From email2ants at gmail.com  Wed May  2 12:38:31 2007
From: email2ants at gmail.com (Anthony Underwood)
Date: Wed, 2 May 2007 17:38:31 +0100
Subject: [BioRuby] EMBL parsing
Message-ID: <9EF29B4E-EDFC-4106-A736-52195314F374@gmail.com>

Dear all,

I am having a problem when parsing EMBL genome files.

embl = open(filename)
entry = embl.gets(Bio::EMBL::DELIMITER)
seq_obj = Bio::EMBL.new(entry)
puts seq_obj.sequence_length


This takes a long time (minutes) and reports a sequence_length of 0

When taking an equivalent genbank file and changing the code  
appropriately it parses the file in seconds and reports the correct  
length. I am new to bioruby having used bioperl until now. Please can  
anybody let me know if they have had similar problems and any  
possible solutions.

Many thanks

Anthony

From n at bioruby.org  Wed May  2 12:47:27 2007
From: n at bioruby.org (Mitsuteru Nakao)
Date: Thu, 3 May 2007 01:47:27 +0900
Subject: [BioRuby] EMBL parsing
In-Reply-To: <9EF29B4E-EDFC-4106-A736-52195314F374@gmail.com>
References: <9EF29B4E-EDFC-4106-A736-52195314F374@gmail.com>
Message-ID: <90ca35f70705020947g66d6edf9pc552d79935973e75@mail.gmail.com>

Hi Anthony,

Thank you for your bug report.
Please let me know the accession numbers of EMBL genome
files you parsed.

Thanks in advance.

Mitsuteru the Bio::EMBL maintainer.
<n at bioruby.org>

> I am having a problem when parsing EMBL genome files.
>
> embl = open(filename)
> entry = embl.gets(Bio::EMBL::DELIMITER)
> seq_obj = Bio::EMBL.new(entry)
> puts seq_obj.sequence_length
>
>
> This takes a long time (minutes) and reports a sequence_length of 0

From email2ants at gmail.com  Thu May  3 07:48:03 2007
From: email2ants at gmail.com (Anthony Underwood)
Date: Thu, 3 May 2007 12:48:03 +0100
Subject: [BioRuby] EMBL parsing
Message-ID: <0AEBC5E8-5128-4448-AE2E-8FA7E8691332@gmail.com>

Hi Mitsiteru,

Any of the embl files downloaded from the ebi site have this problem.

for example http://www.ebi.ac.uk/cgi-bin/dbfetch? 
db=embl&style=raw&id=CP000360

Ruby takes all of the cpu power :(


But with the equivalent file from NCBI in genbank format there is no  
problem.

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi? 
cmd=Retrieve&db=Nucleotide&list_uids=94549081&dopt=GenBank

Many thanks for having a look at this


Anthony


From jdudley at stanford.edu  Thu May  3 09:51:52 2007
From: jdudley at stanford.edu (Joel Dudley)
Date: Thu, 3 May 2007 06:51:52 -0700
Subject: [BioRuby] Ruby in Science
Message-ID: <D8E63F00-CB20-41BB-BFD9-8E3D9C10F457@stanford.edu>

I'm giving a talk tonight at the SDForum Ruby SIG at Google  
Headquarters on the topic of Ruby and Ruby on Rails in scientific  
computing. For part of the talk I am going to highlight companies,  
research groups, products, and other resources that are deployed or  
currently under development using Ruby and/or Ruby on Rails. If  
you've got a scientific application or resource that fits this and  
would like me to give it mention to please send me the details off- 
list. I can't guarantee that I'll mention it (time for the talk is  
limited), but I'll do my best.

Thanks,

Joel Dudley
Stanford Medical Informatics

From s-merchant at northwestern.edu  Fri May  4 17:52:11 2007
From: s-merchant at northwestern.edu (Sohel Merchant)
Date: Fri, 4 May 2007 16:52:11 -0500
Subject: [BioRuby] BOF at Ruby on Rails conference
Message-ID: <000601c78e96$77f5bb20$c2987ca5@pc13>

Hello Everyone,

  I am organizing a Birds of a Feather (BoF) session at the upcoming Rails
conference in Portland, Oregon. Here are the details: 

 

Venue: Rails conf 2007, Oregon Convention Center (OCC)

Date: Saturday, May 19 

Time: 7:30-8:30pm 

Room: c125.

 

I hope to meet some of you guys there.

 

Cheers,

Sohel Merchant.


From ngoto at gen-info.osaka-u.ac.jp  Sat May  5 02:57:28 2007
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Sat, 5 May 2007 15:57:28 +0900
Subject: [BioRuby] EMBL parsing
In-Reply-To: <0AEBC5E8-5128-4448-AE2E-8FA7E8691332@gmail.com>
References: <0AEBC5E8-5128-4448-AE2E-8FA7E8691332@gmail.com>
Message-ID: <20070505065729.4ECD41CBC510@idnmail.gen-info.osaka-u.ac.jp>

Hi,

On Thu, 3 May 2007 12:48:03 +0100
Anthony Underwood <email2ants at gmail.com> wrote:

> Hi Mitsiteru,
> 
> Any of the embl files downloaded from the ebi site have this problem.
> 
> for example http://www.ebi.ac.uk/cgi-bin/dbfetch? 
> db=embl&style=raw&id=CP000360
> 
> Ruby takes all of the cpu power :(

It seems it is caused by thousands of iterations of str1 += str2
because it creates a new string object every time.
A patch is attached. (Ruby 1.8.0 or newer version required)

--- lib/bio/db.rb       5 Apr 2007 23:35:39 -0000       0.37
+++ lib/bio/db.rb       5 May 2007 06:08:39 -0000
@@ -313,12 +313,12 @@

   # Returns the contents of the entry as a Hash.
   def entry2hash(entry)
-    hash = Hash.new('')
+    hash = Hash.new { |h, k| h[k] = '' }
     entry.each_line do |line|
       tag = tag_get(line)
       next if tag == 'XX'
       tag = 'R' if tag =~ /^R./        # Reference lines
-      hash[tag] += line
+      hash[tag].concat line
     end
     return hash
   end


Naohisa Goto
ng at bioruby.org

From email2ants at gmail.com  Tue May  8 07:53:37 2007
From: email2ants at gmail.com (Anthony Underwood)
Date: Tue, 8 May 2007 12:53:37 +0100
Subject: [BioRuby] EMBL parsing
In-Reply-To: <20070505065729.4ECD41CBC510@idnmail.gen-info.osaka-u.ac.jp>
References: <0AEBC5E8-5128-4448-AE2E-8FA7E8691332@gmail.com>
	<20070505065729.4ECD41CBC510@idnmail.gen-info.osaka-u.ac.jp>
Message-ID: <4045DF0D-6F4C-47DF-A4D7-1B31D61C3A7D@gmail.com>

Hi Naohisa,

Thanks for the patch. This certainly appears to solve the problem of  
slow embl entry reading. However the sequence length is still  
reported as 0.

I found this was due to the idline not being interpreted correctly

on line 97
tmp['SEQUENCE_LENGTH'] = idline[3].strip.split(' ').first.to_i

was changed to

tmp['SEQUENCE_LENGTH'] = idline.last.strip.split(' ').first.to_i

This was OK for my purposes, but I think the whole idline  
interpretation needs to be looked at see (http://www.ebi.ac.uk/embl/ 
Documentation/User_manual/usrman.html#3_4_1). I could have a look at  
this if appropriate.

Thanks

Anthony


On 5 May 2007, at 07:57, Naohisa GOTO wrote:

> Hi,
>
> On Thu, 3 May 2007 12:48:03 +0100
> Anthony Underwood <email2ants at gmail.com> wrote:
>
>> Hi Mitsiteru,
>>
>> Any of the embl files downloaded from the ebi site have this problem.
>>
>> for example http://www.ebi.ac.uk/cgi-bin/dbfetch?
>> db=embl&style=raw&id=CP000360
>>
>> Ruby takes all of the cpu power :(
>
> It seems it is caused by thousands of iterations of str1 += str2
> because it creates a new string object every time.
> A patch is attached. (Ruby 1.8.0 or newer version required)
>
> --- lib/bio/db.rb       5 Apr 2007 23:35:39 -0000       0.37
> +++ lib/bio/db.rb       5 May 2007 06:08:39 -0000
> @@ -313,12 +313,12 @@
>
>    # Returns the contents of the entry as a Hash.
>    def entry2hash(entry)
> -    hash = Hash.new('')
> +    hash = Hash.new { |h, k| h[k] = '' }
>      entry.each_line do |line|
>        tag = tag_get(line)
>        next if tag == 'XX'
>        tag = 'R' if tag =~ /^R./        # Reference lines
> -      hash[tag] += line
> +      hash[tag].concat line
>      end
>      return hash
>    end
>
>
> Naohisa Goto
> ng at bioruby.org
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby


From n at bioruby.org  Tue May  8 13:09:47 2007
From: n at bioruby.org (Mitsuteru Nakao)
Date: Wed, 9 May 2007 02:09:47 +0900
Subject: [BioRuby] EMBL parsing
In-Reply-To: <4045DF0D-6F4C-47DF-A4D7-1B31D61C3A7D@gmail.com>
References: <0AEBC5E8-5128-4448-AE2E-8FA7E8691332@gmail.com>
	<20070505065729.4ECD41CBC510@idnmail.gen-info.osaka-u.ac.jp>
	<4045DF0D-6F4C-47DF-A4D7-1B31D61C3A7D@gmail.com>
Message-ID: <90ca35f70705081009r7719c562u36a902a84f88566c@mail.gmail.com>

Hi Anthony,

Thank you for your suggestions.
You can use the bioruby CVS HEAD which contains new idline
parser for EMBL rel89.



> This was OK for my purposes, but I think the whole idline
> interpretation needs to be looked at see (http://www.ebi.ac.uk/embl/
> Documentation/User_manual/usrman.html#3_4_1). I could have a look at
> this if appropriate.

Thanks

Mitsuteru
-
Mitsuteur Nakao
n at bioruby.org

From jan.aerts at bbsrc.ac.uk  Wed May  9 09:14:52 2007
From: jan.aerts at bbsrc.ac.uk (jan aerts (RI))
Date: Wed, 9 May 2007 14:14:52 +0100
Subject: [BioRuby] Ensembl API
Message-ID: <84DA9D8AC9B05F4B889E7C70238CB45104FB16F3@rie2ksrv1.ri.bbsrc.ac.uk>

Has anyone worked on an Ensembl API? There is a perl API and the
database schema is well-documented. On first impression, it seems
straightforward to make one using ActiveRecord, but I wouldn't want to
waste efforts on that if someone else is already working on it.

See http://www.ensembl.org/info/software/core/index.html

Dr Jan Aerts
Bioinformatics Group
Roslin Institute
Roslin EH25 9PS
Scotland, UK
tel: +44 131 527 4198
skype: aerts_ri

----...and the obligatory disclaimer----
Roslin Institute is a company limited by guarantee, registered in
Scotland (registered number SC157100) and a Scottish Charity (registered
number SC023592). Our registered office is at Roslin, Midlothian, EH25
9PS. VAT registration number 847380013.

The information contained in this e-mail (including any attachments) is
confidential and is intended for the use of  the addressee only. The
opinions expressed within this e-mail (including any attachments) are
the opinions of the sender and do not necessarily constitute those of
Roslin Institute (Edinburgh) ("the Institute") unless specifically
stated by a sender who is duly authorised to do so on behalf of the
Institute.


From jan.aerts at bbsrc.ac.uk  Wed May  9 09:49:50 2007
From: jan.aerts at bbsrc.ac.uk (jan aerts (RI))
Date: Wed, 9 May 2007 14:49:50 +0100
Subject: [BioRuby] Ensembl API
In-Reply-To: <1E75E5B2-D515-4EE4-9B2D-2E2D034E1EA1@sanger.ac.uk>
Message-ID: <84DA9D8AC9B05F4B889E7C70238CB45104FB16F6@rie2ksrv1.ri.bbsrc.ac.uk>

A post (in Japanese) about this shows a good primer:
http://itoshi.tv/d/?date=20060829

I'm testing this out on some tables of the Ensembl core and variation
databases, and things look promising... As you say it might well be that
we can't cover everything, but at least we can get quite far.

jan. 

-----Original Message-----
From: Michael Han [mailto:mh6 at sanger.ac.uk] 
Sent: 09 May 2007 14:38
To: jan aerts (RI)
Subject: Re: [BioRuby] Ensembl API

On 9 May 2007, at 14:14, jan aerts ((RI)) wrote:
> Has anyone worked on an Ensembl API? There is a perl API and the 
> database schema is well-documented. On first impression, it seems 
> straightforward to make one using ActiveRecord, but I wouldn't want to

> waste efforts on that if someone else is already working on it.
>
> See http://www.ensembl.org/info/software/core/index.html
>
> Dr Jan Aerts
> Bioinformatics Group

Hi Jan,

I am not sure if you can cover everything with a the default active-
record behavior.
But I would be a happy user of a ruby EnsEMBL API.
If you need/want help with it, I would also volunteer.

Michael


From jan.aerts at bbsrc.ac.uk  Wed May  9 10:10:24 2007
From: jan.aerts at bbsrc.ac.uk (jan aerts (RI))
Date: Wed, 9 May 2007 15:10:24 +0100
Subject: [BioRuby] Ensembl API
In-Reply-To: <58E34B0F-64FF-4CEB-9E36-7AF0B7159D08@sanger.ac.uk>
Message-ID: <84DA9D8AC9B05F4B889E7C70238CB45104FB16F9@rie2ksrv1.ri.bbsrc.ac.uk>

I've tried a connection similar to the ones used by the perl API and am
able to connect directly to the core and other databases. Am currently
playing around with the cow features, actually :-)

jan. 

-----Original Message-----
From: Michael Han [mailto:mh6 at sanger.ac.uk] 
Sent: 09 May 2007 14:57
To: jan aerts (RI)
Cc: bioruby at lists.open-bio.org
Subject: Re: [BioRuby] Ensembl API


On 9 May 2007, at 14:49, jan aerts ((RI)) wrote:
> A post (in Japanese) about this shows a good primer:
> http://itoshi.tv/d/?date=20060829

my Japanese is not so good, but isn't that run on a BioMart and not an
ensembl-core schema?

> I'm testing this out on some tables of the Ensembl core and variation 
> databases, and things look promising... As you say it might well be 
> that we can't cover everything, but at least we can get quite far.
>
> jan.
>
> -----Original Message-----
> From: Michael Han [mailto:mh6 at sanger.ac.uk]
> Sent: 09 May 2007 14:38
> To: jan aerts (RI)
> Subject: Re: [BioRuby] Ensembl API
>
> On 9 May 2007, at 14:14, jan aerts ((RI)) wrote:
>> Has anyone worked on an Ensembl API? There is a perl API and the 
>> database schema is well-documented. On first impression, it seems 
>> straightforward to make one using ActiveRecord, but I wouldn't want 
>> to
>
>> waste efforts on that if someone else is already working on it.
>>
>> See http://www.ensembl.org/info/software/core/index.html
>>
>> Dr Jan Aerts
>> Bioinformatics Group
>
> Hi Jan,
>
> I am not sure if you can cover everything with a the default active- 
> record behavior.
> But I would be a happy user of a ruby EnsEMBL API.
> If you need/want help with it, I would also volunteer.
>
> Michael



From mh6 at sanger.ac.uk  Wed May  9 09:57:18 2007
From: mh6 at sanger.ac.uk (Michael Han)
Date: Wed, 9 May 2007 14:57:18 +0100
Subject: [BioRuby] Ensembl API
In-Reply-To: <84DA9D8AC9B05F4B889E7C70238CB45104FB16F6@rie2ksrv1.ri.bbsrc.ac.uk>
References: <84DA9D8AC9B05F4B889E7C70238CB45104FB16F6@rie2ksrv1.ri.bbsrc.ac.uk>
Message-ID: <58E34B0F-64FF-4CEB-9E36-7AF0B7159D08@sanger.ac.uk>


On 9 May 2007, at 14:49, jan aerts ((RI)) wrote:
> A post (in Japanese) about this shows a good primer:
> http://itoshi.tv/d/?date=20060829

my Japanese is not so good, but isn't that run on a BioMart and not  
an ensembl-core schema?

> I'm testing this out on some tables of the Ensembl core and variation
> databases, and things look promising... As you say it might well be  
> that
> we can't cover everything, but at least we can get quite far.
>
> jan.
>
> -----Original Message-----
> From: Michael Han [mailto:mh6 at sanger.ac.uk]
> Sent: 09 May 2007 14:38
> To: jan aerts (RI)
> Subject: Re: [BioRuby] Ensembl API
>
> On 9 May 2007, at 14:14, jan aerts ((RI)) wrote:
>> Has anyone worked on an Ensembl API? There is a perl API and the
>> database schema is well-documented. On first impression, it seems
>> straightforward to make one using ActiveRecord, but I wouldn't  
>> want to
>
>> waste efforts on that if someone else is already working on it.
>>
>> See http://www.ensembl.org/info/software/core/index.html
>>
>> Dr Jan Aerts
>> Bioinformatics Group
>
> Hi Jan,
>
> I am not sure if you can cover everything with a the default active-
> record behavior.
> But I would be a happy user of a ruby EnsEMBL API.
> If you need/want help with it, I would also volunteer.
>
> Michael


From jan.aerts at bbsrc.ac.uk  Thu May 10 03:58:02 2007
From: jan.aerts at bbsrc.ac.uk (jan aerts (RI))
Date: Thu, 10 May 2007 08:58:02 +0100
Subject: [BioRuby] Ensembl API
In-Reply-To: <1E75E5B2-D515-4EE4-9B2D-2E2D034E1EA1@sanger.ac.uk>
Message-ID: <84DA9D8AC9B05F4B889E7C70238CB45104FB16FE@rie2ksrv1.ri.bbsrc.ac.uk>

Michael,

As you mention that we maybe won't be able to cover everything with the
default activerecord behaviour: what problems are you thinking of?

Note: I'd like to use the perl API as a guide. And indeed working out
the Slice object was quite simple...

jan.

-----Original Message-----
From: Michael Han [mailto:mh6 at sanger.ac.uk] 
Sent: 09 May 2007 14:38
To: jan aerts (RI)
Subject: Re: [BioRuby] Ensembl API

On 9 May 2007, at 14:14, jan aerts ((RI)) wrote:
> Has anyone worked on an Ensembl API? There is a perl API and the 
> database schema is well-documented. On first impression, it seems 
> straightforward to make one using ActiveRecord, but I wouldn't want to

> waste efforts on that if someone else is already working on it.
>
> See http://www.ensembl.org/info/software/core/index.html
>
> Dr Jan Aerts
> Bioinformatics Group

Hi Jan,

I am not sure if you can cover everything with a the default active-
record behavior.
But I would be a happy user of a ruby EnsEMBL API.
If you need/want help with it, I would also volunteer.

Michael


From jan.aerts at bbsrc.ac.uk  Thu May 10 05:09:50 2007
From: jan.aerts at bbsrc.ac.uk (jan aerts (RI))
Date: Thu, 10 May 2007 10:09:50 +0100
Subject: [BioRuby] Ensembl API
In-Reply-To: <834748BE-64D8-4642-AF70-5098589F91EB@sanger.ac.uk>
Message-ID: <84DA9D8AC9B05F4B889E7C70238CB45104FB1701@rie2ksrv1.ri.bbsrc.ac.uk>

I actually just started working on this API last night (in between some
deadlines I got to catch), so haven't gotten so far as to think about
caching. I'm basically working through the perl API tutorial
(http://www.ensembl.org/info/software/core/core_tutorial.html) and try
to implement all those examples. (At the moment, I'm at the bit that
says "Break chromosomal slices into smaller 100k component slices"...)

Some hurdles that I see coming are the caching and projecting features
from one coord system to another. We'll see what happens when we get
there.

As for a public place: I would _very_ much appreciate help with the API,
although

QUESTION FOR BIORUBY COMMUNITY AND DEVELOPERS:
* Do you think it would be best to create a sourceforge project for
this, or should I add it directly into bioruby (e.g. Bio::Api::Ensembl)?
I suppose the second option would be best, but the stuff I have is
probably not polished enough yet... and *far* from complete.
* Secondly: if a new release is coming: would it be best to wait untill
_after_ that release?

jan.


-----Original Message-----
From: Michael Han [mailto:mh6 at sanger.ac.uk] 
Sent: 10 May 2007 09:51
To: jan aerts (RI)
Subject: Re: [BioRuby] Ensembl API


On 10 May 2007, at 08:58, jan aerts ((RI)) wrote:
> Michael,
>
> As you mention that we maybe won't be able to cover everything with 
> the default activerecord behaviour: what problems are you thinking of?
>
> Note: I'd like to use the perl API as a guide. And indeed working out 
> the Slice object was quite simple...

Yes, I was thinking of the slices in combination with the different
assembly levels.
A change to the mapping part of that broke the last EnsEMBL release.
There were some cases where a seq_region maps one-to-many to other
seq_regions (also with gaps).
Did you put all the caching stuff from the Perl API into it? And if not,
is the performance ok?

It would be also great if you could put the code into some public place
(RubyForge as example), then it would be easier to see what is already
working/being worked at and what not.

> jan.
>
> -----Original Message-----
> From: Michael Han [mailto:mh6 at sanger.ac.uk]
> Sent: 09 May 2007 14:38
> To: jan aerts (RI)
> Subject: Re: [BioRuby] Ensembl API
>
> On 9 May 2007, at 14:14, jan aerts ((RI)) wrote:
>> Has anyone worked on an Ensembl API? There is a perl API and the 
>> database schema is well-documented. On first impression, it seems 
>> straightforward to make one using ActiveRecord, but I wouldn't want 
>> to
>
>> waste efforts on that if someone else is already working on it.
>>
>> See http://www.ensembl.org/info/software/core/index.html
>>
>> Dr Jan Aerts
>> Bioinformatics Group
>
> Hi Jan,
>
> I am not sure if you can cover everything with a the default active- 
> record behavior.
> But I would be a happy user of a ruby EnsEMBL API.
> If you need/want help with it, I would also volunteer.
>
> Michael



From jan.aerts at bbsrc.ac.uk  Thu May 10 06:18:22 2007
From: jan.aerts at bbsrc.ac.uk (jan aerts (RI))
Date: Thu, 10 May 2007 11:18:22 +0100
Subject: [BioRuby] Ensembl API
In-Reply-To: <BE63A0A3-726A-4A06-BF3A-2E292A120816@hgc.jp>
Message-ID: <84DA9D8AC9B05F4B889E7C70238CB45104FB1703@rie2ksrv1.ri.bbsrc.ac.uk>

OK. 

-----Original Message-----
From: Toshiaki Katayama [mailto:ktym at hgc.jp] 
Sent: 10 May 2007 11:14
To: jan aerts (RI)
Cc: Michael Han; bioruby at lists.open-bio.org
Subject: Re: [BioRuby] Ensembl API

Jan,

In that case, I would like you to consider to use the rubyforge
repository 'bioruby-annex' which Nakao-san had set up.

  http://lists.open-bio.org/pipermail/bioruby/2007-April/000355.html

When your modules matured and we, core developers, have decided how to
integrate Rails dependent modules in BioRuby, you can put them in the
BioRuby distribution.

Toshiaki

On 2007/05/10, at 18:09, jan aerts (RI) wrote:

> I actually just started working on this API last night (in between 
> some deadlines I got to catch), so haven't gotten so far as to think 
> about caching. I'm basically working through the perl API tutorial
> (http://www.ensembl.org/info/software/core/core_tutorial.html) and try

> to implement all those examples. (At the moment, I'm at the bit that 
> says "Break chromosomal slices into smaller 100k component slices"...)
>
> Some hurdles that I see coming are the caching and projecting features

> from one coord system to another. We'll see what happens when we get 
> there.
>
> As for a public place: I would _very_ much appreciate help with the 
> API, although
>
> QUESTION FOR BIORUBY COMMUNITY AND DEVELOPERS:
> * Do you think it would be best to create a sourceforge project for 
> this, or should I add it directly into bioruby (e.g.
Bio::Api::Ensembl)?
> I suppose the second option would be best, but the stuff I have is 
> probably not polished enough yet... and *far* from complete.
> * Secondly: if a new release is coming: would it be best to wait 
> untill _after_ that release?
>
> jan.
>
>
> -----Original Message-----
> From: Michael Han [mailto:mh6 at sanger.ac.uk]
> Sent: 10 May 2007 09:51
> To: jan aerts (RI)
> Subject: Re: [BioRuby] Ensembl API
>
>
> On 10 May 2007, at 08:58, jan aerts ((RI)) wrote:
>> Michael,
>>
>> As you mention that we maybe won't be able to cover everything with 
>> the default activerecord behaviour: what problems are you thinking
of?
>>
>> Note: I'd like to use the perl API as a guide. And indeed working out

>> the Slice object was quite simple...
>
> Yes, I was thinking of the slices in combination with the different 
> assembly levels.
> A change to the mapping part of that broke the last EnsEMBL release.
> There were some cases where a seq_region maps one-to-many to other 
> seq_regions (also with gaps).
> Did you put all the caching stuff from the Perl API into it? And if 
> not, is the performance ok?
>
> It would be also great if you could put the code into some public 
> place (RubyForge as example), then it would be easier to see what is 
> already working/being worked at and what not.
>
>> jan.
>>
>> -----Original Message-----
>> From: Michael Han [mailto:mh6 at sanger.ac.uk]
>> Sent: 09 May 2007 14:38
>> To: jan aerts (RI)
>> Subject: Re: [BioRuby] Ensembl API
>>
>> On 9 May 2007, at 14:14, jan aerts ((RI)) wrote:
>>> Has anyone worked on an Ensembl API? There is a perl API and the 
>>> database schema is well-documented. On first impression, it seems 
>>> straightforward to make one using ActiveRecord, but I wouldn't want 
>>> to
>>
>>> waste efforts on that if someone else is already working on it.
>>>
>>> See http://www.ensembl.org/info/software/core/index.html
>>>
>>> Dr Jan Aerts
>>> Bioinformatics Group
>>
>> Hi Jan,
>>
>> I am not sure if you can cover everything with a the default active- 
>> record behavior.
>> But I would be a happy user of a ruby EnsEMBL API.
>> If you need/want help with it, I would also volunteer.
>>
>> Michael
>



From ktym at hgc.jp  Thu May 10 06:13:34 2007
From: ktym at hgc.jp (Toshiaki Katayama)
Date: Thu, 10 May 2007 19:13:34 +0900
Subject: [BioRuby] Ensembl API
In-Reply-To: <84DA9D8AC9B05F4B889E7C70238CB45104FB1701@rie2ksrv1.ri.bbsrc.ac.uk>
References: <84DA9D8AC9B05F4B889E7C70238CB45104FB1701@rie2ksrv1.ri.bbsrc.ac.uk>
Message-ID: <BE63A0A3-726A-4A06-BF3A-2E292A120816@hgc.jp>

Jan,

In that case, I would like you to consider to use the rubyforge repository
'bioruby-annex' which Nakao-san had set up.

  http://lists.open-bio.org/pipermail/bioruby/2007-April/000355.html

When your modules matured and we, core developers, have decided how to integrate
Rails dependent modules in BioRuby, you can put them in the BioRuby distribution.

Toshiaki

On 2007/05/10, at 18:09, jan aerts (RI) wrote:

> I actually just started working on this API last night (in between some
> deadlines I got to catch), so haven't gotten so far as to think about
> caching. I'm basically working through the perl API tutorial
> (http://www.ensembl.org/info/software/core/core_tutorial.html) and try
> to implement all those examples. (At the moment, I'm at the bit that
> says "Break chromosomal slices into smaller 100k component slices"...)
>
> Some hurdles that I see coming are the caching and projecting features
> from one coord system to another. We'll see what happens when we get
> there.
>
> As for a public place: I would _very_ much appreciate help with the API,
> although
>
> QUESTION FOR BIORUBY COMMUNITY AND DEVELOPERS:
> * Do you think it would be best to create a sourceforge project for
> this, or should I add it directly into bioruby (e.g. Bio::Api::Ensembl)?
> I suppose the second option would be best, but the stuff I have is
> probably not polished enough yet... and *far* from complete.
> * Secondly: if a new release is coming: would it be best to wait untill
> _after_ that release?
>
> jan.
>
>
> -----Original Message-----
> From: Michael Han [mailto:mh6 at sanger.ac.uk] 
> Sent: 10 May 2007 09:51
> To: jan aerts (RI)
> Subject: Re: [BioRuby] Ensembl API
>
>
> On 10 May 2007, at 08:58, jan aerts ((RI)) wrote:
>> Michael,
>>
>> As you mention that we maybe won't be able to cover everything with 
>> the default activerecord behaviour: what problems are you thinking of?
>>
>> Note: I'd like to use the perl API as a guide. And indeed working out 
>> the Slice object was quite simple...
>
> Yes, I was thinking of the slices in combination with the different
> assembly levels.
> A change to the mapping part of that broke the last EnsEMBL release.
> There were some cases where a seq_region maps one-to-many to other
> seq_regions (also with gaps).
> Did you put all the caching stuff from the Perl API into it? And if not,
> is the performance ok?
>
> It would be also great if you could put the code into some public place
> (RubyForge as example), then it would be easier to see what is already
> working/being worked at and what not.
>
>> jan.
>>
>> -----Original Message-----
>> From: Michael Han [mailto:mh6 at sanger.ac.uk]
>> Sent: 09 May 2007 14:38
>> To: jan aerts (RI)
>> Subject: Re: [BioRuby] Ensembl API
>>
>> On 9 May 2007, at 14:14, jan aerts ((RI)) wrote:
>>> Has anyone worked on an Ensembl API? There is a perl API and the 
>>> database schema is well-documented. On first impression, it seems 
>>> straightforward to make one using ActiveRecord, but I wouldn't want 
>>> to
>>
>>> waste efforts on that if someone else is already working on it.
>>>
>>> See http://www.ensembl.org/info/software/core/index.html
>>>
>>> Dr Jan Aerts
>>> Bioinformatics Group
>>
>> Hi Jan,
>>
>> I am not sure if you can cover everything with a the default active- 
>> record behavior.
>> But I would be a happy user of a ruby EnsEMBL API.
>> If you need/want help with it, I would also volunteer.
>>
>> Michael
>


From ktym at hgc.jp  Thu May 10 07:42:53 2007
From: ktym at hgc.jp (Toshiaki Katayama)
Date: Thu, 10 May 2007 20:42:53 +0900
Subject: [BioRuby] Ensembl API
In-Reply-To: <84DA9D8AC9B05F4B889E7C70238CB45104FB1706@rie2ksrv1.ri.bbsrc.ac.uk>
References: <84DA9D8AC9B05F4B889E7C70238CB45104FB1706@rie2ksrv1.ri.bbsrc.ac.uk>
Message-ID: <B312993D-DFFA-4869-9F1E-890D04093A9C@hgc.jp>

Jan,

You are added as a annex developer.

> I noticed that the bioruby-annex repository is for bioruby *rails*
> plugins. However, the Ensembl API would have nothing to do with rails

When I discussed with Nakao-san previously, we have agreed to 
include any Rails (or ActiveRecord etc.) dependent bioinformatics
projects in the bioruby-annex repository (maybe we need to
refine

The purpose is

1. The number of codes which depend on Rails related libraries
   is increasing, but we have not yet decided how to integrate
   such modules in BioRuby.

2. We thought correcting various add-ons to BioRuby in one place
   might be useful (so that users can find your bioinformatics
   modules easily, and/or some of them might be integrated into
   core BioRuby library in the future).

> (apart from the fact that it uses ActiveRecord in the background).

So, I thought your project is appropriate to be included.

> This might get confusing for possible users.

Yes, we may need to re-write our project description to clarify.
Volunteers?

As the bioruby-annex seems to be functioning now, we need to discuss
some rules for how to develop, release, and use sub products in it.

My idea is still vague, but how about to have codes in SVN as

  /bioruby-annex/rails/plugins <- for Rails' script/plugin source
  /bioruby-annex/project1/
  /bioruby-annex/project2/
    :

and each sub projects will release the package as a gem (or tar.gz) file
prefixed with 'bioruby-' or 'bioruby-annex-' so that, for instance,
you could release

  bioruby-ensembl-api-1.0.gem

for downlaod from

  http://rubyforge.org/projects/bioruby-annex/

Toshiaki

On 2007/05/10, at 19:34, jan aerts (RI) wrote:

> Toshiaki,
>
> I noticed that the bioruby-annex repository is for bioruby *rails*
> plugins. However, the Ensembl API would have nothing to do with rails
> (apart from the fact that it uses ActiveRecord in the background).
> This might get confusing for possible users.
>
> jan. 
>
> -----Original Message-----
> From: Toshiaki Katayama [mailto:ktym at hgc.jp] 
> Sent: 10 May 2007 11:14
> To: jan aerts (RI)
> Cc: Michael Han; bioruby at lists.open-bio.org
> Subject: Re: [BioRuby] Ensembl API
>
> Jan,
>
> In that case, I would like you to consider to use the rubyforge
> repository 'bioruby-annex' which Nakao-san had set up.
>
>   http://lists.open-bio.org/pipermail/bioruby/2007-April/000355.html
>
> When your modules matured and we, core developers, have decided how to
> integrate Rails dependent modules in BioRuby, you can put them in the
> BioRuby distribution.
>
> Toshiaki
>
> On 2007/05/10, at 18:09, jan aerts (RI) wrote:
>
>> I actually just started working on this API last night (in between 
>> some deadlines I got to catch), so haven't gotten so far as to think 
>> about caching. I'm basically working through the perl API tutorial
>> (http://www.ensembl.org/info/software/core/core_tutorial.html) and try
>
>> to implement all those examples. (At the moment, I'm at the bit that 
>> says "Break chromosomal slices into smaller 100k component slices"...)
>>
>> Some hurdles that I see coming are the caching and projecting features
>
>> from one coord system to another. We'll see what happens when we get 
>> there.
>>
>> As for a public place: I would _very_ much appreciate help with the 
>> API, although
>>
>> QUESTION FOR BIORUBY COMMUNITY AND DEVELOPERS:
>> * Do you think it would be best to create a sourceforge project for 
>> this, or should I add it directly into bioruby (e.g.
> Bio::Api::Ensembl)?
>> I suppose the second option would be best, but the stuff I have is 
>> probably not polished enough yet... and *far* from complete.
>> * Secondly: if a new release is coming: would it be best to wait 
>> untill _after_ that release?
>>
>> jan.
>>
>>
>> -----Original Message-----
>> From: Michael Han [mailto:mh6 at sanger.ac.uk]
>> Sent: 10 May 2007 09:51
>> To: jan aerts (RI)
>> Subject: Re: [BioRuby] Ensembl API
>>
>>
>> On 10 May 2007, at 08:58, jan aerts ((RI)) wrote:
>>> Michael,
>>>
>>> As you mention that we maybe won't be able to cover everything with 
>>> the default activerecord behaviour: what problems are you thinking
> of?
>>>
>>> Note: I'd like to use the perl API as a guide. And indeed working out
>
>>> the Slice object was quite simple...
>>
>> Yes, I was thinking of the slices in combination with the different 
>> assembly levels.
>> A change to the mapping part of that broke the last EnsEMBL release.
>> There were some cases where a seq_region maps one-to-many to other 
>> seq_regions (also with gaps).
>> Did you put all the caching stuff from the Perl API into it? And if 
>> not, is the performance ok?
>>
>> It would be also great if you could put the code into some public 
>> place (RubyForge as example), then it would be easier to see what is 
>> already working/being worked at and what not.
>>
>>> jan.
>>>
>>> -----Original Message-----
>>> From: Michael Han [mailto:mh6 at sanger.ac.uk]
>>> Sent: 09 May 2007 14:38
>>> To: jan aerts (RI)
>>> Subject: Re: [BioRuby] Ensembl API
>>>
>>> On 9 May 2007, at 14:14, jan aerts ((RI)) wrote:
>>>> Has anyone worked on an Ensembl API? There is a perl API and the 
>>>> database schema is well-documented. On first impression, it seems 
>>>> straightforward to make one using ActiveRecord, but I wouldn't want 
>>>> to
>>>
>>>> waste efforts on that if someone else is already working on it.
>>>>
>>>> See http://www.ensembl.org/info/software/core/index.html
>>>>
>>>> Dr Jan Aerts
>>>> Bioinformatics Group
>>>
>>> Hi Jan,
>>>
>>> I am not sure if you can cover everything with a the default active- 
>>> record behavior.
>>> But I would be a happy user of a ruby EnsEMBL API.
>>> If you need/want help with it, I would also volunteer.
>>>
>>> Michael
>>
>


From ktym at hgc.jp  Thu May 10 07:45:40 2007
From: ktym at hgc.jp (Toshiaki Katayama)
Date: Thu, 10 May 2007 20:45:40 +0900
Subject: [BioRuby] Ensembl API
In-Reply-To: <B312993D-DFFA-4869-9F1E-890D04093A9C@hgc.jp>
References: <84DA9D8AC9B05F4B889E7C70238CB45104FB1706@rie2ksrv1.ri.bbsrc.ac.uk>
	<B312993D-DFFA-4869-9F1E-890D04093A9C@hgc.jp>
Message-ID: <057D48B5-57EC-464E-ABB7-05B059569253@hgc.jp>

On 2007/05/10, at 20:42, Toshiaki Katayama wrote:
> When I discussed with Nakao-san previously, we have agreed to 
> include any Rails (or ActiveRecord etc.) dependent bioinformatics
> projects in the bioruby-annex repository (maybe we need to
> refine

refine the project description).

Toshiaki


From ktym at hgc.jp  Thu May 10 07:49:15 2007
From: ktym at hgc.jp (Toshiaki Katayama)
Date: Thu, 10 May 2007 20:49:15 +0900
Subject: [BioRuby] Ensembl API
In-Reply-To: <B312993D-DFFA-4869-9F1E-890D04093A9C@hgc.jp>
References: <84DA9D8AC9B05F4B889E7C70238CB45104FB1706@rie2ksrv1.ri.bbsrc.ac.uk>
	<B312993D-DFFA-4869-9F1E-890D04093A9C@hgc.jp>
Message-ID: <38E0CF6A-14CD-4905-947E-410D389F9CD9@hgc.jp>

On 2007/05/10, at 20:42, Toshiaki Katayama wrote:
> 2. We thought correcting various add-ons to BioRuby in one place

s/correct/collect/ ... there might be many other mistakes as always :)

Toshiaki



From jan.aerts at bbsrc.ac.uk  Thu May 10 09:29:01 2007
From: jan.aerts at bbsrc.ac.uk (jan aerts (RI))
Date: Thu, 10 May 2007 14:29:01 +0100
Subject: [BioRuby] Ensembl API
In-Reply-To: <B312993D-DFFA-4869-9F1E-890D04093A9C@hgc.jp>
Message-ID: <84DA9D8AC9B05F4B889E7C70238CB45104FB170C@rie2ksrv1.ri.bbsrc.ac.uk>

Removing the 'rails' from the project description would be a good idea.
It would be great if this repository could also be the home for modules
like Bio::Graphics (which is completely unrelated to rails or
activerecord)

jan. 

-----Original Message-----
From: Toshiaki Katayama [mailto:ktym at hgc.jp] 
Sent: 10 May 2007 12:43
To: jan aerts (RI)
Cc: BioRubyML
Subject: Re: [BioRuby] Ensembl API

Jan,

You are added as a annex developer.

> I noticed that the bioruby-annex repository is for bioruby *rails* 
> plugins. However, the Ensembl API would have nothing to do with rails

When I discussed with Nakao-san previously, we have agreed to include
any Rails (or ActiveRecord etc.) dependent bioinformatics projects in
the bioruby-annex repository (maybe we need to refine

The purpose is

1. The number of codes which depend on Rails related libraries
   is increasing, but we have not yet decided how to integrate
   such modules in BioRuby.

2. We thought correcting various add-ons to BioRuby in one place
   might be useful (so that users can find your bioinformatics
   modules easily, and/or some of them might be integrated into
   core BioRuby library in the future).

> (apart from the fact that it uses ActiveRecord in the background).

So, I thought your project is appropriate to be included.

> This might get confusing for possible users.

Yes, we may need to re-write our project description to clarify.
Volunteers?

As the bioruby-annex seems to be functioning now, we need to discuss
some rules for how to develop, release, and use sub products in it.

My idea is still vague, but how about to have codes in SVN as

  /bioruby-annex/rails/plugins <- for Rails' script/plugin source
  /bioruby-annex/project1/
  /bioruby-annex/project2/
    :

and each sub projects will release the package as a gem (or tar.gz) file
prefixed with 'bioruby-' or 'bioruby-annex-' so that, for instance, you
could release

  bioruby-ensembl-api-1.0.gem

for downlaod from

  http://rubyforge.org/projects/bioruby-annex/

Toshiaki

On 2007/05/10, at 19:34, jan aerts (RI) wrote:

> Toshiaki,
>
> I noticed that the bioruby-annex repository is for bioruby *rails* 
> plugins. However, the Ensembl API would have nothing to do with rails 
> (apart from the fact that it uses ActiveRecord in the background).
> This might get confusing for possible users.
>
> jan. 
>
> -----Original Message-----
> From: Toshiaki Katayama [mailto:ktym at hgc.jp]
> Sent: 10 May 2007 11:14
> To: jan aerts (RI)
> Cc: Michael Han; bioruby at lists.open-bio.org
> Subject: Re: [BioRuby] Ensembl API
>
> Jan,
>
> In that case, I would like you to consider to use the rubyforge 
> repository 'bioruby-annex' which Nakao-san had set up.
>
>   http://lists.open-bio.org/pipermail/bioruby/2007-April/000355.html
>
> When your modules matured and we, core developers, have decided how to

> integrate Rails dependent modules in BioRuby, you can put them in the 
> BioRuby distribution.
>
> Toshiaki
>
> On 2007/05/10, at 18:09, jan aerts (RI) wrote:
>
>> I actually just started working on this API last night (in between 
>> some deadlines I got to catch), so haven't gotten so far as to think 
>> about caching. I'm basically working through the perl API tutorial
>> (http://www.ensembl.org/info/software/core/core_tutorial.html) and 
>> try
>
>> to implement all those examples. (At the moment, I'm at the bit that 
>> says "Break chromosomal slices into smaller 100k component 
>> slices"...)
>>
>> Some hurdles that I see coming are the caching and projecting 
>> features
>
>> from one coord system to another. We'll see what happens when we get 
>> there.
>>
>> As for a public place: I would _very_ much appreciate help with the 
>> API, although
>>
>> QUESTION FOR BIORUBY COMMUNITY AND DEVELOPERS:
>> * Do you think it would be best to create a sourceforge project for 
>> this, or should I add it directly into bioruby (e.g.
> Bio::Api::Ensembl)?
>> I suppose the second option would be best, but the stuff I have is 
>> probably not polished enough yet... and *far* from complete.
>> * Secondly: if a new release is coming: would it be best to wait 
>> untill _after_ that release?
>>
>> jan.
>>
>>
>> -----Original Message-----
>> From: Michael Han [mailto:mh6 at sanger.ac.uk]
>> Sent: 10 May 2007 09:51
>> To: jan aerts (RI)
>> Subject: Re: [BioRuby] Ensembl API
>>
>>
>> On 10 May 2007, at 08:58, jan aerts ((RI)) wrote:
>>> Michael,
>>>
>>> As you mention that we maybe won't be able to cover everything with 
>>> the default activerecord behaviour: what problems are you thinking
> of?
>>>
>>> Note: I'd like to use the perl API as a guide. And indeed working 
>>> out
>
>>> the Slice object was quite simple...
>>
>> Yes, I was thinking of the slices in combination with the different 
>> assembly levels.
>> A change to the mapping part of that broke the last EnsEMBL release.
>> There were some cases where a seq_region maps one-to-many to other 
>> seq_regions (also with gaps).
>> Did you put all the caching stuff from the Perl API into it? And if 
>> not, is the performance ok?
>>
>> It would be also great if you could put the code into some public 
>> place (RubyForge as example), then it would be easier to see what is 
>> already working/being worked at and what not.
>>
>>> jan.
>>>
>>> -----Original Message-----
>>> From: Michael Han [mailto:mh6 at sanger.ac.uk]
>>> Sent: 09 May 2007 14:38
>>> To: jan aerts (RI)
>>> Subject: Re: [BioRuby] Ensembl API
>>>
>>> On 9 May 2007, at 14:14, jan aerts ((RI)) wrote:
>>>> Has anyone worked on an Ensembl API? There is a perl API and the 
>>>> database schema is well-documented. On first impression, it seems 
>>>> straightforward to make one using ActiveRecord, but I wouldn't want

>>>> to
>>>
>>>> waste efforts on that if someone else is already working on it.
>>>>
>>>> See http://www.ensembl.org/info/software/core/index.html
>>>>
>>>> Dr Jan Aerts
>>>> Bioinformatics Group
>>>
>>> Hi Jan,
>>>
>>> I am not sure if you can cover everything with a the default active-

>>> record behavior.
>>> But I would be a happy user of a ruby EnsEMBL API.
>>> If you need/want help with it, I would also volunteer.
>>>
>>> Michael
>>
>



From jan.aerts at bbsrc.ac.uk  Thu May 10 09:32:22 2007
From: jan.aerts at bbsrc.ac.uk (jan aerts (RI))
Date: Thu, 10 May 2007 14:32:22 +0100
Subject: [BioRuby] Ensembl API
In-Reply-To: <B312993D-DFFA-4869-9F1E-890D04093A9C@hgc.jp>
Message-ID: <84DA9D8AC9B05F4B889E7C70238CB45104FB170D@rie2ksrv1.ri.bbsrc.ac.uk>

Toshiaki,

Your idea of a directory structure as this seems a good choice.
  /bioruby-annex/rails/plugins <- for Rails' script/plugin source
  /bioruby-annex/project1/
  /bioruby-annex/project2/
    :

OK if I add a subdirectory for 'ensembl_api'? (so that would be:
/bioruby-annex/ensembl_api/)

jan.

-----Original Message-----
From: Toshiaki Katayama [mailto:ktym at hgc.jp] 
Sent: 10 May 2007 12:43
To: jan aerts (RI)
Cc: BioRubyML
Subject: Re: [BioRuby] Ensembl API

Jan,

You are added as a annex developer.

> I noticed that the bioruby-annex repository is for bioruby *rails* 
> plugins. However, the Ensembl API would have nothing to do with rails

When I discussed with Nakao-san previously, we have agreed to include
any Rails (or ActiveRecord etc.) dependent bioinformatics projects in
the bioruby-annex repository (maybe we need to refine

The purpose is

1. The number of codes which depend on Rails related libraries
   is increasing, but we have not yet decided how to integrate
   such modules in BioRuby.

2. We thought correcting various add-ons to BioRuby in one place
   might be useful (so that users can find your bioinformatics
   modules easily, and/or some of them might be integrated into
   core BioRuby library in the future).

> (apart from the fact that it uses ActiveRecord in the background).

So, I thought your project is appropriate to be included.

> This might get confusing for possible users.

Yes, we may need to re-write our project description to clarify.
Volunteers?

As the bioruby-annex seems to be functioning now, we need to discuss
some rules for how to develop, release, and use sub products in it.

My idea is still vague, but how about to have codes in SVN as

  /bioruby-annex/rails/plugins <- for Rails' script/plugin source
  /bioruby-annex/project1/
  /bioruby-annex/project2/
    :

and each sub projects will release the package as a gem (or tar.gz) file
prefixed with 'bioruby-' or 'bioruby-annex-' so that, for instance, you
could release

  bioruby-ensembl-api-1.0.gem

for downlaod from

  http://rubyforge.org/projects/bioruby-annex/

Toshiaki

On 2007/05/10, at 19:34, jan aerts (RI) wrote:

> Toshiaki,
>
> I noticed that the bioruby-annex repository is for bioruby *rails* 
> plugins. However, the Ensembl API would have nothing to do with rails 
> (apart from the fact that it uses ActiveRecord in the background).
> This might get confusing for possible users.
>
> jan. 
>
> -----Original Message-----
> From: Toshiaki Katayama [mailto:ktym at hgc.jp]
> Sent: 10 May 2007 11:14
> To: jan aerts (RI)
> Cc: Michael Han; bioruby at lists.open-bio.org
> Subject: Re: [BioRuby] Ensembl API
>
> Jan,
>
> In that case, I would like you to consider to use the rubyforge 
> repository 'bioruby-annex' which Nakao-san had set up.
>
>   http://lists.open-bio.org/pipermail/bioruby/2007-April/000355.html
>
> When your modules matured and we, core developers, have decided how to

> integrate Rails dependent modules in BioRuby, you can put them in the 
> BioRuby distribution.
>
> Toshiaki
>
> On 2007/05/10, at 18:09, jan aerts (RI) wrote:
>
>> I actually just started working on this API last night (in between 
>> some deadlines I got to catch), so haven't gotten so far as to think 
>> about caching. I'm basically working through the perl API tutorial
>> (http://www.ensembl.org/info/software/core/core_tutorial.html) and 
>> try
>
>> to implement all those examples. (At the moment, I'm at the bit that 
>> says "Break chromosomal slices into smaller 100k component 
>> slices"...)
>>
>> Some hurdles that I see coming are the caching and projecting 
>> features
>
>> from one coord system to another. We'll see what happens when we get 
>> there.
>>
>> As for a public place: I would _very_ much appreciate help with the 
>> API, although
>>
>> QUESTION FOR BIORUBY COMMUNITY AND DEVELOPERS:
>> * Do you think it would be best to create a sourceforge project for 
>> this, or should I add it directly into bioruby (e.g.
> Bio::Api::Ensembl)?
>> I suppose the second option would be best, but the stuff I have is 
>> probably not polished enough yet... and *far* from complete.
>> * Secondly: if a new release is coming: would it be best to wait 
>> untill _after_ that release?
>>
>> jan.
>>
>>
>> -----Original Message-----
>> From: Michael Han [mailto:mh6 at sanger.ac.uk]
>> Sent: 10 May 2007 09:51
>> To: jan aerts (RI)
>> Subject: Re: [BioRuby] Ensembl API
>>
>>
>> On 10 May 2007, at 08:58, jan aerts ((RI)) wrote:
>>> Michael,
>>>
>>> As you mention that we maybe won't be able to cover everything with 
>>> the default activerecord behaviour: what problems are you thinking
> of?
>>>
>>> Note: I'd like to use the perl API as a guide. And indeed working 
>>> out
>
>>> the Slice object was quite simple...
>>
>> Yes, I was thinking of the slices in combination with the different 
>> assembly levels.
>> A change to the mapping part of that broke the last EnsEMBL release.
>> There were some cases where a seq_region maps one-to-many to other 
>> seq_regions (also with gaps).
>> Did you put all the caching stuff from the Perl API into it? And if 
>> not, is the performance ok?
>>
>> It would be also great if you could put the code into some public 
>> place (RubyForge as example), then it would be easier to see what is 
>> already working/being worked at and what not.
>>
>>> jan.
>>>
>>> -----Original Message-----
>>> From: Michael Han [mailto:mh6 at sanger.ac.uk]
>>> Sent: 09 May 2007 14:38
>>> To: jan aerts (RI)
>>> Subject: Re: [BioRuby] Ensembl API
>>>
>>> On 9 May 2007, at 14:14, jan aerts ((RI)) wrote:
>>>> Has anyone worked on an Ensembl API? There is a perl API and the 
>>>> database schema is well-documented. On first impression, it seems 
>>>> straightforward to make one using ActiveRecord, but I wouldn't want

>>>> to
>>>
>>>> waste efforts on that if someone else is already working on it.
>>>>
>>>> See http://www.ensembl.org/info/software/core/index.html
>>>>
>>>> Dr Jan Aerts
>>>> Bioinformatics Group
>>>
>>> Hi Jan,
>>>
>>> I am not sure if you can cover everything with a the default active-

>>> record behavior.
>>> But I would be a happy user of a ruby EnsEMBL API.
>>> If you need/want help with it, I would also volunteer.
>>>
>>> Michael
>>
>



From fredjoha at bioreg.kyushu-u.ac.jp  Tue May 15 01:54:46 2007
From: fredjoha at bioreg.kyushu-u.ac.jp (Fredrik Johansson)
Date: Tue, 15 May 2007 14:54:46 +0900
Subject: [BioRuby] Bio::Blast not fully functional?
Message-ID: <1179208486.7335.39.camel@fred-kyudai>

Hello all,
I am reading in the tutorial at
http://dev.bioruby.org/wiki/en/?Tutorial.rd
about BLAST and I try to use it according to this tutorial (see the code
below).
However, many of the entries in the 'hit' variable in the code below
seems to be nil. hit.identity and hit.target_seq are for example two
methods that just answer nil when I call them. Am I missing something?

#!/usr/bin/env ruby
require 'bio'
factory = Bio::Blast.remote('blastp', 'nr-aa')
Bio::FlatFile.open(Bio::FastaFormat, '/home/fred/pdb/test.fasta.txt') do
|ff|
  ff.each do |entry|
    report = factory.query(entry)
    report.each do |hit|
      if hit.evalue < 0.001
         puts hit.target_id
         puts hit.target_seq
      end
    end
  end
end

Thanks for any help!
Best regards,
Fredrik Johansson


From hienle at club-internet.fr  Tue May 15 11:30:27 2007
From: hienle at club-internet.fr (hienle at club-internet.fr)
Date: Tue, 15 May 2007 17:30:27 +0200
Subject: [BioRuby] Parsing GFF3 attributes
Message-ID: <mnet1.1179243027.27796.hienle@club-internet.fr>

Hello all,

I am working with a GFF3-formatted file and have noticed that the attributes field is not parsed properly.

In bio/db/gff.rb, 

    75      def parse_attributes(attributes)
    76        hash = Hash.new
    77        attributes.split(/[^\\];/).each do |atr|
    78          key, value = atr.split(' ', 2)
    79          hash[key] = value
    80        end
    81        return hash
    82      end
    83    end

I changed :
    78          key, value = atr.split(' ', 2)
to:
    78          key, value = atr.split('=', 2)

and it now appears to behave properly. However, I am not certain if this is appropriate for backward compatibility with GFF and GFF2. Is anyone working on parsing GFF3 files?

Thank you in advance for your help,
-Hien



From mh6 at sanger.ac.uk  Tue May 15 12:10:20 2007
From: mh6 at sanger.ac.uk (Michael Han)
Date: Tue, 15 May 2007 17:10:20 +0100
Subject: [BioRuby] Parsing GFF3 attributes
In-Reply-To: <mnet1.1179243027.27796.hienle@club-internet.fr>
References: <mnet1.1179243027.27796.hienle@club-internet.fr>
Message-ID: <ACEE88FC-0094-4B17-AC2F-34E56CF072D1@sanger.ac.uk>


On 15 May 2007, at 16:30, hienle at club-internet.fr wrote:
> Hello all,
>
> I am working with a GFF3-formatted file and have noticed that the  
> attributes field is not parsed properly.
>
> In bio/db/gff.rb,
>
>     75      def parse_attributes(attributes)
>     76        hash = Hash.new
>     77        attributes.split(/[^\\];/).each do |atr|
>     78          key, value = atr.split(' ', 2)
>     79          hash[key] = value
>     80        end
>     81        return hash
>     82      end
>     83    end
>
> I changed :
>     78          key, value = atr.split(' ', 2)
> to:
>     78          key, value = atr.split('=', 2)
>
> and it now appears to behave properly. However, I am not certain if  
> this is appropriate for backward compatibility with GFF and GFF2.

I use normally spaces between the key and the value of the attributes  
for GFF2 like: Gene "1234" ; Transcript "1234"
as described in <"http://www.sanger.ac.uk/Software/formats/GFF/ 
GFF_Spec.shtml">

so it would break  GFF2 / GFF parsing.
Maybe you could create a separate GFF3 parser inheriting from the  
gff.rb .

some GFF3 reference (note: last version from a few weeks ago)
<"http://www.sequenceontology.org/gff3.shtml">

> Is anyone working on parsing GFF3 files?
>
> Thank you in advance for your help,
> -Hien

MIchael

From hien.le at mail.mcgill.ca  Wed May 16 03:01:54 2007
From: hien.le at mail.mcgill.ca (Hien Le)
Date: Wed, 16 May 2007 03:01:54 -0400
Subject: [BioRuby] Parsing GFF3 attributes
In-Reply-To: <ACEE88FC-0094-4B17-AC2F-34E56CF072D1@sanger.ac.uk>
References: <mnet1.1179243027.27796.hienle@club-internet.fr>
	<ACEE88FC-0094-4B17-AC2F-34E56CF072D1@sanger.ac.uk>
Message-ID: <20070516030154.esps58l1ws8c8o00@webmail.mcgill.ca>

Quoting Michael Han <mh6 at sanger.ac.uk>:

> so it would break  GFF2 / GFF parsing.
> Maybe you could create a separate GFF3 parser inheriting from the
> gff.rb .

OK, thanks Michael for the advice!
-Hien

From cihan at cihan.us  Wed May 16 10:44:14 2007
From: cihan at cihan.us (cihan inan)
Date: Wed, 16 May 2007 17:44:14 +0300
Subject: [BioRuby] Translate docs
Message-ID: <5584352e0705160744w429281b6v3ccf3e8f105cac17@mail.gmail.com>

hi I am cihan inan and I am from Turkey. I am a student at Biology. I am new
in Ruby language. I want to translate some docs to Turkish. But I think I
have to get permission. But I dont know who gives that permission? please
help me about this topic. ( tell me the docs to start give me a way sth. )
thanks a lot.

From fredjoha at bioreg.kyushu-u.ac.jp  Thu May 17 21:17:12 2007
From: fredjoha at bioreg.kyushu-u.ac.jp (Fredrik Johansson)
Date: Fri, 18 May 2007 10:17:12 +0900
Subject: [BioRuby] FASTA problem
Message-ID: <1179451032.29172.33.camel@fred-kyudai>

Hello,
I had problem running a fasta search locally on my computer, and it
turned out that Kernel.exec(*cmd) is not very happy to get the array cmd
with nil as one of its element. This is however what happens in
bio/app/fasta.rb, if ktup is not set. I changed this to make it work :

--- fasta.rb.old        2007-05-18 09:55:01.000000000 +0900
+++ fasta.rb    2007-05-18 09:55:37.000000000 +0900
@@ -114,7 +114,8 @@
 
   def exec_local(query)
     cmd = [ @program, *@options ]
-    cmd.concat([ '@', @db, @ktup ])
+    cmd.concat([ '@', @db])
+    cmd.push(@ktup) if @ktup
 
     report = nil
 
Something to submit to the repository?

Best regards,
Fredrik


From ktym at hgc.jp  Fri May 18 11:23:41 2007
From: ktym at hgc.jp (Toshiaki Katayama)
Date: Sat, 19 May 2007 00:23:41 +0900
Subject: [BioRuby] FASTA problem
In-Reply-To: <1179451032.29172.33.camel@fred-kyudai>
References: <1179451032.29172.33.camel@fred-kyudai>
Message-ID: <FCA0A706-457C-4C23-944E-65DD07DEE9BF@hgc.jp>

Hello Fredrik,

Thank you for your fix!
I have commited your patch to the CVS.

Regards,
Toshiaki Katayama


On 2007/05/18, at 10:17, Fredrik Johansson wrote:

> Hello,
> I had problem running a fasta search locally on my computer, and it
> turned out that Kernel.exec(*cmd) is not very happy to get the array cmd
> with nil as one of its element. This is however what happens in
> bio/app/fasta.rb, if ktup is not set. I changed this to make it work :
>
> --- fasta.rb.old        2007-05-18 09:55:01.000000000 +0900
> +++ fasta.rb    2007-05-18 09:55:37.000000000 +0900
> @@ -114,7 +114,8 @@
>
>    def exec_local(query)
>      cmd = [ @program, *@options ]
> -    cmd.concat([ '@', @db, @ktup ])
> +    cmd.concat([ '@', @db])
> +    cmd.push(@ktup) if @ktup
>
>      report = nil
>
> Something to submit to the repository?
>
> Best regards,
> Fredrik
>
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby


From ktym at hgc.jp  Fri May 18 11:24:24 2007
From: ktym at hgc.jp (Toshiaki Katayama)
Date: Sat, 19 May 2007 00:24:24 +0900
Subject: [BioRuby] Translate docs
In-Reply-To: <5584352e0705160744w429281b6v3ccf3e8f105cac17@mail.gmail.com>
References: <5584352e0705160744w429281b6v3ccf3e8f105cac17@mail.gmail.com>
Message-ID: <852FFA12-3475-46B7-82C6-250ACD7A6BD0@hgc.jp>

Hi,

You are free to translate the documents in the bioruby-x.x.x/doc/ directory or on web (wiki) pages.
I apologize the main document, bioruby tutorial, is not updated
(I've lost updated version with disk crash in this Feb and not restarted yet).

Regards,
Toshiaki Katayama

On 2007/05/16, at 23:44, cihan inan wrote:

> hi I am cihan inan and I am from Turkey. I am a student at Biology. I am new
> in Ruby language. I want to translate some docs to Turkish. But I think I
> have to get permission. But I dont know who gives that permission? please
> help me about this topic. ( tell me the docs to start give me a way sth. )
> thanks a lot.
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby


From ktym at hgc.jp  Fri May 18 11:23:51 2007
From: ktym at hgc.jp (Toshiaki Katayama)
Date: Sat, 19 May 2007 00:23:51 +0900
Subject: [BioRuby] Parsing GFF3 attributes
In-Reply-To: <ACEE88FC-0094-4B17-AC2F-34E56CF072D1@sanger.ac.uk>
References: <mnet1.1179243027.27796.hienle@club-internet.fr>
	<ACEE88FC-0094-4B17-AC2F-34E56CF072D1@sanger.ac.uk>
Message-ID: <10A4A7B4-063F-459F-B9D6-56222F8C26E9@hgc.jp>

Hien,

Thank you for your report.

In bio/db/gff.rb, we have Bio::GFF::GFF2 for version 2 spec and Bio::GFF::GFF3 for version 3
and I added your modification to the Bio::GFF::GFF3 class.

Personally, I have not yet use GFF3 intensively, so if you think the class
should have more functionality to support new features in GFF3, please propose.

Toshiaki

On 2007/05/16, at 1:10, Michael Han wrote:

>
> On 15 May 2007, at 16:30, hienle at club-internet.fr wrote:
>> Hello all,
>>
>> I am working with a GFF3-formatted file and have noticed that the  
>> attributes field is not parsed properly.
>>
>> In bio/db/gff.rb,
>>
>>     75      def parse_attributes(attributes)
>>     76        hash = Hash.new
>>     77        attributes.split(/[^\\];/).each do |atr|
>>     78          key, value = atr.split(' ', 2)
>>     79          hash[key] = value
>>     80        end
>>     81        return hash
>>     82      end
>>     83    end
>>
>> I changed :
>>     78          key, value = atr.split(' ', 2)
>> to:
>>     78          key, value = atr.split('=', 2)
>>
>> and it now appears to behave properly. However, I am not certain if  
>> this is appropriate for backward compatibility with GFF and GFF2.
>
> I use normally spaces between the key and the value of the attributes  
> for GFF2 like: Gene "1234" ; Transcript "1234"
> as described in <"http://www.sanger.ac.uk/Software/formats/GFF/ 
> GFF_Spec.shtml">
>
> so it would break  GFF2 / GFF parsing.
> Maybe you could create a separate GFF3 parser inheriting from the  
> gff.rb .
>
> some GFF3 reference (note: last version from a few weeks ago)
> <"http://www.sequenceontology.org/gff3.shtml">
>
>> Is anyone working on parsing GFF3 files?
>>
>> Thank you in advance for your help,
>> -Hien
>
> MIchael
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby


From ktym at hgc.jp  Fri May 18 12:00:33 2007
From: ktym at hgc.jp (Toshiaki Katayama)
Date: Sat, 19 May 2007 01:00:33 +0900
Subject: [BioRuby] Bio::Blast not fully functional?
In-Reply-To: <1179208486.7335.39.camel@fred-kyudai>
References: <1179208486.7335.39.camel@fred-kyudai>
Message-ID: <8B741702-DB3E-49D5-9920-9420336F4E61@hgc.jp>


Fredrik,

This is because Bio::Blast.remote uses '-m 8' option
which returns a tabular output format without target sequences.

You can use XML output for your purpose by changing the following line

> factory = Bio::Blast.remote('blastp', 'nr-aa')

to

factory = Bio::Blast.remote('blastp', 'nr-aa', '-m 7')

Regards,
Toshiaki

On 2007/05/15, at 14:54, Fredrik Johansson wrote:

> Hello all,
> I am reading in the tutorial at
> http://dev.bioruby.org/wiki/en/?Tutorial.rd
> about BLAST and I try to use it according to this tutorial (see the code
> below).
> However, many of the entries in the 'hit' variable in the code below
> seems to be nil. hit.identity and hit.target_seq are for example two
> methods that just answer nil when I call them. Am I missing something?
>
> #!/usr/bin/env ruby
> require 'bio'
> factory = Bio::Blast.remote('blastp', 'nr-aa')
> Bio::FlatFile.open(Bio::FastaFormat, '/home/fred/pdb/test.fasta.txt') do
> |ff|
>   ff.each do |entry|
>     report = factory.query(entry)
>     report.each do |hit|
>       if hit.evalue < 0.001
>          puts hit.target_id
>          puts hit.target_seq
>       end
>     end
>   end
> end
>
> Thanks for any help!
> Best regards,
> Fredrik Johansson
>
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby


From fredjoha at bioreg.kyushu-u.ac.jp  Mon May 21 04:16:31 2007
From: fredjoha at bioreg.kyushu-u.ac.jp (Fredrik Johansson)
Date: Mon, 21 May 2007 17:16:31 +0900
Subject: [BioRuby] Parsing FASTA result
Message-ID: <1179735391.29172.91.camel@fred-kyudai>

I have encountered a problem again when running FASTA. I got a huge
amount of homologs from fasta (25 MB data) for one sequence, and then
the Bio::Fasta::Report class gets this error when initializing:

format10.rb:21:in `sub!': failed to allocate memory (NoMemoryError)

so I made the following changes to my code. It is just a quick fix, and
I am not sure about that 'else' case that I took away. It does not seem
to be covered by the line that I added. Also I did not bother about the
@list variable since it does not seem to be used anywhere.

/Fredrik

The patch:

--- fasta/format10.rb   2007-05-21 16:50:38.000000000 +0900
+++ fasta/format10.new.rb       2007-05-21 16:52:55.000000000 +0900
@@ -17,13 +17,7 @@
 
   def initialize(data)
     # header lines - brief list of the hits
-    if data.sub!(/.*\nThe best scores are/m, '')
-      data.sub!(/(.*)\n\n>>>/m, '')
-      @list = "The best scores are" + $1
-    else 
-      data.sub!(/.*\n!!\s+/m, '')
-      data.sub!(/.*/) { |x| @list = x; '' }
-    end
+    data = data[data.index("\n\n>>>")+5..data.size]
 
     # body lines - fasta execution result
     program, *hits = data.split(/\n>>/)



From jan.aerts at bbsrc.ac.uk  Mon May 21 10:05:17 2007
From: jan.aerts at bbsrc.ac.uk (jan aerts (RI))
Date: Mon, 21 May 2007 15:05:17 +0100
Subject: [BioRuby] Ensembl API for ruby
Message-ID: <84DA9D8AC9B05F4B889E7C70238CB45104FB1784@rie2ksrv1.ri.bbsrc.ac.uk>

All,

I committed the first version of a ruby API to the bioruby-annex SVN on
rubyforge. Although it is far from completed, it does already have its
uses. Thought it would be good to commit as soon as possible so you guys
get an idea of what the API would look like.
I would like to follow the excellent perl API as much as possible
(http://www.ensembl.org/info/software/core/core_tutorial.html).


What it does at the moment:
* All tables of the core database are covered by ActiveRecord classes.
* A Slice object represents a continuous region of a genome. Slices can
be used to obtain sequence, features or other information from a
particular region of interest.
* Coordinates can be transfered from one coordinate system to another. I
hope I tested this thorougly enough (but still am a bit squeemish about
it).

What is not implemented yet:
* A whole bunch of methods that are available to the perl objects that I
would like to 'copy' to the ruby API.
* The Variation and Compara databases.
* The 'project' and 'transform' methods for features and slices (as
explained on the perl tutorial mentioned above).

To get this code, please go to
http://rubyforge.org/projects/bioruby-annex/ You can export the code
using SVN with the following command (without quotes):
"svn checkout svn://rubyforge.org/var/svn/bioruby-annex". There should
be a subdirectory 'ensembl-api', containing the API itself, the sample
script, tests and of course all documentation.

I've created a gem (available in the top-directory of the SVN export),
but can't test if it actually works. Can someone please test it for me?

Toshiaki: if the code works and the gem can be installed on other
systems, could you please do a file release for the gem-file?

Others: if people are interested to help me to develop this API, please
let me know.

Thanks,
jan.

Dr Jan Aerts
Bioinformatics Group
Roslin Institute
Roslin EH25 9PS
Scotland, UK
tel: +44 131 527 4198
skype: aerts_ri

----...and the obligatory disclaimer----
Roslin Institute is a company limited by guarantee, registered in
Scotland (registered number SC157100) and a Scottish Charity (registered
number SC023592). Our registered office is at Roslin, Midlothian, EH25
9PS. VAT registration number 847380013.

The information contained in this e-mail (including any attachments) is
confidential and is intended for the use of  the addressee only. The
opinions expressed within this e-mail (including any attachments) are
the opinions of the sender and do not necessarily constitute those of
Roslin Institute (Edinburgh) ("the Institute") unless specifically
stated by a sender who is duly authorised to do so on behalf of the
Institute.


From hien.le at mail.mcgill.ca  Tue May 22 03:33:26 2007
From: hien.le at mail.mcgill.ca (Hien Le)
Date: Tue, 22 May 2007 03:33:26 -0400
Subject: [BioRuby] Parsing GFF3 attributes
Message-ID: <20070522033326.1zpegb2scgg0skws@webmail.mcgill.ca>

On May 18, 2007, at 17:23, Toshiaki Katayama wrote:

> and I added your modification to the Bio::GFF::GFF3 class.

OK Thanks!

> Personally, I have not yet use GFF3 intensively, so if you think the
> class should have more functionality to support new features in GFF3, 
> please propose.

Same for myself, I have just recently started using GFF3 formats. I'll 
let you know if I think the class needs added functionality.

-Hien

From christophercyll at gmail.com  Thu May 24 18:22:56 2007
From: christophercyll at gmail.com (Topher Cyll)
Date: Thu, 24 May 2007 18:22:56 -0400
Subject: [BioRuby] looking for a cool project to do using bioruby
Message-ID: <2599499e0705241522k4e674a26q28ddc2bd021e17a8@mail.gmail.com>

Hi BioRubyers,

I'm a long time reader of this list, but I think this might be my first post.

I'm in the process of writing a Ruby project book.  Each chapter
guides the reader through a new and unusual project they can code in
Ruby. For comparison, in other chapters we do things like compose
music, build a game, run simulations, implement Lisp, etc.

I'd really like to include a project using BioRuby (since I think a
lot of Rubyists would find it exciting).  But with only one
undergraduate bio-informatics class under my belt, I'm a little stuck
on ideas for fun and interesting projects.

So I thought I'd ask the experts!

Can anyone think of a fun, interesting use for BioRuby that I could
walk readers through?  I like to have each project produce a final
product, instead of just doing a tutorial, so I'm looking for a idea
that would have some implementation work, but wouldn't be too, too
difficult.

Any ideas?
Toph

From s-merchant at northwestern.edu  Fri May 25 11:39:55 2007
From: s-merchant at northwestern.edu (Sohel Merchant)
Date: Fri, 25 May 2007 10:39:55 -0500
Subject: [BioRuby] looking for a cool project to do using bioruby
In-Reply-To: <2599499e0705241522k4e674a26q28ddc2bd021e17a8@mail.gmail.com>
References: <2599499e0705241522k4e674a26q28ddc2bd021e17a8@mail.gmail.com>
Message-ID: <000001c79ee2$f1eda7b0$c2987ca5@pc13>

Hi Toph,
  I would say one of fun things to implement in Ruby would be Ontology
visualization. The tool could be used to visualize any kind of ontology such
as GO. It would be cool if this could be integrated in to a Rails app. Look
at QuickGo which visualizes the Gene Ontology

http://www.ebi.ac.uk/ego/DisplayGoTerm?id=GO:0042351

Hope this helps. Let me know if you any questions.

Cheers,
Sohel.



-----Original Message-----
From: bioruby-bounces at lists.open-bio.org
[mailto:bioruby-bounces at lists.open-bio.org] On Behalf Of Topher Cyll
Sent: Thursday, May 24, 2007 5:23 PM
To: bioruby at lists.open-bio.org
Subject: [BioRuby] looking for a cool project to do using bioruby

Hi BioRubyers,

I'm a long time reader of this list, but I think this might be my first
post.

I'm in the process of writing a Ruby project book.  Each chapter
guides the reader through a new and unusual project they can code in
Ruby. For comparison, in other chapters we do things like compose
music, build a game, run simulations, implement Lisp, etc.

I'd really like to include a project using BioRuby (since I think a
lot of Rubyists would find it exciting).  But with only one
undergraduate bio-informatics class under my belt, I'm a little stuck
on ideas for fun and interesting projects.

So I thought I'd ask the experts!

Can anyone think of a fun, interesting use for BioRuby that I could
walk readers through?  I like to have each project produce a final
product, instead of just doing a tutorial, so I'm looking for a idea
that would have some implementation work, but wouldn't be too, too
difficult.

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



From email2ants at gmail.com  Wed May  2 16:38:31 2007
From: email2ants at gmail.com (Anthony Underwood)
Date: Wed, 2 May 2007 17:38:31 +0100
Subject: [BioRuby] EMBL parsing
Message-ID: <9EF29B4E-EDFC-4106-A736-52195314F374@gmail.com>

Dear all,

I am having a problem when parsing EMBL genome files.

embl = open(filename)
entry = embl.gets(Bio::EMBL::DELIMITER)
seq_obj = Bio::EMBL.new(entry)
puts seq_obj.sequence_length


This takes a long time (minutes) and reports a sequence_length of 0

When taking an equivalent genbank file and changing the code  
appropriately it parses the file in seconds and reports the correct  
length. I am new to bioruby having used bioperl until now. Please can  
anybody let me know if they have had similar problems and any  
possible solutions.

Many thanks

Anthony


From n at bioruby.org  Wed May  2 16:47:27 2007
From: n at bioruby.org (Mitsuteru Nakao)
Date: Thu, 3 May 2007 01:47:27 +0900
Subject: [BioRuby] EMBL parsing
In-Reply-To: <9EF29B4E-EDFC-4106-A736-52195314F374@gmail.com>
References: <9EF29B4E-EDFC-4106-A736-52195314F374@gmail.com>
Message-ID: <90ca35f70705020947g66d6edf9pc552d79935973e75@mail.gmail.com>

Hi Anthony,

Thank you for your bug report.
Please let me know the accession numbers of EMBL genome
files you parsed.

Thanks in advance.

Mitsuteru the Bio::EMBL maintainer.
<n at bioruby.org>

> I am having a problem when parsing EMBL genome files.
>
> embl = open(filename)
> entry = embl.gets(Bio::EMBL::DELIMITER)
> seq_obj = Bio::EMBL.new(entry)
> puts seq_obj.sequence_length
>
>
> This takes a long time (minutes) and reports a sequence_length of 0


From email2ants at gmail.com  Thu May  3 11:48:03 2007
From: email2ants at gmail.com (Anthony Underwood)
Date: Thu, 3 May 2007 12:48:03 +0100
Subject: [BioRuby] EMBL parsing
Message-ID: <0AEBC5E8-5128-4448-AE2E-8FA7E8691332@gmail.com>

Hi Mitsiteru,

Any of the embl files downloaded from the ebi site have this problem.

for example http://www.ebi.ac.uk/cgi-bin/dbfetch? 
db=embl&style=raw&id=CP000360

Ruby takes all of the cpu power :(


But with the equivalent file from NCBI in genbank format there is no  
problem.

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi? 
cmd=Retrieve&db=Nucleotide&list_uids=94549081&dopt=GenBank

Many thanks for having a look at this


Anthony



From jdudley at stanford.edu  Thu May  3 13:51:52 2007
From: jdudley at stanford.edu (Joel Dudley)
Date: Thu, 3 May 2007 06:51:52 -0700
Subject: [BioRuby] Ruby in Science
Message-ID: <D8E63F00-CB20-41BB-BFD9-8E3D9C10F457@stanford.edu>

I'm giving a talk tonight at the SDForum Ruby SIG at Google  
Headquarters on the topic of Ruby and Ruby on Rails in scientific  
computing. For part of the talk I am going to highlight companies,  
research groups, products, and other resources that are deployed or  
currently under development using Ruby and/or Ruby on Rails. If  
you've got a scientific application or resource that fits this and  
would like me to give it mention to please send me the details off- 
list. I can't guarantee that I'll mention it (time for the talk is  
limited), but I'll do my best.

Thanks,

Joel Dudley
Stanford Medical Informatics


From s-merchant at northwestern.edu  Fri May  4 21:52:11 2007
From: s-merchant at northwestern.edu (Sohel Merchant)
Date: Fri, 4 May 2007 16:52:11 -0500
Subject: [BioRuby] BOF at Ruby on Rails conference
Message-ID: <000601c78e96$77f5bb20$c2987ca5@pc13>

Hello Everyone,

  I am organizing a Birds of a Feather (BoF) session at the upcoming Rails
conference in Portland, Oregon. Here are the details: 

 

Venue: Rails conf 2007, Oregon Convention Center (OCC)

Date: Saturday, May 19 

Time: 7:30-8:30pm 

Room: c125.

 

I hope to meet some of you guys there.

 

Cheers,

Sohel Merchant.



From ngoto at gen-info.osaka-u.ac.jp  Sat May  5 06:57:28 2007
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Sat, 5 May 2007 15:57:28 +0900
Subject: [BioRuby] EMBL parsing
In-Reply-To: <0AEBC5E8-5128-4448-AE2E-8FA7E8691332@gmail.com>
References: <0AEBC5E8-5128-4448-AE2E-8FA7E8691332@gmail.com>
Message-ID: <20070505065729.4ECD41CBC510@idnmail.gen-info.osaka-u.ac.jp>

Hi,

On Thu, 3 May 2007 12:48:03 +0100
Anthony Underwood <email2ants at gmail.com> wrote:

> Hi Mitsiteru,
> 
> Any of the embl files downloaded from the ebi site have this problem.
> 
> for example http://www.ebi.ac.uk/cgi-bin/dbfetch? 
> db=embl&style=raw&id=CP000360
> 
> Ruby takes all of the cpu power :(

It seems it is caused by thousands of iterations of str1 += str2
because it creates a new string object every time.
A patch is attached. (Ruby 1.8.0 or newer version required)

--- lib/bio/db.rb       5 Apr 2007 23:35:39 -0000       0.37
+++ lib/bio/db.rb       5 May 2007 06:08:39 -0000
@@ -313,12 +313,12 @@

   # Returns the contents of the entry as a Hash.
   def entry2hash(entry)
-    hash = Hash.new('')
+    hash = Hash.new { |h, k| h[k] = '' }
     entry.each_line do |line|
       tag = tag_get(line)
       next if tag == 'XX'
       tag = 'R' if tag =~ /^R./        # Reference lines
-      hash[tag] += line
+      hash[tag].concat line
     end
     return hash
   end


Naohisa Goto
ng at bioruby.org


From email2ants at gmail.com  Tue May  8 11:53:37 2007
From: email2ants at gmail.com (Anthony Underwood)
Date: Tue, 8 May 2007 12:53:37 +0100
Subject: [BioRuby] EMBL parsing
In-Reply-To: <20070505065729.4ECD41CBC510@idnmail.gen-info.osaka-u.ac.jp>
References: <0AEBC5E8-5128-4448-AE2E-8FA7E8691332@gmail.com>
	<20070505065729.4ECD41CBC510@idnmail.gen-info.osaka-u.ac.jp>
Message-ID: <4045DF0D-6F4C-47DF-A4D7-1B31D61C3A7D@gmail.com>

Hi Naohisa,

Thanks for the patch. This certainly appears to solve the problem of  
slow embl entry reading. However the sequence length is still  
reported as 0.

I found this was due to the idline not being interpreted correctly

on line 97
tmp['SEQUENCE_LENGTH'] = idline[3].strip.split(' ').first.to_i

was changed to

tmp['SEQUENCE_LENGTH'] = idline.last.strip.split(' ').first.to_i

This was OK for my purposes, but I think the whole idline  
interpretation needs to be looked at see (http://www.ebi.ac.uk/embl/ 
Documentation/User_manual/usrman.html#3_4_1). I could have a look at  
this if appropriate.

Thanks

Anthony


On 5 May 2007, at 07:57, Naohisa GOTO wrote:

> Hi,
>
> On Thu, 3 May 2007 12:48:03 +0100
> Anthony Underwood <email2ants at gmail.com> wrote:
>
>> Hi Mitsiteru,
>>
>> Any of the embl files downloaded from the ebi site have this problem.
>>
>> for example http://www.ebi.ac.uk/cgi-bin/dbfetch?
>> db=embl&style=raw&id=CP000360
>>
>> Ruby takes all of the cpu power :(
>
> It seems it is caused by thousands of iterations of str1 += str2
> because it creates a new string object every time.
> A patch is attached. (Ruby 1.8.0 or newer version required)
>
> --- lib/bio/db.rb       5 Apr 2007 23:35:39 -0000       0.37
> +++ lib/bio/db.rb       5 May 2007 06:08:39 -0000
> @@ -313,12 +313,12 @@
>
>    # Returns the contents of the entry as a Hash.
>    def entry2hash(entry)
> -    hash = Hash.new('')
> +    hash = Hash.new { |h, k| h[k] = '' }
>      entry.each_line do |line|
>        tag = tag_get(line)
>        next if tag == 'XX'
>        tag = 'R' if tag =~ /^R./        # Reference lines
> -      hash[tag] += line
> +      hash[tag].concat line
>      end
>      return hash
>    end
>
>
> Naohisa Goto
> ng at bioruby.org
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby



From n at bioruby.org  Tue May  8 17:09:47 2007
From: n at bioruby.org (Mitsuteru Nakao)
Date: Wed, 9 May 2007 02:09:47 +0900
Subject: [BioRuby] EMBL parsing
In-Reply-To: <4045DF0D-6F4C-47DF-A4D7-1B31D61C3A7D@gmail.com>
References: <0AEBC5E8-5128-4448-AE2E-8FA7E8691332@gmail.com>
	<20070505065729.4ECD41CBC510@idnmail.gen-info.osaka-u.ac.jp>
	<4045DF0D-6F4C-47DF-A4D7-1B31D61C3A7D@gmail.com>
Message-ID: <90ca35f70705081009r7719c562u36a902a84f88566c@mail.gmail.com>

Hi Anthony,

Thank you for your suggestions.
You can use the bioruby CVS HEAD which contains new idline
parser for EMBL rel89.



> This was OK for my purposes, but I think the whole idline
> interpretation needs to be looked at see (http://www.ebi.ac.uk/embl/
> Documentation/User_manual/usrman.html#3_4_1). I could have a look at
> this if appropriate.

Thanks

Mitsuteru
-
Mitsuteur Nakao
n at bioruby.org


From jan.aerts at bbsrc.ac.uk  Wed May  9 13:14:52 2007
From: jan.aerts at bbsrc.ac.uk (jan aerts (RI))
Date: Wed, 9 May 2007 14:14:52 +0100
Subject: [BioRuby] Ensembl API
Message-ID: <84DA9D8AC9B05F4B889E7C70238CB45104FB16F3@rie2ksrv1.ri.bbsrc.ac.uk>

Has anyone worked on an Ensembl API? There is a perl API and the
database schema is well-documented. On first impression, it seems
straightforward to make one using ActiveRecord, but I wouldn't want to
waste efforts on that if someone else is already working on it.

See http://www.ensembl.org/info/software/core/index.html

Dr Jan Aerts
Bioinformatics Group
Roslin Institute
Roslin EH25 9PS
Scotland, UK
tel: +44 131 527 4198
skype: aerts_ri

----...and the obligatory disclaimer----
Roslin Institute is a company limited by guarantee, registered in
Scotland (registered number SC157100) and a Scottish Charity (registered
number SC023592). Our registered office is at Roslin, Midlothian, EH25
9PS. VAT registration number 847380013.

The information contained in this e-mail (including any attachments) is
confidential and is intended for the use of  the addressee only. The
opinions expressed within this e-mail (including any attachments) are
the opinions of the sender and do not necessarily constitute those of
Roslin Institute (Edinburgh) ("the Institute") unless specifically
stated by a sender who is duly authorised to do so on behalf of the
Institute.



From jan.aerts at bbsrc.ac.uk  Wed May  9 13:49:50 2007
From: jan.aerts at bbsrc.ac.uk (jan aerts (RI))
Date: Wed, 9 May 2007 14:49:50 +0100
Subject: [BioRuby] Ensembl API
In-Reply-To: <1E75E5B2-D515-4EE4-9B2D-2E2D034E1EA1@sanger.ac.uk>
Message-ID: <84DA9D8AC9B05F4B889E7C70238CB45104FB16F6@rie2ksrv1.ri.bbsrc.ac.uk>

A post (in Japanese) about this shows a good primer:
http://itoshi.tv/d/?date=20060829

I'm testing this out on some tables of the Ensembl core and variation
databases, and things look promising... As you say it might well be that
we can't cover everything, but at least we can get quite far.

jan. 

-----Original Message-----
From: Michael Han [mailto:mh6 at sanger.ac.uk] 
Sent: 09 May 2007 14:38
To: jan aerts (RI)
Subject: Re: [BioRuby] Ensembl API

On 9 May 2007, at 14:14, jan aerts ((RI)) wrote:
> Has anyone worked on an Ensembl API? There is a perl API and the 
> database schema is well-documented. On first impression, it seems 
> straightforward to make one using ActiveRecord, but I wouldn't want to

> waste efforts on that if someone else is already working on it.
>
> See http://www.ensembl.org/info/software/core/index.html
>
> Dr Jan Aerts
> Bioinformatics Group

Hi Jan,

I am not sure if you can cover everything with a the default active-
record behavior.
But I would be a happy user of a ruby EnsEMBL API.
If you need/want help with it, I would also volunteer.

Michael



From jan.aerts at bbsrc.ac.uk  Wed May  9 14:10:24 2007
From: jan.aerts at bbsrc.ac.uk (jan aerts (RI))
Date: Wed, 9 May 2007 15:10:24 +0100
Subject: [BioRuby] Ensembl API
In-Reply-To: <58E34B0F-64FF-4CEB-9E36-7AF0B7159D08@sanger.ac.uk>
Message-ID: <84DA9D8AC9B05F4B889E7C70238CB45104FB16F9@rie2ksrv1.ri.bbsrc.ac.uk>

I've tried a connection similar to the ones used by the perl API and am
able to connect directly to the core and other databases. Am currently
playing around with the cow features, actually :-)

jan. 

-----Original Message-----
From: Michael Han [mailto:mh6 at sanger.ac.uk] 
Sent: 09 May 2007 14:57
To: jan aerts (RI)
Cc: bioruby at lists.open-bio.org
Subject: Re: [BioRuby] Ensembl API


On 9 May 2007, at 14:49, jan aerts ((RI)) wrote:
> A post (in Japanese) about this shows a good primer:
> http://itoshi.tv/d/?date=20060829

my Japanese is not so good, but isn't that run on a BioMart and not an
ensembl-core schema?

> I'm testing this out on some tables of the Ensembl core and variation 
> databases, and things look promising... As you say it might well be 
> that we can't cover everything, but at least we can get quite far.
>
> jan.
>
> -----Original Message-----
> From: Michael Han [mailto:mh6 at sanger.ac.uk]
> Sent: 09 May 2007 14:38
> To: jan aerts (RI)
> Subject: Re: [BioRuby] Ensembl API
>
> On 9 May 2007, at 14:14, jan aerts ((RI)) wrote:
>> Has anyone worked on an Ensembl API? There is a perl API and the 
>> database schema is well-documented. On first impression, it seems 
>> straightforward to make one using ActiveRecord, but I wouldn't want 
>> to
>
>> waste efforts on that if someone else is already working on it.
>>
>> See http://www.ensembl.org/info/software/core/index.html
>>
>> Dr Jan Aerts
>> Bioinformatics Group
>
> Hi Jan,
>
> I am not sure if you can cover everything with a the default active- 
> record behavior.
> But I would be a happy user of a ruby EnsEMBL API.
> If you need/want help with it, I would also volunteer.
>
> Michael




From mh6 at sanger.ac.uk  Wed May  9 13:57:18 2007
From: mh6 at sanger.ac.uk (Michael Han)
Date: Wed, 9 May 2007 14:57:18 +0100
Subject: [BioRuby] Ensembl API
In-Reply-To: <84DA9D8AC9B05F4B889E7C70238CB45104FB16F6@rie2ksrv1.ri.bbsrc.ac.uk>
References: <84DA9D8AC9B05F4B889E7C70238CB45104FB16F6@rie2ksrv1.ri.bbsrc.ac.uk>
Message-ID: <58E34B0F-64FF-4CEB-9E36-7AF0B7159D08@sanger.ac.uk>


On 9 May 2007, at 14:49, jan aerts ((RI)) wrote:
> A post (in Japanese) about this shows a good primer:
> http://itoshi.tv/d/?date=20060829

my Japanese is not so good, but isn't that run on a BioMart and not  
an ensembl-core schema?

> I'm testing this out on some tables of the Ensembl core and variation
> databases, and things look promising... As you say it might well be  
> that
> we can't cover everything, but at least we can get quite far.
>
> jan.
>
> -----Original Message-----
> From: Michael Han [mailto:mh6 at sanger.ac.uk]
> Sent: 09 May 2007 14:38
> To: jan aerts (RI)
> Subject: Re: [BioRuby] Ensembl API
>
> On 9 May 2007, at 14:14, jan aerts ((RI)) wrote:
>> Has anyone worked on an Ensembl API? There is a perl API and the
>> database schema is well-documented. On first impression, it seems
>> straightforward to make one using ActiveRecord, but I wouldn't  
>> want to
>
>> waste efforts on that if someone else is already working on it.
>>
>> See http://www.ensembl.org/info/software/core/index.html
>>
>> Dr Jan Aerts
>> Bioinformatics Group
>
> Hi Jan,
>
> I am not sure if you can cover everything with a the default active-
> record behavior.
> But I would be a happy user of a ruby EnsEMBL API.
> If you need/want help with it, I would also volunteer.
>
> Michael



From jan.aerts at bbsrc.ac.uk  Thu May 10 07:58:02 2007
From: jan.aerts at bbsrc.ac.uk (jan aerts (RI))
Date: Thu, 10 May 2007 08:58:02 +0100
Subject: [BioRuby] Ensembl API
In-Reply-To: <1E75E5B2-D515-4EE4-9B2D-2E2D034E1EA1@sanger.ac.uk>
Message-ID: <84DA9D8AC9B05F4B889E7C70238CB45104FB16FE@rie2ksrv1.ri.bbsrc.ac.uk>

Michael,

As you mention that we maybe won't be able to cover everything with the
default activerecord behaviour: what problems are you thinking of?

Note: I'd like to use the perl API as a guide. And indeed working out
the Slice object was quite simple...

jan.

-----Original Message-----
From: Michael Han [mailto:mh6 at sanger.ac.uk] 
Sent: 09 May 2007 14:38
To: jan aerts (RI)
Subject: Re: [BioRuby] Ensembl API

On 9 May 2007, at 14:14, jan aerts ((RI)) wrote:
> Has anyone worked on an Ensembl API? There is a perl API and the 
> database schema is well-documented. On first impression, it seems 
> straightforward to make one using ActiveRecord, but I wouldn't want to

> waste efforts on that if someone else is already working on it.
>
> See http://www.ensembl.org/info/software/core/index.html
>
> Dr Jan Aerts
> Bioinformatics Group

Hi Jan,

I am not sure if you can cover everything with a the default active-
record behavior.
But I would be a happy user of a ruby EnsEMBL API.
If you need/want help with it, I would also volunteer.

Michael



From jan.aerts at bbsrc.ac.uk  Thu May 10 09:09:50 2007
From: jan.aerts at bbsrc.ac.uk (jan aerts (RI))
Date: Thu, 10 May 2007 10:09:50 +0100
Subject: [BioRuby] Ensembl API
In-Reply-To: <834748BE-64D8-4642-AF70-5098589F91EB@sanger.ac.uk>
Message-ID: <84DA9D8AC9B05F4B889E7C70238CB45104FB1701@rie2ksrv1.ri.bbsrc.ac.uk>

I actually just started working on this API last night (in between some
deadlines I got to catch), so haven't gotten so far as to think about
caching. I'm basically working through the perl API tutorial
(http://www.ensembl.org/info/software/core/core_tutorial.html) and try
to implement all those examples. (At the moment, I'm at the bit that
says "Break chromosomal slices into smaller 100k component slices"...)

Some hurdles that I see coming are the caching and projecting features
from one coord system to another. We'll see what happens when we get
there.

As for a public place: I would _very_ much appreciate help with the API,
although

QUESTION FOR BIORUBY COMMUNITY AND DEVELOPERS:
* Do you think it would be best to create a sourceforge project for
this, or should I add it directly into bioruby (e.g. Bio::Api::Ensembl)?
I suppose the second option would be best, but the stuff I have is
probably not polished enough yet... and *far* from complete.
* Secondly: if a new release is coming: would it be best to wait untill
_after_ that release?

jan.


-----Original Message-----
From: Michael Han [mailto:mh6 at sanger.ac.uk] 
Sent: 10 May 2007 09:51
To: jan aerts (RI)
Subject: Re: [BioRuby] Ensembl API


On 10 May 2007, at 08:58, jan aerts ((RI)) wrote:
> Michael,
>
> As you mention that we maybe won't be able to cover everything with 
> the default activerecord behaviour: what problems are you thinking of?
>
> Note: I'd like to use the perl API as a guide. And indeed working out 
> the Slice object was quite simple...

Yes, I was thinking of the slices in combination with the different
assembly levels.
A change to the mapping part of that broke the last EnsEMBL release.
There were some cases where a seq_region maps one-to-many to other
seq_regions (also with gaps).
Did you put all the caching stuff from the Perl API into it? And if not,
is the performance ok?

It would be also great if you could put the code into some public place
(RubyForge as example), then it would be easier to see what is already
working/being worked at and what not.

> jan.
>
> -----Original Message-----
> From: Michael Han [mailto:mh6 at sanger.ac.uk]
> Sent: 09 May 2007 14:38
> To: jan aerts (RI)
> Subject: Re: [BioRuby] Ensembl API
>
> On 9 May 2007, at 14:14, jan aerts ((RI)) wrote:
>> Has anyone worked on an Ensembl API? There is a perl API and the 
>> database schema is well-documented. On first impression, it seems 
>> straightforward to make one using ActiveRecord, but I wouldn't want 
>> to
>
>> waste efforts on that if someone else is already working on it.
>>
>> See http://www.ensembl.org/info/software/core/index.html
>>
>> Dr Jan Aerts
>> Bioinformatics Group
>
> Hi Jan,
>
> I am not sure if you can cover everything with a the default active- 
> record behavior.
> But I would be a happy user of a ruby EnsEMBL API.
> If you need/want help with it, I would also volunteer.
>
> Michael




From jan.aerts at bbsrc.ac.uk  Thu May 10 10:18:22 2007
From: jan.aerts at bbsrc.ac.uk (jan aerts (RI))
Date: Thu, 10 May 2007 11:18:22 +0100
Subject: [BioRuby] Ensembl API
In-Reply-To: <BE63A0A3-726A-4A06-BF3A-2E292A120816@hgc.jp>
Message-ID: <84DA9D8AC9B05F4B889E7C70238CB45104FB1703@rie2ksrv1.ri.bbsrc.ac.uk>

OK. 

-----Original Message-----
From: Toshiaki Katayama [mailto:ktym at hgc.jp] 
Sent: 10 May 2007 11:14
To: jan aerts (RI)
Cc: Michael Han; bioruby at lists.open-bio.org
Subject: Re: [BioRuby] Ensembl API

Jan,

In that case, I would like you to consider to use the rubyforge
repository 'bioruby-annex' which Nakao-san had set up.

  http://lists.open-bio.org/pipermail/bioruby/2007-April/000355.html

When your modules matured and we, core developers, have decided how to
integrate Rails dependent modules in BioRuby, you can put them in the
BioRuby distribution.

Toshiaki

On 2007/05/10, at 18:09, jan aerts (RI) wrote:

> I actually just started working on this API last night (in between 
> some deadlines I got to catch), so haven't gotten so far as to think 
> about caching. I'm basically working through the perl API tutorial
> (http://www.ensembl.org/info/software/core/core_tutorial.html) and try

> to implement all those examples. (At the moment, I'm at the bit that 
> says "Break chromosomal slices into smaller 100k component slices"...)
>
> Some hurdles that I see coming are the caching and projecting features

> from one coord system to another. We'll see what happens when we get 
> there.
>
> As for a public place: I would _very_ much appreciate help with the 
> API, although
>
> QUESTION FOR BIORUBY COMMUNITY AND DEVELOPERS:
> * Do you think it would be best to create a sourceforge project for 
> this, or should I add it directly into bioruby (e.g.
Bio::Api::Ensembl)?
> I suppose the second option would be best, but the stuff I have is 
> probably not polished enough yet... and *far* from complete.
> * Secondly: if a new release is coming: would it be best to wait 
> untill _after_ that release?
>
> jan.
>
>
> -----Original Message-----
> From: Michael Han [mailto:mh6 at sanger.ac.uk]
> Sent: 10 May 2007 09:51
> To: jan aerts (RI)
> Subject: Re: [BioRuby] Ensembl API
>
>
> On 10 May 2007, at 08:58, jan aerts ((RI)) wrote:
>> Michael,
>>
>> As you mention that we maybe won't be able to cover everything with 
>> the default activerecord behaviour: what problems are you thinking
of?
>>
>> Note: I'd like to use the perl API as a guide. And indeed working out

>> the Slice object was quite simple...
>
> Yes, I was thinking of the slices in combination with the different 
> assembly levels.
> A change to the mapping part of that broke the last EnsEMBL release.
> There were some cases where a seq_region maps one-to-many to other 
> seq_regions (also with gaps).
> Did you put all the caching stuff from the Perl API into it? And if 
> not, is the performance ok?
>
> It would be also great if you could put the code into some public 
> place (RubyForge as example), then it would be easier to see what is 
> already working/being worked at and what not.
>
>> jan.
>>
>> -----Original Message-----
>> From: Michael Han [mailto:mh6 at sanger.ac.uk]
>> Sent: 09 May 2007 14:38
>> To: jan aerts (RI)
>> Subject: Re: [BioRuby] Ensembl API
>>
>> On 9 May 2007, at 14:14, jan aerts ((RI)) wrote:
>>> Has anyone worked on an Ensembl API? There is a perl API and the 
>>> database schema is well-documented. On first impression, it seems 
>>> straightforward to make one using ActiveRecord, but I wouldn't want 
>>> to
>>
>>> waste efforts on that if someone else is already working on it.
>>>
>>> See http://www.ensembl.org/info/software/core/index.html
>>>
>>> Dr Jan Aerts
>>> Bioinformatics Group
>>
>> Hi Jan,
>>
>> I am not sure if you can cover everything with a the default active- 
>> record behavior.
>> But I would be a happy user of a ruby EnsEMBL API.
>> If you need/want help with it, I would also volunteer.
>>
>> Michael
>




From ktym at hgc.jp  Thu May 10 10:13:34 2007
From: ktym at hgc.jp (Toshiaki Katayama)
Date: Thu, 10 May 2007 19:13:34 +0900
Subject: [BioRuby] Ensembl API
In-Reply-To: <84DA9D8AC9B05F4B889E7C70238CB45104FB1701@rie2ksrv1.ri.bbsrc.ac.uk>
References: <84DA9D8AC9B05F4B889E7C70238CB45104FB1701@rie2ksrv1.ri.bbsrc.ac.uk>
Message-ID: <BE63A0A3-726A-4A06-BF3A-2E292A120816@hgc.jp>

Jan,

In that case, I would like you to consider to use the rubyforge repository
'bioruby-annex' which Nakao-san had set up.

  http://lists.open-bio.org/pipermail/bioruby/2007-April/000355.html

When your modules matured and we, core developers, have decided how to integrate
Rails dependent modules in BioRuby, you can put them in the BioRuby distribution.

Toshiaki

On 2007/05/10, at 18:09, jan aerts (RI) wrote:

> I actually just started working on this API last night (in between some
> deadlines I got to catch), so haven't gotten so far as to think about
> caching. I'm basically working through the perl API tutorial
> (http://www.ensembl.org/info/software/core/core_tutorial.html) and try
> to implement all those examples. (At the moment, I'm at the bit that
> says "Break chromosomal slices into smaller 100k component slices"...)
>
> Some hurdles that I see coming are the caching and projecting features
> from one coord system to another. We'll see what happens when we get
> there.
>
> As for a public place: I would _very_ much appreciate help with the API,
> although
>
> QUESTION FOR BIORUBY COMMUNITY AND DEVELOPERS:
> * Do you think it would be best to create a sourceforge project for
> this, or should I add it directly into bioruby (e.g. Bio::Api::Ensembl)?
> I suppose the second option would be best, but the stuff I have is
> probably not polished enough yet... and *far* from complete.
> * Secondly: if a new release is coming: would it be best to wait untill
> _after_ that release?
>
> jan.
>
>
> -----Original Message-----
> From: Michael Han [mailto:mh6 at sanger.ac.uk] 
> Sent: 10 May 2007 09:51
> To: jan aerts (RI)
> Subject: Re: [BioRuby] Ensembl API
>
>
> On 10 May 2007, at 08:58, jan aerts ((RI)) wrote:
>> Michael,
>>
>> As you mention that we maybe won't be able to cover everything with 
>> the default activerecord behaviour: what problems are you thinking of?
>>
>> Note: I'd like to use the perl API as a guide. And indeed working out 
>> the Slice object was quite simple...
>
> Yes, I was thinking of the slices in combination with the different
> assembly levels.
> A change to the mapping part of that broke the last EnsEMBL release.
> There were some cases where a seq_region maps one-to-many to other
> seq_regions (also with gaps).
> Did you put all the caching stuff from the Perl API into it? And if not,
> is the performance ok?
>
> It would be also great if you could put the code into some public place
> (RubyForge as example), then it would be easier to see what is already
> working/being worked at and what not.
>
>> jan.
>>
>> -----Original Message-----
>> From: Michael Han [mailto:mh6 at sanger.ac.uk]
>> Sent: 09 May 2007 14:38
>> To: jan aerts (RI)
>> Subject: Re: [BioRuby] Ensembl API
>>
>> On 9 May 2007, at 14:14, jan aerts ((RI)) wrote:
>>> Has anyone worked on an Ensembl API? There is a perl API and the 
>>> database schema is well-documented. On first impression, it seems 
>>> straightforward to make one using ActiveRecord, but I wouldn't want 
>>> to
>>
>>> waste efforts on that if someone else is already working on it.
>>>
>>> See http://www.ensembl.org/info/software/core/index.html
>>>
>>> Dr Jan Aerts
>>> Bioinformatics Group
>>
>> Hi Jan,
>>
>> I am not sure if you can cover everything with a the default active- 
>> record behavior.
>> But I would be a happy user of a ruby EnsEMBL API.
>> If you need/want help with it, I would also volunteer.
>>
>> Michael
>



From ktym at hgc.jp  Thu May 10 11:42:53 2007
From: ktym at hgc.jp (Toshiaki Katayama)
Date: Thu, 10 May 2007 20:42:53 +0900
Subject: [BioRuby] Ensembl API
In-Reply-To: <84DA9D8AC9B05F4B889E7C70238CB45104FB1706@rie2ksrv1.ri.bbsrc.ac.uk>
References: <84DA9D8AC9B05F4B889E7C70238CB45104FB1706@rie2ksrv1.ri.bbsrc.ac.uk>
Message-ID: <B312993D-DFFA-4869-9F1E-890D04093A9C@hgc.jp>

Jan,

You are added as a annex developer.

> I noticed that the bioruby-annex repository is for bioruby *rails*
> plugins. However, the Ensembl API would have nothing to do with rails

When I discussed with Nakao-san previously, we have agreed to 
include any Rails (or ActiveRecord etc.) dependent bioinformatics
projects in the bioruby-annex repository (maybe we need to
refine

The purpose is

1. The number of codes which depend on Rails related libraries
   is increasing, but we have not yet decided how to integrate
   such modules in BioRuby.

2. We thought correcting various add-ons to BioRuby in one place
   might be useful (so that users can find your bioinformatics
   modules easily, and/or some of them might be integrated into
   core BioRuby library in the future).

> (apart from the fact that it uses ActiveRecord in the background).

So, I thought your project is appropriate to be included.

> This might get confusing for possible users.

Yes, we may need to re-write our project description to clarify.
Volunteers?

As the bioruby-annex seems to be functioning now, we need to discuss
some rules for how to develop, release, and use sub products in it.

My idea is still vague, but how about to have codes in SVN as

  /bioruby-annex/rails/plugins <- for Rails' script/plugin source
  /bioruby-annex/project1/
  /bioruby-annex/project2/
    :

and each sub projects will release the package as a gem (or tar.gz) file
prefixed with 'bioruby-' or 'bioruby-annex-' so that, for instance,
you could release

  bioruby-ensembl-api-1.0.gem

for downlaod from

  http://rubyforge.org/projects/bioruby-annex/

Toshiaki

On 2007/05/10, at 19:34, jan aerts (RI) wrote:

> Toshiaki,
>
> I noticed that the bioruby-annex repository is for bioruby *rails*
> plugins. However, the Ensembl API would have nothing to do with rails
> (apart from the fact that it uses ActiveRecord in the background).
> This might get confusing for possible users.
>
> jan. 
>
> -----Original Message-----
> From: Toshiaki Katayama [mailto:ktym at hgc.jp] 
> Sent: 10 May 2007 11:14
> To: jan aerts (RI)
> Cc: Michael Han; bioruby at lists.open-bio.org
> Subject: Re: [BioRuby] Ensembl API
>
> Jan,
>
> In that case, I would like you to consider to use the rubyforge
> repository 'bioruby-annex' which Nakao-san had set up.
>
>   http://lists.open-bio.org/pipermail/bioruby/2007-April/000355.html
>
> When your modules matured and we, core developers, have decided how to
> integrate Rails dependent modules in BioRuby, you can put them in the
> BioRuby distribution.
>
> Toshiaki
>
> On 2007/05/10, at 18:09, jan aerts (RI) wrote:
>
>> I actually just started working on this API last night (in between 
>> some deadlines I got to catch), so haven't gotten so far as to think 
>> about caching. I'm basically working through the perl API tutorial
>> (http://www.ensembl.org/info/software/core/core_tutorial.html) and try
>
>> to implement all those examples. (At the moment, I'm at the bit that 
>> says "Break chromosomal slices into smaller 100k component slices"...)
>>
>> Some hurdles that I see coming are the caching and projecting features
>
>> from one coord system to another. We'll see what happens when we get 
>> there.
>>
>> As for a public place: I would _very_ much appreciate help with the 
>> API, although
>>
>> QUESTION FOR BIORUBY COMMUNITY AND DEVELOPERS:
>> * Do you think it would be best to create a sourceforge project for 
>> this, or should I add it directly into bioruby (e.g.
> Bio::Api::Ensembl)?
>> I suppose the second option would be best, but the stuff I have is 
>> probably not polished enough yet... and *far* from complete.
>> * Secondly: if a new release is coming: would it be best to wait 
>> untill _after_ that release?
>>
>> jan.
>>
>>
>> -----Original Message-----
>> From: Michael Han [mailto:mh6 at sanger.ac.uk]
>> Sent: 10 May 2007 09:51
>> To: jan aerts (RI)
>> Subject: Re: [BioRuby] Ensembl API
>>
>>
>> On 10 May 2007, at 08:58, jan aerts ((RI)) wrote:
>>> Michael,
>>>
>>> As you mention that we maybe won't be able to cover everything with 
>>> the default activerecord behaviour: what problems are you thinking
> of?
>>>
>>> Note: I'd like to use the perl API as a guide. And indeed working out
>
>>> the Slice object was quite simple...
>>
>> Yes, I was thinking of the slices in combination with the different 
>> assembly levels.
>> A change to the mapping part of that broke the last EnsEMBL release.
>> There were some cases where a seq_region maps one-to-many to other 
>> seq_regions (also with gaps).
>> Did you put all the caching stuff from the Perl API into it? And if 
>> not, is the performance ok?
>>
>> It would be also great if you could put the code into some public 
>> place (RubyForge as example), then it would be easier to see what is 
>> already working/being worked at and what not.
>>
>>> jan.
>>>
>>> -----Original Message-----
>>> From: Michael Han [mailto:mh6 at sanger.ac.uk]
>>> Sent: 09 May 2007 14:38
>>> To: jan aerts (RI)
>>> Subject: Re: [BioRuby] Ensembl API
>>>
>>> On 9 May 2007, at 14:14, jan aerts ((RI)) wrote:
>>>> Has anyone worked on an Ensembl API? There is a perl API and the 
>>>> database schema is well-documented. On first impression, it seems 
>>>> straightforward to make one using ActiveRecord, but I wouldn't want 
>>>> to
>>>
>>>> waste efforts on that if someone else is already working on it.
>>>>
>>>> See http://www.ensembl.org/info/software/core/index.html
>>>>
>>>> Dr Jan Aerts
>>>> Bioinformatics Group
>>>
>>> Hi Jan,
>>>
>>> I am not sure if you can cover everything with a the default active- 
>>> record behavior.
>>> But I would be a happy user of a ruby EnsEMBL API.
>>> If you need/want help with it, I would also volunteer.
>>>
>>> Michael
>>
>



From ktym at hgc.jp  Thu May 10 11:45:40 2007
From: ktym at hgc.jp (Toshiaki Katayama)
Date: Thu, 10 May 2007 20:45:40 +0900
Subject: [BioRuby] Ensembl API
In-Reply-To: <B312993D-DFFA-4869-9F1E-890D04093A9C@hgc.jp>
References: <84DA9D8AC9B05F4B889E7C70238CB45104FB1706@rie2ksrv1.ri.bbsrc.ac.uk>
	<B312993D-DFFA-4869-9F1E-890D04093A9C@hgc.jp>
Message-ID: <057D48B5-57EC-464E-ABB7-05B059569253@hgc.jp>

On 2007/05/10, at 20:42, Toshiaki Katayama wrote:
> When I discussed with Nakao-san previously, we have agreed to 
> include any Rails (or ActiveRecord etc.) dependent bioinformatics
> projects in the bioruby-annex repository (maybe we need to
> refine

refine the project description).

Toshiaki



From ktym at hgc.jp  Thu May 10 11:49:15 2007
From: ktym at hgc.jp (Toshiaki Katayama)
Date: Thu, 10 May 2007 20:49:15 +0900
Subject: [BioRuby] Ensembl API
In-Reply-To: <B312993D-DFFA-4869-9F1E-890D04093A9C@hgc.jp>
References: <84DA9D8AC9B05F4B889E7C70238CB45104FB1706@rie2ksrv1.ri.bbsrc.ac.uk>
	<B312993D-DFFA-4869-9F1E-890D04093A9C@hgc.jp>
Message-ID: <38E0CF6A-14CD-4905-947E-410D389F9CD9@hgc.jp>

On 2007/05/10, at 20:42, Toshiaki Katayama wrote:
> 2. We thought correcting various add-ons to BioRuby in one place

s/correct/collect/ ... there might be many other mistakes as always :)

Toshiaki




From jan.aerts at bbsrc.ac.uk  Thu May 10 13:29:01 2007
From: jan.aerts at bbsrc.ac.uk (jan aerts (RI))
Date: Thu, 10 May 2007 14:29:01 +0100
Subject: [BioRuby] Ensembl API
In-Reply-To: <B312993D-DFFA-4869-9F1E-890D04093A9C@hgc.jp>
Message-ID: <84DA9D8AC9B05F4B889E7C70238CB45104FB170C@rie2ksrv1.ri.bbsrc.ac.uk>

Removing the 'rails' from the project description would be a good idea.
It would be great if this repository could also be the home for modules
like Bio::Graphics (which is completely unrelated to rails or
activerecord)

jan. 

-----Original Message-----
From: Toshiaki Katayama [mailto:ktym at hgc.jp] 
Sent: 10 May 2007 12:43
To: jan aerts (RI)
Cc: BioRubyML
Subject: Re: [BioRuby] Ensembl API

Jan,

You are added as a annex developer.

> I noticed that the bioruby-annex repository is for bioruby *rails* 
> plugins. However, the Ensembl API would have nothing to do with rails

When I discussed with Nakao-san previously, we have agreed to include
any Rails (or ActiveRecord etc.) dependent bioinformatics projects in
the bioruby-annex repository (maybe we need to refine

The purpose is

1. The number of codes which depend on Rails related libraries
   is increasing, but we have not yet decided how to integrate
   such modules in BioRuby.

2. We thought correcting various add-ons to BioRuby in one place
   might be useful (so that users can find your bioinformatics
   modules easily, and/or some of them might be integrated into
   core BioRuby library in the future).

> (apart from the fact that it uses ActiveRecord in the background).

So, I thought your project is appropriate to be included.

> This might get confusing for possible users.

Yes, we may need to re-write our project description to clarify.
Volunteers?

As the bioruby-annex seems to be functioning now, we need to discuss
some rules for how to develop, release, and use sub products in it.

My idea is still vague, but how about to have codes in SVN as

  /bioruby-annex/rails/plugins <- for Rails' script/plugin source
  /bioruby-annex/project1/
  /bioruby-annex/project2/
    :

and each sub projects will release the package as a gem (or tar.gz) file
prefixed with 'bioruby-' or 'bioruby-annex-' so that, for instance, you
could release

  bioruby-ensembl-api-1.0.gem

for downlaod from

  http://rubyforge.org/projects/bioruby-annex/

Toshiaki

On 2007/05/10, at 19:34, jan aerts (RI) wrote:

> Toshiaki,
>
> I noticed that the bioruby-annex repository is for bioruby *rails* 
> plugins. However, the Ensembl API would have nothing to do with rails 
> (apart from the fact that it uses ActiveRecord in the background).
> This might get confusing for possible users.
>
> jan. 
>
> -----Original Message-----
> From: Toshiaki Katayama [mailto:ktym at hgc.jp]
> Sent: 10 May 2007 11:14
> To: jan aerts (RI)
> Cc: Michael Han; bioruby at lists.open-bio.org
> Subject: Re: [BioRuby] Ensembl API
>
> Jan,
>
> In that case, I would like you to consider to use the rubyforge 
> repository 'bioruby-annex' which Nakao-san had set up.
>
>   http://lists.open-bio.org/pipermail/bioruby/2007-April/000355.html
>
> When your modules matured and we, core developers, have decided how to

> integrate Rails dependent modules in BioRuby, you can put them in the 
> BioRuby distribution.
>
> Toshiaki
>
> On 2007/05/10, at 18:09, jan aerts (RI) wrote:
>
>> I actually just started working on this API last night (in between 
>> some deadlines I got to catch), so haven't gotten so far as to think 
>> about caching. I'm basically working through the perl API tutorial
>> (http://www.ensembl.org/info/software/core/core_tutorial.html) and 
>> try
>
>> to implement all those examples. (At the moment, I'm at the bit that 
>> says "Break chromosomal slices into smaller 100k component 
>> slices"...)
>>
>> Some hurdles that I see coming are the caching and projecting 
>> features
>
>> from one coord system to another. We'll see what happens when we get 
>> there.
>>
>> As for a public place: I would _very_ much appreciate help with the 
>> API, although
>>
>> QUESTION FOR BIORUBY COMMUNITY AND DEVELOPERS:
>> * Do you think it would be best to create a sourceforge project for 
>> this, or should I add it directly into bioruby (e.g.
> Bio::Api::Ensembl)?
>> I suppose the second option would be best, but the stuff I have is 
>> probably not polished enough yet... and *far* from complete.
>> * Secondly: if a new release is coming: would it be best to wait 
>> untill _after_ that release?
>>
>> jan.
>>
>>
>> -----Original Message-----
>> From: Michael Han [mailto:mh6 at sanger.ac.uk]
>> Sent: 10 May 2007 09:51
>> To: jan aerts (RI)
>> Subject: Re: [BioRuby] Ensembl API
>>
>>
>> On 10 May 2007, at 08:58, jan aerts ((RI)) wrote:
>>> Michael,
>>>
>>> As you mention that we maybe won't be able to cover everything with 
>>> the default activerecord behaviour: what problems are you thinking
> of?
>>>
>>> Note: I'd like to use the perl API as a guide. And indeed working 
>>> out
>
>>> the Slice object was quite simple...
>>
>> Yes, I was thinking of the slices in combination with the different 
>> assembly levels.
>> A change to the mapping part of that broke the last EnsEMBL release.
>> There were some cases where a seq_region maps one-to-many to other 
>> seq_regions (also with gaps).
>> Did you put all the caching stuff from the Perl API into it? And if 
>> not, is the performance ok?
>>
>> It would be also great if you could put the code into some public 
>> place (RubyForge as example), then it would be easier to see what is 
>> already working/being worked at and what not.
>>
>>> jan.
>>>
>>> -----Original Message-----
>>> From: Michael Han [mailto:mh6 at sanger.ac.uk]
>>> Sent: 09 May 2007 14:38
>>> To: jan aerts (RI)
>>> Subject: Re: [BioRuby] Ensembl API
>>>
>>> On 9 May 2007, at 14:14, jan aerts ((RI)) wrote:
>>>> Has anyone worked on an Ensembl API? There is a perl API and the 
>>>> database schema is well-documented. On first impression, it seems 
>>>> straightforward to make one using ActiveRecord, but I wouldn't want

>>>> to
>>>
>>>> waste efforts on that if someone else is already working on it.
>>>>
>>>> See http://www.ensembl.org/info/software/core/index.html
>>>>
>>>> Dr Jan Aerts
>>>> Bioinformatics Group
>>>
>>> Hi Jan,
>>>
>>> I am not sure if you can cover everything with a the default active-

>>> record behavior.
>>> But I would be a happy user of a ruby EnsEMBL API.
>>> If you need/want help with it, I would also volunteer.
>>>
>>> Michael
>>
>




From jan.aerts at bbsrc.ac.uk  Thu May 10 13:32:22 2007
From: jan.aerts at bbsrc.ac.uk (jan aerts (RI))
Date: Thu, 10 May 2007 14:32:22 +0100
Subject: [BioRuby] Ensembl API
In-Reply-To: <B312993D-DFFA-4869-9F1E-890D04093A9C@hgc.jp>
Message-ID: <84DA9D8AC9B05F4B889E7C70238CB45104FB170D@rie2ksrv1.ri.bbsrc.ac.uk>

Toshiaki,

Your idea of a directory structure as this seems a good choice.
  /bioruby-annex/rails/plugins <- for Rails' script/plugin source
  /bioruby-annex/project1/
  /bioruby-annex/project2/
    :

OK if I add a subdirectory for 'ensembl_api'? (so that would be:
/bioruby-annex/ensembl_api/)

jan.

-----Original Message-----
From: Toshiaki Katayama [mailto:ktym at hgc.jp] 
Sent: 10 May 2007 12:43
To: jan aerts (RI)
Cc: BioRubyML
Subject: Re: [BioRuby] Ensembl API

Jan,

You are added as a annex developer.

> I noticed that the bioruby-annex repository is for bioruby *rails* 
> plugins. However, the Ensembl API would have nothing to do with rails

When I discussed with Nakao-san previously, we have agreed to include
any Rails (or ActiveRecord etc.) dependent bioinformatics projects in
the bioruby-annex repository (maybe we need to refine

The purpose is

1. The number of codes which depend on Rails related libraries
   is increasing, but we have not yet decided how to integrate
   such modules in BioRuby.

2. We thought correcting various add-ons to BioRuby in one place
   might be useful (so that users can find your bioinformatics
   modules easily, and/or some of them might be integrated into
   core BioRuby library in the future).

> (apart from the fact that it uses ActiveRecord in the background).

So, I thought your project is appropriate to be included.

> This might get confusing for possible users.

Yes, we may need to re-write our project description to clarify.
Volunteers?

As the bioruby-annex seems to be functioning now, we need to discuss
some rules for how to develop, release, and use sub products in it.

My idea is still vague, but how about to have codes in SVN as

  /bioruby-annex/rails/plugins <- for Rails' script/plugin source
  /bioruby-annex/project1/
  /bioruby-annex/project2/
    :

and each sub projects will release the package as a gem (or tar.gz) file
prefixed with 'bioruby-' or 'bioruby-annex-' so that, for instance, you
could release

  bioruby-ensembl-api-1.0.gem

for downlaod from

  http://rubyforge.org/projects/bioruby-annex/

Toshiaki

On 2007/05/10, at 19:34, jan aerts (RI) wrote:

> Toshiaki,
>
> I noticed that the bioruby-annex repository is for bioruby *rails* 
> plugins. However, the Ensembl API would have nothing to do with rails 
> (apart from the fact that it uses ActiveRecord in the background).
> This might get confusing for possible users.
>
> jan. 
>
> -----Original Message-----
> From: Toshiaki Katayama [mailto:ktym at hgc.jp]
> Sent: 10 May 2007 11:14
> To: jan aerts (RI)
> Cc: Michael Han; bioruby at lists.open-bio.org
> Subject: Re: [BioRuby] Ensembl API
>
> Jan,
>
> In that case, I would like you to consider to use the rubyforge 
> repository 'bioruby-annex' which Nakao-san had set up.
>
>   http://lists.open-bio.org/pipermail/bioruby/2007-April/000355.html
>
> When your modules matured and we, core developers, have decided how to

> integrate Rails dependent modules in BioRuby, you can put them in the 
> BioRuby distribution.
>
> Toshiaki
>
> On 2007/05/10, at 18:09, jan aerts (RI) wrote:
>
>> I actually just started working on this API last night (in between 
>> some deadlines I got to catch), so haven't gotten so far as to think 
>> about caching. I'm basically working through the perl API tutorial
>> (http://www.ensembl.org/info/software/core/core_tutorial.html) and 
>> try
>
>> to implement all those examples. (At the moment, I'm at the bit that 
>> says "Break chromosomal slices into smaller 100k component 
>> slices"...)
>>
>> Some hurdles that I see coming are the caching and projecting 
>> features
>
>> from one coord system to another. We'll see what happens when we get 
>> there.
>>
>> As for a public place: I would _very_ much appreciate help with the 
>> API, although
>>
>> QUESTION FOR BIORUBY COMMUNITY AND DEVELOPERS:
>> * Do you think it would be best to create a sourceforge project for 
>> this, or should I add it directly into bioruby (e.g.
> Bio::Api::Ensembl)?
>> I suppose the second option would be best, but the stuff I have is 
>> probably not polished enough yet... and *far* from complete.
>> * Secondly: if a new release is coming: would it be best to wait 
>> untill _after_ that release?
>>
>> jan.
>>
>>
>> -----Original Message-----
>> From: Michael Han [mailto:mh6 at sanger.ac.uk]
>> Sent: 10 May 2007 09:51
>> To: jan aerts (RI)
>> Subject: Re: [BioRuby] Ensembl API
>>
>>
>> On 10 May 2007, at 08:58, jan aerts ((RI)) wrote:
>>> Michael,
>>>
>>> As you mention that we maybe won't be able to cover everything with 
>>> the default activerecord behaviour: what problems are you thinking
> of?
>>>
>>> Note: I'd like to use the perl API as a guide. And indeed working 
>>> out
>
>>> the Slice object was quite simple...
>>
>> Yes, I was thinking of the slices in combination with the different 
>> assembly levels.
>> A change to the mapping part of that broke the last EnsEMBL release.
>> There were some cases where a seq_region maps one-to-many to other 
>> seq_regions (also with gaps).
>> Did you put all the caching stuff from the Perl API into it? And if 
>> not, is the performance ok?
>>
>> It would be also great if you could put the code into some public 
>> place (RubyForge as example), then it would be easier to see what is 
>> already working/being worked at and what not.
>>
>>> jan.
>>>
>>> -----Original Message-----
>>> From: Michael Han [mailto:mh6 at sanger.ac.uk]
>>> Sent: 09 May 2007 14:38
>>> To: jan aerts (RI)
>>> Subject: Re: [BioRuby] Ensembl API
>>>
>>> On 9 May 2007, at 14:14, jan aerts ((RI)) wrote:
>>>> Has anyone worked on an Ensembl API? There is a perl API and the 
>>>> database schema is well-documented. On first impression, it seems 
>>>> straightforward to make one using ActiveRecord, but I wouldn't want

>>>> to
>>>
>>>> waste efforts on that if someone else is already working on it.
>>>>
>>>> See http://www.ensembl.org/info/software/core/index.html
>>>>
>>>> Dr Jan Aerts
>>>> Bioinformatics Group
>>>
>>> Hi Jan,
>>>
>>> I am not sure if you can cover everything with a the default active-

>>> record behavior.
>>> But I would be a happy user of a ruby EnsEMBL API.
>>> If you need/want help with it, I would also volunteer.
>>>
>>> Michael
>>
>




From fredjoha at bioreg.kyushu-u.ac.jp  Tue May 15 05:54:46 2007
From: fredjoha at bioreg.kyushu-u.ac.jp (Fredrik Johansson)
Date: Tue, 15 May 2007 14:54:46 +0900
Subject: [BioRuby] Bio::Blast not fully functional?
Message-ID: <1179208486.7335.39.camel@fred-kyudai>

Hello all,
I am reading in the tutorial at
http://dev.bioruby.org/wiki/en/?Tutorial.rd
about BLAST and I try to use it according to this tutorial (see the code
below).
However, many of the entries in the 'hit' variable in the code below
seems to be nil. hit.identity and hit.target_seq are for example two
methods that just answer nil when I call them. Am I missing something?

#!/usr/bin/env ruby
require 'bio'
factory = Bio::Blast.remote('blastp', 'nr-aa')
Bio::FlatFile.open(Bio::FastaFormat, '/home/fred/pdb/test.fasta.txt') do
|ff|
  ff.each do |entry|
    report = factory.query(entry)
    report.each do |hit|
      if hit.evalue < 0.001
         puts hit.target_id
         puts hit.target_seq
      end
    end
  end
end

Thanks for any help!
Best regards,
Fredrik Johansson



From hienle at club-internet.fr  Tue May 15 15:30:27 2007
From: hienle at club-internet.fr (hienle at club-internet.fr)
Date: Tue, 15 May 2007 17:30:27 +0200
Subject: [BioRuby] Parsing GFF3 attributes
Message-ID: <mnet1.1179243027.27796.hienle@club-internet.fr>

Hello all,

I am working with a GFF3-formatted file and have noticed that the attributes field is not parsed properly.

In bio/db/gff.rb, 

    75      def parse_attributes(attributes)
    76        hash = Hash.new
    77        attributes.split(/[^\\];/).each do |atr|
    78          key, value = atr.split(' ', 2)
    79          hash[key] = value
    80        end
    81        return hash
    82      end
    83    end

I changed :
    78          key, value = atr.split(' ', 2)
to:
    78          key, value = atr.split('=', 2)

and it now appears to behave properly. However, I am not certain if this is appropriate for backward compatibility with GFF and GFF2. Is anyone working on parsing GFF3 files?

Thank you in advance for your help,
-Hien




From mh6 at sanger.ac.uk  Tue May 15 16:10:20 2007
From: mh6 at sanger.ac.uk (Michael Han)
Date: Tue, 15 May 2007 17:10:20 +0100
Subject: [BioRuby] Parsing GFF3 attributes
In-Reply-To: <mnet1.1179243027.27796.hienle@club-internet.fr>
References: <mnet1.1179243027.27796.hienle@club-internet.fr>
Message-ID: <ACEE88FC-0094-4B17-AC2F-34E56CF072D1@sanger.ac.uk>


On 15 May 2007, at 16:30, hienle at club-internet.fr wrote:
> Hello all,
>
> I am working with a GFF3-formatted file and have noticed that the  
> attributes field is not parsed properly.
>
> In bio/db/gff.rb,
>
>     75      def parse_attributes(attributes)
>     76        hash = Hash.new
>     77        attributes.split(/[^\\];/).each do |atr|
>     78          key, value = atr.split(' ', 2)
>     79          hash[key] = value
>     80        end
>     81        return hash
>     82      end
>     83    end
>
> I changed :
>     78          key, value = atr.split(' ', 2)
> to:
>     78          key, value = atr.split('=', 2)
>
> and it now appears to behave properly. However, I am not certain if  
> this is appropriate for backward compatibility with GFF and GFF2.

I use normally spaces between the key and the value of the attributes  
for GFF2 like: Gene "1234" ; Transcript "1234"
as described in <"http://www.sanger.ac.uk/Software/formats/GFF/ 
GFF_Spec.shtml">

so it would break  GFF2 / GFF parsing.
Maybe you could create a separate GFF3 parser inheriting from the  
gff.rb .

some GFF3 reference (note: last version from a few weeks ago)
<"http://www.sequenceontology.org/gff3.shtml">

> Is anyone working on parsing GFF3 files?
>
> Thank you in advance for your help,
> -Hien

MIchael


From hien.le at mail.mcgill.ca  Wed May 16 07:01:54 2007
From: hien.le at mail.mcgill.ca (Hien Le)
Date: Wed, 16 May 2007 03:01:54 -0400
Subject: [BioRuby] Parsing GFF3 attributes
In-Reply-To: <ACEE88FC-0094-4B17-AC2F-34E56CF072D1@sanger.ac.uk>
References: <mnet1.1179243027.27796.hienle@club-internet.fr>
	<ACEE88FC-0094-4B17-AC2F-34E56CF072D1@sanger.ac.uk>
Message-ID: <20070516030154.esps58l1ws8c8o00@webmail.mcgill.ca>

Quoting Michael Han <mh6 at sanger.ac.uk>:

> so it would break  GFF2 / GFF parsing.
> Maybe you could create a separate GFF3 parser inheriting from the
> gff.rb .

OK, thanks Michael for the advice!
-Hien


From cihan at cihan.us  Wed May 16 14:44:14 2007
From: cihan at cihan.us (cihan inan)
Date: Wed, 16 May 2007 17:44:14 +0300
Subject: [BioRuby] Translate docs
Message-ID: <5584352e0705160744w429281b6v3ccf3e8f105cac17@mail.gmail.com>

hi I am cihan inan and I am from Turkey. I am a student at Biology. I am new
in Ruby language. I want to translate some docs to Turkish. But I think I
have to get permission. But I dont know who gives that permission? please
help me about this topic. ( tell me the docs to start give me a way sth. )
thanks a lot.


From fredjoha at bioreg.kyushu-u.ac.jp  Fri May 18 01:17:12 2007
From: fredjoha at bioreg.kyushu-u.ac.jp (Fredrik Johansson)
Date: Fri, 18 May 2007 10:17:12 +0900
Subject: [BioRuby] FASTA problem
Message-ID: <1179451032.29172.33.camel@fred-kyudai>

Hello,
I had problem running a fasta search locally on my computer, and it
turned out that Kernel.exec(*cmd) is not very happy to get the array cmd
with nil as one of its element. This is however what happens in
bio/app/fasta.rb, if ktup is not set. I changed this to make it work :

--- fasta.rb.old        2007-05-18 09:55:01.000000000 +0900
+++ fasta.rb    2007-05-18 09:55:37.000000000 +0900
@@ -114,7 +114,8 @@
 
   def exec_local(query)
     cmd = [ @program, *@options ]
-    cmd.concat([ '@', @db, @ktup ])
+    cmd.concat([ '@', @db])
+    cmd.push(@ktup) if @ktup
 
     report = nil
 
Something to submit to the repository?

Best regards,
Fredrik



From ktym at hgc.jp  Fri May 18 15:23:41 2007
From: ktym at hgc.jp (Toshiaki Katayama)
Date: Sat, 19 May 2007 00:23:41 +0900
Subject: [BioRuby] FASTA problem
In-Reply-To: <1179451032.29172.33.camel@fred-kyudai>
References: <1179451032.29172.33.camel@fred-kyudai>
Message-ID: <FCA0A706-457C-4C23-944E-65DD07DEE9BF@hgc.jp>

Hello Fredrik,

Thank you for your fix!
I have commited your patch to the CVS.

Regards,
Toshiaki Katayama


On 2007/05/18, at 10:17, Fredrik Johansson wrote:

> Hello,
> I had problem running a fasta search locally on my computer, and it
> turned out that Kernel.exec(*cmd) is not very happy to get the array cmd
> with nil as one of its element. This is however what happens in
> bio/app/fasta.rb, if ktup is not set. I changed this to make it work :
>
> --- fasta.rb.old        2007-05-18 09:55:01.000000000 +0900
> +++ fasta.rb    2007-05-18 09:55:37.000000000 +0900
> @@ -114,7 +114,8 @@
>
>    def exec_local(query)
>      cmd = [ @program, *@options ]
> -    cmd.concat([ '@', @db, @ktup ])
> +    cmd.concat([ '@', @db])
> +    cmd.push(@ktup) if @ktup
>
>      report = nil
>
> Something to submit to the repository?
>
> Best regards,
> Fredrik
>
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby



From ktym at hgc.jp  Fri May 18 15:24:24 2007
From: ktym at hgc.jp (Toshiaki Katayama)
Date: Sat, 19 May 2007 00:24:24 +0900
Subject: [BioRuby] Translate docs
In-Reply-To: <5584352e0705160744w429281b6v3ccf3e8f105cac17@mail.gmail.com>
References: <5584352e0705160744w429281b6v3ccf3e8f105cac17@mail.gmail.com>
Message-ID: <852FFA12-3475-46B7-82C6-250ACD7A6BD0@hgc.jp>

Hi,

You are free to translate the documents in the bioruby-x.x.x/doc/ directory or on web (wiki) pages.
I apologize the main document, bioruby tutorial, is not updated
(I've lost updated version with disk crash in this Feb and not restarted yet).

Regards,
Toshiaki Katayama

On 2007/05/16, at 23:44, cihan inan wrote:

> hi I am cihan inan and I am from Turkey. I am a student at Biology. I am new
> in Ruby language. I want to translate some docs to Turkish. But I think I
> have to get permission. But I dont know who gives that permission? please
> help me about this topic. ( tell me the docs to start give me a way sth. )
> thanks a lot.
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby



From ktym at hgc.jp  Fri May 18 15:23:51 2007
From: ktym at hgc.jp (Toshiaki Katayama)
Date: Sat, 19 May 2007 00:23:51 +0900
Subject: [BioRuby] Parsing GFF3 attributes
In-Reply-To: <ACEE88FC-0094-4B17-AC2F-34E56CF072D1@sanger.ac.uk>
References: <mnet1.1179243027.27796.hienle@club-internet.fr>
	<ACEE88FC-0094-4B17-AC2F-34E56CF072D1@sanger.ac.uk>
Message-ID: <10A4A7B4-063F-459F-B9D6-56222F8C26E9@hgc.jp>

Hien,

Thank you for your report.

In bio/db/gff.rb, we have Bio::GFF::GFF2 for version 2 spec and Bio::GFF::GFF3 for version 3
and I added your modification to the Bio::GFF::GFF3 class.

Personally, I have not yet use GFF3 intensively, so if you think the class
should have more functionality to support new features in GFF3, please propose.

Toshiaki

On 2007/05/16, at 1:10, Michael Han wrote:

>
> On 15 May 2007, at 16:30, hienle at club-internet.fr wrote:
>> Hello all,
>>
>> I am working with a GFF3-formatted file and have noticed that the  
>> attributes field is not parsed properly.
>>
>> In bio/db/gff.rb,
>>
>>     75      def parse_attributes(attributes)
>>     76        hash = Hash.new
>>     77        attributes.split(/[^\\];/).each do |atr|
>>     78          key, value = atr.split(' ', 2)
>>     79          hash[key] = value
>>     80        end
>>     81        return hash
>>     82      end
>>     83    end
>>
>> I changed :
>>     78          key, value = atr.split(' ', 2)
>> to:
>>     78          key, value = atr.split('=', 2)
>>
>> and it now appears to behave properly. However, I am not certain if  
>> this is appropriate for backward compatibility with GFF and GFF2.
>
> I use normally spaces between the key and the value of the attributes  
> for GFF2 like: Gene "1234" ; Transcript "1234"
> as described in <"http://www.sanger.ac.uk/Software/formats/GFF/ 
> GFF_Spec.shtml">
>
> so it would break  GFF2 / GFF parsing.
> Maybe you could create a separate GFF3 parser inheriting from the  
> gff.rb .
>
> some GFF3 reference (note: last version from a few weeks ago)
> <"http://www.sequenceontology.org/gff3.shtml">
>
>> Is anyone working on parsing GFF3 files?
>>
>> Thank you in advance for your help,
>> -Hien
>
> MIchael
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby



From ktym at hgc.jp  Fri May 18 16:00:33 2007
From: ktym at hgc.jp (Toshiaki Katayama)
Date: Sat, 19 May 2007 01:00:33 +0900
Subject: [BioRuby] Bio::Blast not fully functional?
In-Reply-To: <1179208486.7335.39.camel@fred-kyudai>
References: <1179208486.7335.39.camel@fred-kyudai>
Message-ID: <8B741702-DB3E-49D5-9920-9420336F4E61@hgc.jp>


Fredrik,

This is because Bio::Blast.remote uses '-m 8' option
which returns a tabular output format without target sequences.

You can use XML output for your purpose by changing the following line

> factory = Bio::Blast.remote('blastp', 'nr-aa')

to

factory = Bio::Blast.remote('blastp', 'nr-aa', '-m 7')

Regards,
Toshiaki

On 2007/05/15, at 14:54, Fredrik Johansson wrote:

> Hello all,
> I am reading in the tutorial at
> http://dev.bioruby.org/wiki/en/?Tutorial.rd
> about BLAST and I try to use it according to this tutorial (see the code
> below).
> However, many of the entries in the 'hit' variable in the code below
> seems to be nil. hit.identity and hit.target_seq are for example two
> methods that just answer nil when I call them. Am I missing something?
>
> #!/usr/bin/env ruby
> require 'bio'
> factory = Bio::Blast.remote('blastp', 'nr-aa')
> Bio::FlatFile.open(Bio::FastaFormat, '/home/fred/pdb/test.fasta.txt') do
> |ff|
>   ff.each do |entry|
>     report = factory.query(entry)
>     report.each do |hit|
>       if hit.evalue < 0.001
>          puts hit.target_id
>          puts hit.target_seq
>       end
>     end
>   end
> end
>
> Thanks for any help!
> Best regards,
> Fredrik Johansson
>
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby



From fredjoha at bioreg.kyushu-u.ac.jp  Mon May 21 08:16:31 2007
From: fredjoha at bioreg.kyushu-u.ac.jp (Fredrik Johansson)
Date: Mon, 21 May 2007 17:16:31 +0900
Subject: [BioRuby] Parsing FASTA result
Message-ID: <1179735391.29172.91.camel@fred-kyudai>

I have encountered a problem again when running FASTA. I got a huge
amount of homologs from fasta (25 MB data) for one sequence, and then
the Bio::Fasta::Report class gets this error when initializing:

format10.rb:21:in `sub!': failed to allocate memory (NoMemoryError)

so I made the following changes to my code. It is just a quick fix, and
I am not sure about that 'else' case that I took away. It does not seem
to be covered by the line that I added. Also I did not bother about the
@list variable since it does not seem to be used anywhere.

/Fredrik

The patch:

--- fasta/format10.rb   2007-05-21 16:50:38.000000000 +0900
+++ fasta/format10.new.rb       2007-05-21 16:52:55.000000000 +0900
@@ -17,13 +17,7 @@
 
   def initialize(data)
     # header lines - brief list of the hits
-    if data.sub!(/.*\nThe best scores are/m, '')
-      data.sub!(/(.*)\n\n>>>/m, '')
-      @list = "The best scores are" + $1
-    else 
-      data.sub!(/.*\n!!\s+/m, '')
-      data.sub!(/.*/) { |x| @list = x; '' }
-    end
+    data = data[data.index("\n\n>>>")+5..data.size]
 
     # body lines - fasta execution result
     program, *hits = data.split(/\n>>/)




From jan.aerts at bbsrc.ac.uk  Mon May 21 14:05:17 2007
From: jan.aerts at bbsrc.ac.uk (jan aerts (RI))
Date: Mon, 21 May 2007 15:05:17 +0100
Subject: [BioRuby] Ensembl API for ruby
Message-ID: <84DA9D8AC9B05F4B889E7C70238CB45104FB1784@rie2ksrv1.ri.bbsrc.ac.uk>

All,

I committed the first version of a ruby API to the bioruby-annex SVN on
rubyforge. Although it is far from completed, it does already have its
uses. Thought it would be good to commit as soon as possible so you guys
get an idea of what the API would look like.
I would like to follow the excellent perl API as much as possible
(http://www.ensembl.org/info/software/core/core_tutorial.html).


What it does at the moment:
* All tables of the core database are covered by ActiveRecord classes.
* A Slice object represents a continuous region of a genome. Slices can
be used to obtain sequence, features or other information from a
particular region of interest.
* Coordinates can be transfered from one coordinate system to another. I
hope I tested this thorougly enough (but still am a bit squeemish about
it).

What is not implemented yet:
* A whole bunch of methods that are available to the perl objects that I
would like to 'copy' to the ruby API.
* The Variation and Compara databases.
* The 'project' and 'transform' methods for features and slices (as
explained on the perl tutorial mentioned above).

To get this code, please go to
http://rubyforge.org/projects/bioruby-annex/ You can export the code
using SVN with the following command (without quotes):
"svn checkout svn://rubyforge.org/var/svn/bioruby-annex". There should
be a subdirectory 'ensembl-api', containing the API itself, the sample
script, tests and of course all documentation.

I've created a gem (available in the top-directory of the SVN export),
but can't test if it actually works. Can someone please test it for me?

Toshiaki: if the code works and the gem can be installed on other
systems, could you please do a file release for the gem-file?

Others: if people are interested to help me to develop this API, please
let me know.

Thanks,
jan.

Dr Jan Aerts
Bioinformatics Group
Roslin Institute
Roslin EH25 9PS
Scotland, UK
tel: +44 131 527 4198
skype: aerts_ri

----...and the obligatory disclaimer----
Roslin Institute is a company limited by guarantee, registered in
Scotland (registered number SC157100) and a Scottish Charity (registered
number SC023592). Our registered office is at Roslin, Midlothian, EH25
9PS. VAT registration number 847380013.

The information contained in this e-mail (including any attachments) is
confidential and is intended for the use of  the addressee only. The
opinions expressed within this e-mail (including any attachments) are
the opinions of the sender and do not necessarily constitute those of
Roslin Institute (Edinburgh) ("the Institute") unless specifically
stated by a sender who is duly authorised to do so on behalf of the
Institute.



From hien.le at mail.mcgill.ca  Tue May 22 07:33:26 2007
From: hien.le at mail.mcgill.ca (Hien Le)
Date: Tue, 22 May 2007 03:33:26 -0400
Subject: [BioRuby] Parsing GFF3 attributes
Message-ID: <20070522033326.1zpegb2scgg0skws@webmail.mcgill.ca>

On May 18, 2007, at 17:23, Toshiaki Katayama wrote:

> and I added your modification to the Bio::GFF::GFF3 class.

OK Thanks!

> Personally, I have not yet use GFF3 intensively, so if you think the
> class should have more functionality to support new features in GFF3, 
> please propose.

Same for myself, I have just recently started using GFF3 formats. I'll 
let you know if I think the class needs added functionality.

-Hien


From christophercyll at gmail.com  Thu May 24 22:22:56 2007
From: christophercyll at gmail.com (Topher Cyll)
Date: Thu, 24 May 2007 18:22:56 -0400
Subject: [BioRuby] looking for a cool project to do using bioruby
Message-ID: <2599499e0705241522k4e674a26q28ddc2bd021e17a8@mail.gmail.com>

Hi BioRubyers,

I'm a long time reader of this list, but I think this might be my first post.

I'm in the process of writing a Ruby project book.  Each chapter
guides the reader through a new and unusual project they can code in
Ruby. For comparison, in other chapters we do things like compose
music, build a game, run simulations, implement Lisp, etc.

I'd really like to include a project using BioRuby (since I think a
lot of Rubyists would find it exciting).  But with only one
undergraduate bio-informatics class under my belt, I'm a little stuck
on ideas for fun and interesting projects.

So I thought I'd ask the experts!

Can anyone think of a fun, interesting use for BioRuby that I could
walk readers through?  I like to have each project produce a final
product, instead of just doing a tutorial, so I'm looking for a idea
that would have some implementation work, but wouldn't be too, too
difficult.

Any ideas?
Toph


From s-merchant at northwestern.edu  Fri May 25 15:39:55 2007
From: s-merchant at northwestern.edu (Sohel Merchant)
Date: Fri, 25 May 2007 10:39:55 -0500
Subject: [BioRuby] looking for a cool project to do using bioruby
In-Reply-To: <2599499e0705241522k4e674a26q28ddc2bd021e17a8@mail.gmail.com>
References: <2599499e0705241522k4e674a26q28ddc2bd021e17a8@mail.gmail.com>
Message-ID: <000001c79ee2$f1eda7b0$c2987ca5@pc13>

Hi Toph,
  I would say one of fun things to implement in Ruby would be Ontology
visualization. The tool could be used to visualize any kind of ontology such
as GO. It would be cool if this could be integrated in to a Rails app. Look
at QuickGo which visualizes the Gene Ontology

http://www.ebi.ac.uk/ego/DisplayGoTerm?id=GO:0042351

Hope this helps. Let me know if you any questions.

Cheers,
Sohel.



-----Original Message-----
From: bioruby-bounces at lists.open-bio.org
[mailto:bioruby-bounces at lists.open-bio.org] On Behalf Of Topher Cyll
Sent: Thursday, May 24, 2007 5:23 PM
To: bioruby at lists.open-bio.org
Subject: [BioRuby] looking for a cool project to do using bioruby

Hi BioRubyers,

I'm a long time reader of this list, but I think this might be my first
post.

I'm in the process of writing a Ruby project book.  Each chapter
guides the reader through a new and unusual project they can code in
Ruby. For comparison, in other chapters we do things like compose
music, build a game, run simulations, implement Lisp, etc.

I'd really like to include a project using BioRuby (since I think a
lot of Rubyists would find it exciting).  But with only one
undergraduate bio-informatics class under my belt, I'm a little stuck
on ideas for fun and interesting projects.

So I thought I'd ask the experts!

Can anyone think of a fun, interesting use for BioRuby that I could
walk readers through?  I like to have each project produce a final
product, instead of just doing a tutorial, so I'm looking for a idea
that would have some implementation work, but wouldn't be too, too
difficult.

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