is to use the Linux "batch" queue
> (http://linux.about.com/library/cmd/blcmdl1_batch.htm). 
> You can just submit jobs to the queue and they are only run when system
> resources are available. Ensure that the results are written into a file
> with a unique job ID in the file name and display a results page with
> some AJAX which keeps querying for the BLAST result file (by its ID) and
> inserts it into the page as soon as it is available.
> 
> Hope this helps.
> 
> Frank
> 
> 
> On Thu, 2010-09-23 at 06:20 -0500, Trevor Wennblom wrote:
>> Hi Yannick,
>> 
>> It's pretty straight-forward. Put your sequences into a blast database as usual with formatdb. Setup a page in Rails with a textarea or file upload submit form. Take the submitted text / sequence, use it to query against your blast database by saving the input to a file and running the commandline tool (such as blastn), and finally return the file containing results.
>> 
>> This is assuming your queries run quickly since the page render will be delayed until blast is complete. If you need to search against a large database there's a bit more work to it.
>> 
>> _______________________________________________
>> BioRuby Project - http://www.bioruby.org/
>> BioRuby mailing list
>> BioRuby at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioruby
> 
> 
> 
> -- 
> The Wellcome Trust Sanger Institute is operated by Genome Research 
> Limited, a charity registered in England with number 1021457 and a 
> company registered in England with number 2742969, whose registered 
> office is 215 Euston Road, London, NW1 2BE. 




From fs5 at sanger.ac.uk  Thu Sep 23 12:49:29 2010
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Thu, 23 Sep 2010 13:49:29 +0100
Subject: [BioRuby] rails blast server
In-Reply-To: <23ACF172-B4D1-4237-81A9-BDE1A70A508C@corevx.com>
References: <1DF3B9FB-24B8-44AC-9791-61A2EBBF7BE0@unil.ch>
	<23ACF172-B4D1-4237-81A9-BDE1A70A508C@corevx.com>
Message-ID: <1285246169.29263.158.camel@deskpro15336.dynamic.sanger.ac.uk>

What Trever describes is how I do it too. If this is all you want then a
Rails app is a bit overkill because this is a very simple cgi script
that doesn't even connect to a database.
Basically, you just need some validation of input and then issue a
system command (blsatall ....).
As Trever pointed out, for larger databses this may be impractical
because there will be no feedback until the search has completed and if
your site is popular then many BLAST searches on a single server may
quickly become a problem. Two possible solutions:
1) automatically send the results by email and just display a page
showing that the search has been submitted. I use Perl for sending such
messages but it should be just as easy in Ruby
2) use a job queueing system and run jobs in the background. The
simplest solution is to use the Linux "batch" queue
(http://linux.about.com/library/cmd/blcmdl1_batch.htm). 
You can just submit jobs to the queue and they are only run when system
resources are available. Ensure that the results are written into a file
with a unique job ID in the file name and display a results page with
some AJAX which keeps querying for the BLAST result file (by its ID) and
inserts it into the page as soon as it is available.

Hope this helps.

Frank


On Thu, 2010-09-23 at 06:20 -0500, Trevor Wennblom wrote:
> Hi Yannick,
> 
> It's pretty straight-forward. Put your sequences into a blast database as usual with formatdb. Setup a page in Rails with a textarea or file upload submit form. Take the submitted text / sequence, use it to query against your blast database by saving the input to a file and running the commandline tool (such as blastn), and finally return the file containing results.
> 
> This is assuming your queries run quickly since the page render will be delayed until blast is complete. If you need to search against a large database there's a bit more work to it.
> 
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From fs5 at sanger.ac.uk  Thu Sep 23 13:44:31 2010
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Thu, 23 Sep 2010 14:44:31 +0100
Subject: [BioRuby] rails blast server
In-Reply-To: <5D9604BB-313A-44B4-A91B-B868873D26C8@unil.ch>
References: <1DF3B9FB-24B8-44AC-9791-61A2EBBF7BE0@unil.ch>
	<23ACF172-B4D1-4237-81A9-BDE1A70A508C@corevx.com>
	<1285246169.29263.158.camel@deskpro15336.dynamic.sanger.ac.uk>
	<5D9604BB-313A-44B4-A91B-B868873D26C8@unil.ch>
Message-ID: <1285249471.29263.166.camel@deskpro15336.dynamic.sanger.ac.uk>

Hi Yannick,

Of course you can do this in Rails but even those additional
requirements won't really get you started actually using Rails' features
because you probably don't want a backend database just to hold a few
names of FASTA files that you can BLAST against (you can either fetch
them directly from a directory listing or a short config text file). The
(simple) autodetection is just one relatively simple regex and to fetch
the original sequences you will probably want to get them straight out
of the flat (FASTA) files using BioRuby methods, so again no database.
Anyway, I don't want to curb your enthusiasm for learning Rails, so good
luck! :-)

Frank


, so learning a new framework might reallz 

On Thu, 2010-09-23 at 20:08 +0700, Yannick Wurm wrote:
> Thanks for the feedback Frank and Trevor
> 
> While I do want something simple, something with a few extra fun features & that can be extended easily wouldn't hurt :)
> Eg: 
>   - autodetection of whether the use entered nucleotide or aminoacid sequence --> autolimited selection of what blast programs are appropriate
>   ---> automatically populated list of available databases
>   - links in the results that let you fetch the original sequences of the database hits (by providing links to hits, and batch download of the database sequences). 
> 
> I've never done any rails before, so its probably a good opportunity. 
> 
> all the best,
> yannick
> 
> On 23 Sep 2010, at 19:49, Frank Schwach wrote:
> 
> > What Trever describes is how I do it too. If this is all you want then a
> > Rails app is a bit overkill because this is a very simple cgi script
> > that doesn't even connect to a database.
> > Basically, you just need some validation of input and then issue a
> > system command (blsatall ....).
> > As Trever pointed out, for larger databses this may be impractical
> > because there will be no feedback until the search has completed and if
> > your site is popular then many BLAST searches on a single server may
> > quickly become a problem. Two possible solutions:
> > 1) automatically send the results by email and just display a page
> > showing that the search has been submitted. I use Perl for sending such
> > messages but it should be just as easy in Ruby
> > 2) use a job queueing system and run jobs in the background. The
> > simplest solution is to use the Linux "batch" queue
> > (http://linux.about.com/library/cmd/blcmdl1_batch.htm). 
> > You can just submit jobs to the queue and they are only run when system
> > resources are available. Ensure that the results are written into a file
> > with a unique job ID in the file name and display a results page with
> > some AJAX which keeps querying for the BLAST result file (by its ID) and
> > inserts it into the page as soon as it is available.
> > 
> > Hope this helps.
> > 
> > Frank
> > 
> > 
> > On Thu, 2010-09-23 at 06:20 -0500, Trevor Wennblom wrote:
> >> Hi Yannick,
> >> 
> >> It's pretty straight-forward. Put your sequences into a blast database as usual with formatdb. Setup a page in Rails with a textarea or file upload submit form. Take the submitted text / sequence, use it to query against your blast database by saving the input to a file and running the commandline tool (such as blastn), and finally return the file containing results.
> >> 
> >> This is assuming your queries run quickly since the page render will be delayed until blast is complete. If you need to search against a large database there's a bit more work to it.
> >> 
> >> _______________________________________________
> >> BioRuby Project - http://www.bioruby.org/
> >> BioRuby mailing list
> >> BioRuby at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioruby
> > 
> > 
> > 
> > -- 
> > The Wellcome Trust Sanger Institute is operated by Genome Research 
> > Limited, a charity registered in England with number 1021457 and a 
> > company registered in England with number 2742969, whose registered 
> > office is 215 Euston Road, London, NW1 2BE. 
> 



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From yannick.wurm at unil.ch  Thu Sep 23 17:14:39 2010
From: yannick.wurm at unil.ch (Yannick Wurm)
Date: Fri, 24 Sep 2010 00:14:39 +0700
Subject: [BioRuby] rails blast server
In-Reply-To: <1285249471.29263.166.camel@deskpro15336.dynamic.sanger.ac.uk>
References: <1DF3B9FB-24B8-44AC-9791-61A2EBBF7BE0@unil.ch>
	<23ACF172-B4D1-4237-81A9-BDE1A70A508C@corevx.com>
	<1285246169.29263.158.camel@deskpro15336.dynamic.sanger.ac.uk>
	<5D9604BB-313A-44B4-A91B-B868873D26C8@unil.ch>
	<1285249471.29263.166.camel@deskpro15336.dynamic.sanger.ac.uk>
Message-ID: <90EA9391-3216-4634-BC69-0960C8D881DF@unil.ch>

Dang I thought Rails would make AJAX stuff easier too? Or is that only if I need a database backend?
Sorry for the noob questions, I haven't done any web dev in a long time...

On 23 Sep 2010, at 20:44, Frank Schwach wrote:

> Hi Yannick,
> 
> Of course you can do this in Rails but even those additional
> requirements won't really get you started actually using Rails' features
> because you probably don't want a backend database just to hold a few
> names of FASTA files that you can BLAST against (you can either fetch
> them directly from a directory listing or a short config text file). The
> (simple) autodetection is just one relatively simple regex and to fetch
> the original sequences you will probably want to get them straight out
> of the flat (FASTA) files using BioRuby methods, so again no database.
> Anyway, I don't want to curb your enthusiasm for learning Rails, so good
> luck! :-)
> 
> Frank
> 
> 
> , so learning a new framework might reallz 
> 
> On Thu, 2010-09-23 at 20:08 +0700, Yannick Wurm wrote:
>> Thanks for the feedback Frank and Trevor
>> 
>> While I do want something simple, something with a few extra fun features & that can be extended easily wouldn't hurt :)
>> Eg: 
>>  - autodetection of whether the use entered nucleotide or aminoacid sequence --> autolimited selection of what blast programs are appropriate
>>  ---> automatically populated list of available databases
>>  - links in the results that let you fetch the original sequences of the database hits (by providing links to hits, and batch download of the database sequences). 
>> 
>> I've never done any rails before, so its probably a good opportunity. 
>> 
>> all the best,
>> yannick
>> 
>> On 23 Sep 2010, at 19:49, Frank Schwach wrote:
>> 
>>> What Trever describes is how I do it too. If this is all you want then a
>>> Rails app is a bit overkill because this is a very simple cgi script
>>> that doesn't even connect to a database.
>>> Basically, you just need some validation of input and then issue a
>>> system command (blsatall ....).
>>> As Trever pointed out, for larger databses this may be impractical
>>> because there will be no feedback until the search has completed and if
>>> your site is popular then many BLAST searches on a single server may
>>> quickly become a problem. Two possible solutions:
>>> 1) automatically send the results by email and just display a page
>>> showing that the search has been submitted. I use Perl for sending such
>>> messages but it should be just as easy in Ruby
>>> 2) use a job queueing system and run jobs in the background. The
>>> simplest solution is to use the Linux "batch" queue
>>> (http://linux.about.com/library/cmd/blcmdl1_batch.htm). 
>>> You can just submit jobs to the queue and they are only run when system
>>> resources are available. Ensure that the results are written into a file
>>> with a unique job ID in the file name and display a results page with
>>> some AJAX which keeps querying for the BLAST result file (by its ID) and
>>> inserts it into the page as soon as it is available.
>>> 
>>> Hope this helps.
>>> 
>>> Frank
>>> 
>>> 
>>> On Thu, 2010-09-23 at 06:20 -0500, Trevor Wennblom wrote:
>>>> Hi Yannick,
>>>> 
>>>> It's pretty straight-forward. Put your sequences into a blast database as usual with formatdb. Setup a page in Rails with a textarea or file upload submit form. Take the submitted text / sequence, use it to query against your blast database by saving the input to a file and running the commandline tool (such as blastn), and finally return the file containing results.
>>>> 
>>>> This is assuming your queries run quickly since the page render will be delayed until blast is complete. If you need to search against a large database there's a bit more work to it.
>>>> 
>>>> _______________________________________________
>>>> BioRuby Project - http://www.bioruby.org/
>>>> BioRuby mailing list
>>>> BioRuby at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioruby
>>> 
>>> 
>>> 
>>> -- 
>>> The Wellcome Trust Sanger Institute is operated by Genome Research 
>>> Limited, a charity registered in England with number 1021457 and a 
>>> company registered in England with number 2742969, whose registered 
>>> office is 215 Euston Road, London, NW1 2BE. 
>> 
> 
> 
> 
> -- 
> The Wellcome Trust Sanger Institute is operated by Genome Research 
> Limited, a charity registered in England with number 1021457 and a 
> company registered in England with number 2742969, whose registered 
> office is 215 Euston Road, London, NW1 2BE. 




From anurag08priyam at gmail.com  Thu Sep 23 18:06:44 2010
From: anurag08priyam at gmail.com (Anurag Priyam)
Date: Thu, 23 Sep 2010 23:36:44 +0530
Subject: [BioRuby] rails blast server
In-Reply-To: <90EA9391-3216-4634-BC69-0960C8D881DF@unil.ch>
References: <1DF3B9FB-24B8-44AC-9791-61A2EBBF7BE0@unil.ch>
	<23ACF172-B4D1-4237-81A9-BDE1A70A508C@corevx.com>
	<1285246169.29263.158.camel@deskpro15336.dynamic.sanger.ac.uk>
	<5D9604BB-313A-44B4-A91B-B868873D26C8@unil.ch>
	<1285249471.29263.166.camel@deskpro15336.dynamic.sanger.ac.uk>
	<90EA9391-3216-4634-BC69-0960C8D881DF@unil.ch>
Message-ID: <AANLkTikWcP45fCERmLReBEgBb0fenHhRQOi1QHtpatrf@mail.gmail.com>

> Dang I thought Rails would make AJAX stuff easier too? Or is that only if I need a database backend?
> Sorry for the noob questions, I haven't done any web dev in a long time...

Yea Rails will help you with AJAX a bit. It will also help you with
the upload process - paperclip plugin.

But yea, as Frank said, for something as simple as this you do not
need something as heavy as Rails. You might just want to write a Ruby
CGI script or perhaps a Sinatra app. To make life simple with AJAX you
can just use jQuery library.

I have got some web development experience; feel free to contact me
off the list :).

-- 
Anurag Priyam,
3rd Year Undergraduate,
Department of Mechanical Engineering,
IIT Kharagpur.
+91-9775550642


From russell.whitaker at gmail.com  Fri Sep 24 07:34:06 2010
From: russell.whitaker at gmail.com (Russell Whitaker)
Date: Fri, 24 Sep 2010 03:34:06 -0400
Subject: [BioRuby] May I contribute a 23andMe flatfile parser?
Message-ID: <AANLkTikgQbSpwxZF4k=5oS4MsUK1v3xR45E3Bu7iaYrW@mail.gmail.com>

Hi all / ???????????????

[Please let me know if my Japanese is mojibake / ????]

I'm a former professional software engineer who left Google 3 years
ago to pursue a degree in biochemistry from Columbia University (which
I did in fact complete, 4 months ago). After having programmed other languages
over a nearly 20 year career - one in Japan, by the way - I switched from
Python to Ruby/Rails at Google, and have committed to continue with that
as primary platform (except for statistical applications, for which I'm doing R
when needed).

I've been researching best platforms for going general bioinformatics
work, and of course discovered BioRuby, which is why I'm here on this list.

A few hours of digging have convinced me that a 23andMe SNP/genotype
flatfile parser does not yet exist in BioRuby. However, I may be wrong, so I'll
ask: does one exist? No mention of "23andMe" exists in the list archives.

Would anyone object to my writing one? I've been familiarizing myself with
the development process for this group, e.g.:

http://lists.open-bio.org/pipermail/bioruby/2010-June/001319.html

I already have a GitHub account, of course.

Thanks in advance for your help, and I look forward to contributing to this
project.

?????????????
????

-- 
Russell Whitaker
http://twitter.com/OrthoNormalRuss


From fs5 at sanger.ac.uk  Fri Sep 24 08:04:19 2010
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Fri, 24 Sep 2010 09:04:19 +0100
Subject: [BioRuby] rails blast server
In-Reply-To: <AANLkTikWcP45fCERmLReBEgBb0fenHhRQOi1QHtpatrf@mail.gmail.com>
References: <1DF3B9FB-24B8-44AC-9791-61A2EBBF7BE0@unil.ch>
	<23ACF172-B4D1-4237-81A9-BDE1A70A508C@corevx.com>
	<1285246169.29263.158.camel@deskpro15336.dynamic.sanger.ac.uk>
	<5D9604BB-313A-44B4-A91B-B868873D26C8@unil.ch>
	<1285249471.29263.166.camel@deskpro15336.dynamic.sanger.ac.uk>
	<90EA9391-3216-4634-BC69-0960C8D881DF@unil.ch>
	<AANLkTikWcP45fCERmLReBEgBb0fenHhRQOi1QHtpatrf@mail.gmail.com>
Message-ID: <1285315459.29263.193.camel@deskpro15336.dynamic.sanger.ac.uk>

Yes, Rails will give you some sugar for the AJAX stuff but, to be
honeest, it isn't that hard to code that "by hand" and if you need to
learn Rails first then it really won't be worth it for this project.
This is a bit off-topic for a BioRuby list but maybe it helps, so
here is what I use on one of my websites to check for the status of a
job. In this case, there is a cgi script that checks the job status
because this is a slightly more complex system, but you could just check
for the existence of the BLAST result file (but see below). You just
populate the job ID in the javascript function below in your template as
you generate the page. 
When my job is finished, I redirect to a different page which displays
the results but you could just as easily simply insert a link to
download the BLAST resutl file on the same page. I use Prototype.

<script  type="text/javascript"
src="../your/path/to/prototype.js"></script>

<script type="text/javascript">
function statusChecker(){
  new Ajax.Updater( 
  { success: 'jobStatus'}, 
  '../cgi-bin/some_job_status_checker.cgi',
    {
      parameters: 'jobid=1234567',
      method    : 'get',
      onComplete : onJobCompleteRedirect
    }
  );
} ;
/* the job_status_checker returns 'complete' if job is ready to download   */
function onJobCompleteRedirect(response){
  var status = response.responseText;
  if( status == 'completed') {
     window.location.href='../cgi-bin/result_page.cgi?jobid=1234567';
  }
} ;

/* this actually runs the StatusChecker every 5 secs */
new PeriodicalExecuter(statusChecker, 5) ;
</script>


Somewhere on the page I have this:
<span id="jobStatus">queued...</span> 

That's the bit that gets updated with whatever
some_job_status_checker.cgi returns. If it returns 'completed' the
results page is loaded.

One thing to bear in mind if you just check for the existence of files
to indicate job status: the BLAST result file exists before the job is
complete. For that reason you need a sysmte command that first runs
BLAST and then does something to indicate the job is finished, something
like "blastall ....; indicate_completeness.sh". 
That could be either to copy the BLAST result into the public download
folder, so your job status checker doesn't see it before it is complete
or to simply "touch" a file in that folder with a name like this:
"JOBID_complete". Then you take the existence of that file as proof that
the job is finished.
Hope this help. Good luck!

Frank




On Thu, 2010-09-23 at 23:36 +0530, Anurag Priyam wrote:
> > Dang I thought Rails would make AJAX stuff easier too? Or is that only if I need a database backend?
> > Sorry for the noob questions, I haven't done any web dev in a long time...
> 
> Yea Rails will help you with AJAX a bit. It will also help you with
> the upload process - paperclip plugin.
> 
> But yea, as Frank said, for something as simple as this you do not
> need something as heavy as Rails. You might just want to write a Ruby
> CGI script or perhaps a Sinatra app. To make life simple with AJAX you
> can just use jQuery library.
> 
> I have got some web development experience; feel free to contact me
> off the list :).
> 



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From yannick.wurm at unil.ch  Sat Sep 25 07:49:39 2010
From: yannick.wurm at unil.ch (Yannick Wurm)
Date: Sat, 25 Sep 2010 14:49:39 +0700
Subject: [BioRuby] rails blast server
In-Reply-To: <1285315459.29263.193.camel@deskpro15336.dynamic.sanger.ac.uk>
References: <1DF3B9FB-24B8-44AC-9791-61A2EBBF7BE0@unil.ch>
	<23ACF172-B4D1-4237-81A9-BDE1A70A508C@corevx.com>
	<1285246169.29263.158.camel@deskpro15336.dynamic.sanger.ac.uk>
	<5D9604BB-313A-44B4-A91B-B868873D26C8@unil.ch>
	<1285249471.29263.166.camel@deskpro15336.dynamic.sanger.ac.uk>
	<90EA9391-3216-4634-BC69-0960C8D881DF@unil.ch>
	<AANLkTikWcP45fCERmLReBEgBb0fenHhRQOi1QHtpatrf@mail.gmail.com>
	<1285315459.29263.193.camel@deskpro15336.dynamic.sanger.ac.uk>
Message-ID: <08DAFC33-6B56-4F3A-8BA7-510ECA2BCD6B@unil.ch>

Thanks guys for the code and advice!

I apologize for taking the list so far off track...

Thanks and regards,
Yannick


On 24 Sep 2010, at 15:04, Frank Schwach wrote:

> Yes, Rails will give you some sugar for the AJAX stuff but, to be
> honeest, it isn't that hard to code that "by hand" and if you need to
> learn Rails first then it really won't be worth it for this project.
> This is a bit off-topic for a BioRuby list but maybe it helps, so
> here is what I use on one of my websites to check for the status of a
> job. In this case, there is a cgi script that checks the job status
> because this is a slightly more complex system, but you could just check
> for the existence of the BLAST result file (but see below). You just
> populate the job ID in the javascript function below in your template as
> you generate the page. 
> When my job is finished, I redirect to a different page which displays
> the results but you could just as easily simply insert a link to
> download the BLAST resutl file on the same page. I use Prototype.
> 
> <script  type="text/javascript"
> src="../your/path/to/prototype.js"></script>
> 
> <script type="text/javascript">
> function statusChecker(){
>  new Ajax.Updater( 
>  { success: 'jobStatus'}, 
>  '../cgi-bin/some_job_status_checker.cgi',
>    {
>      parameters: 'jobid=1234567',
>      method    : 'get',
>      onComplete : onJobCompleteRedirect
>    }
>  );
> } ;
> /* the job_status_checker returns 'complete' if job is ready to download   */
> function onJobCompleteRedirect(response){
>  var status = response.responseText;
>  if( status == 'completed') {
>     window.location.href='../cgi-bin/result_page.cgi?jobid=1234567';
>  }
> } ;
> 
> /* this actually runs the StatusChecker every 5 secs */
> new PeriodicalExecuter(statusChecker, 5) ;
> </script>
> 
> 
> Somewhere on the page I have this:
> <span id="jobStatus">queued...</span> 
> 
> That's the bit that gets updated with whatever
> some_job_status_checker.cgi returns. If it returns 'completed' the
> results page is loaded.
> 
> One thing to bear in mind if you just check for the existence of files
> to indicate job status: the BLAST result file exists before the job is
> complete. For that reason you need a sysmte command that first runs
> BLAST and then does something to indicate the job is finished, something
> like "blastall ....; indicate_completeness.sh". 
> That could be either to copy the BLAST result into the public download
> folder, so your job status checker doesn't see it before it is complete
> or to simply "touch" a file in that folder with a name like this:
> "JOBID_complete". Then you take the existence of that file as proof that
> the job is finished.
> Hope this help. Good luck!
> 
> Frank
> 
> 
> 
> 
> On Thu, 2010-09-23 at 23:36 +0530, Anurag Priyam wrote:
>>> Dang I thought Rails would make AJAX stuff easier too? Or is that only if I need a database backend?
>>> Sorry for the noob questions, I haven't done any web dev in a long time...
>> 
>> Yea Rails will help you with AJAX a bit. It will also help you with
>> the upload process - paperclip plugin.
>> 
>> But yea, as Frank said, for something as simple as this you do not
>> need something as heavy as Rails. You might just want to write a Ruby
>> CGI script or perhaps a Sinatra app. To make life simple with AJAX you
>> can just use jQuery library.
>> 
>> I have got some web development experience; feel free to contact me
>> off the list :).
>> 
> 
> 
> 
> -- 
> The Wellcome Trust Sanger Institute is operated by Genome Research 
> Limited, a charity registered in England with number 1021457 and a 
> company registered in England with number 2742969, whose registered 
> office is 215 Euston Road, London, NW1 2BE. 



--------------------------------------------
          yannick . wurm @ unil . ch
Ant Genomics, Ecology & Evolution @ Lausanne
   http://www.unil.ch/dee/page28685_fr.html





From protasdeo at yahoo.com  Sat Sep 25 19:15:39 2010
From: protasdeo at yahoo.com (protasdeo at yahoo.com)
Date: Sat, 25 Sep 2010 19:15:39 +0000
Subject: [BioRuby] Bioruby mailing list
Message-ID: <490907.92596.qm@smtp106-mob.biz.mail.ird.yahoo.com>

Bioruby mailing lists subscribe.




From russell.whitaker at gmail.com  Sat Sep 25 19:47:52 2010
From: russell.whitaker at gmail.com (Russell Whitaker)
Date: Sat, 25 Sep 2010 15:47:52 -0400
Subject: [BioRuby] Bioruby mailing list
In-Reply-To: <490907.92596.qm@smtp106-mob.biz.mail.ird.yahoo.com>
References: <490907.92596.qm@smtp106-mob.biz.mail.ird.yahoo.com>
Message-ID: <0FA7D197-9154-4959-8AFA-90DACDC68E7A@gmail.com>

Wonder Twin powers activate!

Russell Whitaker
Sent from my iPhone

On Sep 25, 2010, at 3:15 PM, "protasdeo at yahoo.com" <protasdeo at yahoo.com> wrote:

> Bioruby mailing lists subscribe.
> 
> 
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby



From protasdeo at yahoo.com  Sun Sep 26 16:06:40 2010
From: protasdeo at yahoo.com (protasdeo at yahoo.com)
Date: Sun, 26 Sep 2010 16:06:40 +0000
Subject: [BioRuby] BioRuby mailing list submission
Message-ID: <686985.30438.qm@smtp106-mob.biz.mail.ird.yahoo.com>



 BioRuby mailing list submissions to
	

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When replying, please edit your Subject line so it is more specific
than "Re: Contents of BioRuby digest..."


Today's Topics:

   1. Bioruby mailing list (protasdeo at yahoo.com)
   2. Re: Bioruby mailing list (Russell Whitaker)


----------------------------------------------------------------------

Message: 1
Date: Sat, 25 Sep 2010 19:15:39 +0000
From: "protasdeo at yahoo.com" <protasdeo at yahoo.com>
Subject: [BioRuby] Bioruby mailing list
To: "bioruby at lists.open-bio.org" <bioruby at lists.open-bio.org>
Message-ID: <490907.92596.qm at smtp106-mob.biz.mail.ird.yahoo.com>
Content-Type: text/plain;	charset="utf-8"

Bioruby mailing lists subscribe.




------------------------------

Message: 2
Date: Sat, 25 Sep 2010 15:47:52 -0400
From: Russell Whitaker <russell.whitaker at gmail.com>
Subject: Re: [BioRuby] Bioruby mailing list
To: "protasdeo at yahoo.com" <protasdeo at yahoo.com>
Cc: "bioruby at lists.open-bio.org" <bioruby at lists.open-bio.org>
Message-ID: <0FA7D197-9154-4959-8AFA-90DACDC68E7A at gmail.com>
Content-Type: text/plain; charset=us-ascii

Wonder Twin powers activate!

Russell Whitaker
Sent from my iPhone

On Sep 25, 2010, at 3:15 PM, "protasdeo at yahoo.com" <protasdeo at yahoo.com> wrote:

> Bioruby mailing lists subscribe.
> 
> 
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby



------------------------------

_______________________________________________
BioRuby mailing list
BioRuby at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioruby


End of BioRuby Digest, Vol 60, Issue 10
***************************************




From bonnalraoul at ingm.it  Mon Sep 27 10:52:50 2010
From: bonnalraoul at ingm.it (Raoul Bonnal)
Date: Mon, 27 Sep 2010 12:52:50 +0200
Subject: [BioRuby] Ruby 1.9.2 and BioRuby
Message-ID: <69b8f26b-7ca6-402a-a559-cea06e5dd4bf@ingm.it>

Hello guys, 
Do you have any idea how to solve this error?
/home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-3.0.0/lib/active_support/dependencies.rb:479:in `load_missing_constant': Bio is not missing constant Sequence! (ArgumentError)
        from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-3.0.0/lib/active_support/dependencies.rb:183:in `block in const_missing'
        from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-3.0.0/lib/active_support/dependencies.rb:181:in `each'
        from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-3.0.0/lib/active_support/dependencies.rb:181:in `const_missing'
        from /home/ra/deve/bioruby/lib/bio/sequence/compat.rb:15:in `<module:Bio>'
        from /home/ra/deve/bioruby/lib/bio/sequence/compat.rb:13:in `<top (required)>'
        from <internal:lib/rubygems/custom_require>:29:in `require'
        from <internal:lib/rubygems/custom_require>:29:in `require'
        from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-3.0.0/lib/active_support/dependencies.rb:239:in `block in require'
        from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-3.0.0/lib/active_support/dependencies.rb:225:in `block in load_dependency'
        from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-3.0.0/lib/active_support/dependencies.rb:591:in `new_constants_in'
        from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-3.0.0/lib/active_support/dependencies.rb:225:in `load_dependency'
        from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-3.0.0/lib/active_support/dependencies.rb:239:in `require'
        from /home/ra/deve/bioruby/lib/bio/sequence.rb:15:in `<top (required)>'
        from /home/ra/deve/bioruby/lib/bio/shell/plugin/midi.rb:20:in `<top (required)>'
        from <internal:lib/rubygems/custom_require>:29:in `require'
        from <internal:lib/rubygems/custom_require>:29:in `require'
        from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-3.0.0/lib/active_support/dependencies.rb:239:in `block in require'
        from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-3.0.0/lib/active_support/dependencies.rb:225:in `block in load_dependency'
        from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-3.0.0/lib/active_support/dependencies.rb:591:in `new_constants_in'
        from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-3.0.0/lib/active_support/dependencies.rb:225:in `load_dependency'
        from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-3.0.0/lib/active_support/dependencies.rb:239:in `require'
        from /home/ra/deve/bioruby/lib/bio/shell.rb:29:in `<module:Shell>'
        from /home/ra/deve/bioruby/lib/bio/shell.rb:17:in `<top (required)>'
        from <internal:lib/rubygems/custom_require>:29:in `require'
        from <internal:lib/rubygems/custom_require>:29:in `require'
        from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-3.0.0/lib/active_support/dependencies.rb:239:in `block in require'
        from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-3.0.0/lib/active_support/dependencies.rb:225:in `block in load_dependency'
        from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-3.0.0/lib/active_support/dependencies.rb:591:in `new_constants_in'
        from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-3.0.0/lib/active_support/dependencies.rb:225:in `load_dependency'
        from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-3.0.0/lib/active_support/dependencies.rb:239:in `require'
        from /home/ra/deve/bioruby/bin/bioruby:18:in `<main>'

--
Raoul J.P. Bonnal
Life Science Informatics
Integrative Biology Program
Fondazione INGM
Via F. Sforza 28
20122 Milano, IT
phone: +39 02 006 623  26
fax: +39 02 006 623 46
http://www.ingm.it






From bonnalraoul at ingm.it  Mon Sep 27 13:10:56 2010
From: bonnalraoul at ingm.it (Raoul Bonnal)
Date: Mon, 27 Sep 2010 15:10:56 +0200
Subject: [BioRuby] R:  Ruby 1.9.2 and BioRuby
In-Reply-To: <69b8f26b-7ca6-402a-a559-cea06e5dd4bf@ingm.it>
References: <69b8f26b-7ca6-402a-a559-cea06e5dd4bf@ingm.it>
Message-ID: <89b0ec08-ad5d-4684-acf9-aa05403be430@ingm.it>

And ... it works on 1.8.7 and 1.9.1

--
Raoul J.P. Bonnal
Life Science Informatics
Integrative Biology Program
Fondazione INGM
Via F. Sforza 28
20122 Milano, IT
phone: +39 02 006 623  26
fax: +39 02 006 623 46
http://www.ingm.it


> -----Messaggio originale-----
> Da: bioruby-bounces at lists.open-bio.org [mailto:bioruby-
> bounces at lists.open-bio.org] Per conto di Raoul Bonnal
> Inviato: luned? 27 settembre 2010 12:53
> A: bioruby at lists.open-bio.org
> Oggetto: [BioRuby] Ruby 1.9.2 and BioRuby
> 
> Hello guys,
> Do you have any idea how to solve this error?
> /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> 3.0.0/lib/active_support/dependencies.rb:479:in
> `load_missing_constant': Bio is not missing constant Sequence!
> (ArgumentError)
>         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> 3.0.0/lib/active_support/dependencies.rb:183:in `block in
> const_missing'
>         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> 3.0.0/lib/active_support/dependencies.rb:181:in `each'
>         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> 3.0.0/lib/active_support/dependencies.rb:181:in `const_missing'
>         from /home/ra/deve/bioruby/lib/bio/sequence/compat.rb:15:in
> `<module:Bio>'
>         from /home/ra/deve/bioruby/lib/bio/sequence/compat.rb:13:in
> `<top (required)>'
>         from <internal:lib/rubygems/custom_require>:29:in `require'
>         from <internal:lib/rubygems/custom_require>:29:in `require'
>         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> 3.0.0/lib/active_support/dependencies.rb:239:in `block in require'
>         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> 3.0.0/lib/active_support/dependencies.rb:225:in `block in
> load_dependency'
>         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> 3.0.0/lib/active_support/dependencies.rb:591:in `new_constants_in'
>         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> 3.0.0/lib/active_support/dependencies.rb:225:in `load_dependency'
>         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> 3.0.0/lib/active_support/dependencies.rb:239:in `require'
>         from /home/ra/deve/bioruby/lib/bio/sequence.rb:15:in `<top
> (required)>'
>         from /home/ra/deve/bioruby/lib/bio/shell/plugin/midi.rb:20:in
> `<top (required)>'
>         from <internal:lib/rubygems/custom_require>:29:in `require'
>         from <internal:lib/rubygems/custom_require>:29:in `require'
>         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> 3.0.0/lib/active_support/dependencies.rb:239:in `block in require'
>         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> 3.0.0/lib/active_support/dependencies.rb:225:in `block in
> load_dependency'
>         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> 3.0.0/lib/active_support/dependencies.rb:591:in `new_constants_in'
>         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> 3.0.0/lib/active_support/dependencies.rb:225:in `load_dependency'
>         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> 3.0.0/lib/active_support/dependencies.rb:239:in `require'
>         from /home/ra/deve/bioruby/lib/bio/shell.rb:29:in
> `<module:Shell>'
>         from /home/ra/deve/bioruby/lib/bio/shell.rb:17:in `<top
> (required)>'
>         from <internal:lib/rubygems/custom_require>:29:in `require'
>         from <internal:lib/rubygems/custom_require>:29:in `require'
>         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> 3.0.0/lib/active_support/dependencies.rb:239:in `block in require'
>         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> 3.0.0/lib/active_support/dependencies.rb:225:in `block in
> load_dependency'
>         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> 3.0.0/lib/active_support/dependencies.rb:591:in `new_constants_in'
>         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> 3.0.0/lib/active_support/dependencies.rb:225:in `load_dependency'
>         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> 3.0.0/lib/active_support/dependencies.rb:239:in `require'
>         from /home/ra/deve/bioruby/bin/bioruby:18:in `<main>'
> 
> --
> Raoul J.P. Bonnal
> Life Science Informatics
> Integrative Biology Program
> Fondazione INGM
> Via F. Sforza 28
> 20122 Milano, IT
> phone: +39 02 006 623  26
> fax: +39 02 006 623 46
> http://www.ingm.it
> 
> 
> 
> 
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby




From bonnalraoul at ingm.it  Mon Sep 27 13:25:00 2010
From: bonnalraoul at ingm.it (Raoul Bonnal)
Date: Mon, 27 Sep 2010 15:25:00 +0200
Subject: [BioRuby] R:  Ruby 1.9.2 and BioRuby
In-Reply-To: <89b0ec08-ad5d-4684-acf9-aa05403be430@ingm.it>
References: <69b8f26b-7ca6-402a-a559-cea06e5dd4bf@ingm.it>
	<89b0ec08-ad5d-4684-acf9-aa05403be430@ingm.it>
Message-ID: <fbda1caf-be6c-4e0b-839c-ad708dfc23de@ingm.it>

It's a problem of loading path. In Ruby 1.9.2 the '.' is not loaded by default.
Adding the $:<<'.' Seems to patch the problem.
I did some test and probably 

In activerecord, for instance, they do in this way.


activesupport_path = File.expand_path('../../../activesupport/lib', __FILE__)
$:.unshift(activesupport_path) if File.directory?(activesupport_path) && !$:.include?(activesupport_path)

activemodel_path = File.expand_path('../../../activemodel/lib', __FILE__)
$:.unshift(activemodel_path) if File.directory?(activemodel_path) && !$:.include?(activemodel_path)

require 'active_support'
require 'active_support/i18n'
require 'active_model'
require 'arel'
--
Raoul J.P. Bonnal
Life Science Informatics
Integrative Biology Program
Fondazione INGM
Via F. Sforza 28
20122 Milano, IT
phone: +39 02 006 623  26
fax: +39 02 006 623 46
http://www.ingm.it


> -----Messaggio originale-----
> Da: Raoul Bonnal [mailto:bonnalraoul at ingm.it]
> Inviato: luned? 27 settembre 2010 15:11
> A: 'Raoul Bonnal'; bioruby at lists.open-bio.org
> Oggetto: R: [BioRuby] Ruby 1.9.2 and BioRuby
> 
> And ... it works on 1.8.7 and 1.9.1
> 
> --
> Raoul J.P. Bonnal
> Life Science Informatics
> Integrative Biology Program
> Fondazione INGM
> Via F. Sforza 28
> 20122 Milano, IT
> phone: +39 02 006 623  26
> fax: +39 02 006 623 46
> http://www.ingm.it
> 
> 
> > -----Messaggio originale-----
> > Da: bioruby-bounces at lists.open-bio.org [mailto:bioruby-
> > bounces at lists.open-bio.org] Per conto di Raoul Bonnal
> > Inviato: luned? 27 settembre 2010 12:53
> > A: bioruby at lists.open-bio.org
> > Oggetto: [BioRuby] Ruby 1.9.2 and BioRuby
> >
> > Hello guys,
> > Do you have any idea how to solve this error?
> > /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> > 3.0.0/lib/active_support/dependencies.rb:479:in
> > `load_missing_constant': Bio is not missing constant Sequence!
> > (ArgumentError)
> >         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> > 3.0.0/lib/active_support/dependencies.rb:183:in `block in
> > const_missing'
> >         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> > 3.0.0/lib/active_support/dependencies.rb:181:in `each'
> >         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> > 3.0.0/lib/active_support/dependencies.rb:181:in `const_missing'
> >         from /home/ra/deve/bioruby/lib/bio/sequence/compat.rb:15:in
> > `<module:Bio>'
> >         from /home/ra/deve/bioruby/lib/bio/sequence/compat.rb:13:in
> > `<top (required)>'
> >         from <internal:lib/rubygems/custom_require>:29:in `require'
> >         from <internal:lib/rubygems/custom_require>:29:in `require'
> >         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> > 3.0.0/lib/active_support/dependencies.rb:239:in `block in require'
> >         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> > 3.0.0/lib/active_support/dependencies.rb:225:in `block in
> > load_dependency'
> >         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> > 3.0.0/lib/active_support/dependencies.rb:591:in `new_constants_in'
> >         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> > 3.0.0/lib/active_support/dependencies.rb:225:in `load_dependency'
> >         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> > 3.0.0/lib/active_support/dependencies.rb:239:in `require'
> >         from /home/ra/deve/bioruby/lib/bio/sequence.rb:15:in `<top
> > (required)>'
> >         from /home/ra/deve/bioruby/lib/bio/shell/plugin/midi.rb:20:in
> > `<top (required)>'
> >         from <internal:lib/rubygems/custom_require>:29:in `require'
> >         from <internal:lib/rubygems/custom_require>:29:in `require'
> >         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> > 3.0.0/lib/active_support/dependencies.rb:239:in `block in require'
> >         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> > 3.0.0/lib/active_support/dependencies.rb:225:in `block in
> > load_dependency'
> >         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> > 3.0.0/lib/active_support/dependencies.rb:591:in `new_constants_in'
> >         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> > 3.0.0/lib/active_support/dependencies.rb:225:in `load_dependency'
> >         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> > 3.0.0/lib/active_support/dependencies.rb:239:in `require'
> >         from /home/ra/deve/bioruby/lib/bio/shell.rb:29:in
> > `<module:Shell>'
> >         from /home/ra/deve/bioruby/lib/bio/shell.rb:17:in `<top
> > (required)>'
> >         from <internal:lib/rubygems/custom_require>:29:in `require'
> >         from <internal:lib/rubygems/custom_require>:29:in `require'
> >         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> > 3.0.0/lib/active_support/dependencies.rb:239:in `block in require'
> >         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> > 3.0.0/lib/active_support/dependencies.rb:225:in `block in
> > load_dependency'
> >         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> > 3.0.0/lib/active_support/dependencies.rb:591:in `new_constants_in'
> >         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> > 3.0.0/lib/active_support/dependencies.rb:225:in `load_dependency'
> >         from /home/ra/.rvm/gems/ruby-1.9.2-p0/gems/activesupport-
> > 3.0.0/lib/active_support/dependencies.rb:239:in `require'
> >         from /home/ra/deve/bioruby/bin/bioruby:18:in `<main>'
> >
> > --
> > Raoul J.P. Bonnal
> > Life Science Informatics
> > Integrative Biology Program
> > Fondazione INGM
> > Via F. Sforza 28
> > 20122 Milano, IT
> > phone: +39 02 006 623  26
> > fax: +39 02 006 623 46
> > http://www.ingm.it
> >
> >
> >
> >
> > _______________________________________________
> > BioRuby Project - http://www.bioruby.org/
> > BioRuby mailing list
> > BioRuby at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioruby