From kpatil at science.uva.nl  Wed Jan  7 08:32:52 2009
From: kpatil at science.uva.nl (K. Patil)
Date: Wed, 7 Jan 2009 14:32:52 +0100 (CET)
Subject: [BioRuby] error with big fasta files
Message-ID: <37628.139.19.75.1.1231335172.squirrel@webmail.science.uva.nl>

Hi,

I am trying to process some big fasta files. I get the following error;

/XXX/rubygems/bioruby-1.2.1/lib/bio/db/fasta.rb:156:in `initialize':
private method `sub' called for nil:NilClass (NoMethodError)

The corresponding file contains only one sequence with 3200227952
characters (there are no new lines in the file except the one after the
header).

Any clues?

Cheers,
Kaustubh




From ngoto at gen-info.osaka-u.ac.jp  Wed Jan  7 21:33:49 2009
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Thu, 8 Jan 2009 11:33:49 +0900
Subject: [BioRuby] error with big fasta files
In-Reply-To: <37628.139.19.75.1.1231335172.squirrel@webmail.science.uva.nl>
References: <37628.139.19.75.1.1231335172.squirrel@webmail.science.uva.nl>
Message-ID: <20090108023351.3088F1CBC4CF@idnmail.gen-info.osaka-u.ac.jp>

On Wed, 7 Jan 2009 14:32:52 +0100 (CET)
"K. Patil" <kpatil at science.uva.nl> wrote:

> Hi,
> 
> I am trying to process some big fasta files. I get the following error;
> 
> /XXX/rubygems/bioruby-1.2.1/lib/bio/db/fasta.rb:156:in `initialize':
> private method `sub' called for nil:NilClass (NoMethodError)
> 
> The corresponding file contains only one sequence with 3200227952
> characters (there are no new lines in the file except the one after the
> header).
> 
> Any clues?
> 
> Cheers,
> Kaustubh

The FastaFormat parser first reads all data into memory.
So, it seems memory exhaust.

In addition, in normal 32-bit OS, maximum memory size given
to an application is about 3GB, and it is possible that the
error might also be caused by a limitation of 32-bit.

Please try again by using 64-bit OS with abundant memory and
running 64-bit compiled Ruby (the newest version is strongly
recommended).

Naohisa Goto
ng at bioruby.org / ngoto at gen-info.osaka-u.ac.jp

From kpatil at science.uva.nl  Wed Jan 21 18:11:53 2009
From: kpatil at science.uva.nl (K. Patil)
Date: Thu, 22 Jan 2009 00:11:53 +0100 (CET)
Subject: [BioRuby] newick tree
Message-ID: <27715.84.58.197.42.1232579513.squirrel@webmail.science.uva.nl>

Hi,

I was trying some simple methods for the Newick tree. I did the following,

>t = Bio::Newick.new("(A,(B,C),D)")
>t.tree.nodes
=>[(Node:43c98a8), (Node:"A"), (Node:"B"), (Node:"D"), (Node:43c91f0),
(Node:"C")]
> t.tree.number_of_nodes
=> 6

Am I doing something wrong? I am using bioruby version 1.2.1 in ruby 1.8.
Any suggestions are welcome.

Cheers,
Kaustubh




From tomoakin at kenroku.kanazawa-u.ac.jp  Wed Jan 21 19:12:00 2009
From: tomoakin at kenroku.kanazawa-u.ac.jp (Tomoaki NISHIYAMA)
Date: Thu, 22 Jan 2009 09:12:00 +0900
Subject: [BioRuby] newick tree
In-Reply-To: <27715.84.58.197.42.1232579513.squirrel@webmail.science.uva.nl>
References: <27715.84.58.197.42.1232579513.squirrel@webmail.science.uva.nl>
Message-ID: <F70C4471-5F9C-4756-85F1-D48698F24F18@kenroku.kanazawa-u.ac.jp>

Hi,

I have not used the Newick feature of bioruby but the behavior
you showed seems doing quite right.
What is your expectation? Or, what do you want?

(A,(B,C),D)
represents the following tree, which have 4 terminal and 2 internal  
nodes.

+------A
|
|   +---B
|   |
+---+
|   |
|   +---C
|
+-----D

The two internal nodes have no label and referred as (Node:43c98a8)
(Node:43c91f0) in the representation.

-- 
Tomoaki NISHIYAMA

Advanced Science Research Center,
Kanazawa University,
13-1 Takara-machi,
Kanazawa, 920-0934, Japan


On 2009/01/22, at 8:11, K. Patil wrote:

> Hi,
>
> I was trying some simple methods for the Newick tree. I did the  
> following,
>
>> t = Bio::Newick.new("(A,(B,C),D)")
>> t.tree.nodes
> =>[(Node:43c98a8), (Node:"A"), (Node:"B"), (Node:"D"), (Node:43c91f0),
> (Node:"C")]
>> t.tree.number_of_nodes
> => 6
>
> Am I doing something wrong? I am using bioruby version 1.2.1 in  
> ruby 1.8.
> Any suggestions are welcome.
>
> Cheers,
> Kaustubh
>
>
>
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>


From donttrustben at gmail.com  Wed Jan 21 21:39:50 2009
From: donttrustben at gmail.com (Ben Woodcroft)
Date: Thu, 22 Jan 2009 12:39:50 +1000
Subject: [BioRuby] newick tree
In-Reply-To: <F70C4471-5F9C-4756-85F1-D48698F24F18@kenroku.kanazawa-u.ac.jp>
References: <27715.84.58.197.42.1232579513.squirrel@webmail.science.uva.nl>
	<F70C4471-5F9C-4756-85F1-D48698F24F18@kenroku.kanazawa-u.ac.jp>
Message-ID: <bb2b67d00901211839w3dda10fev63854fd1e5ee72bd@mail.gmail.com>

I had the same problem - managed to solve it, but it wasn't the best. It
used something like this:

count = 0
tree.each_node do |node|
  #I get internal nodes here - not sure how else to skip
  next if node.name.nil? or node.name.length == 0

  count += 1
end
count

2009/1/22 Tomoaki NISHIYAMA <tomoakin at kenroku.kanazawa-u.ac.jp>

> Hi,
>
> I have not used the Newick feature of bioruby but the behavior
> you showed seems doing quite right.
> What is your expectation? Or, what do you want?
>
> (A,(B,C),D)
> represents the following tree, which have 4 terminal and 2 internal nodes.
>
> +------A
> |
> |   +---B
> |   |
> +---+
> |   |
> |   +---C
> |
> +-----D
>
> The two internal nodes have no label and referred as (Node:43c98a8)
> (Node:43c91f0) in the representation.
>
> --
> Tomoaki NISHIYAMA
>
> Advanced Science Research Center,
> Kanazawa University,
> 13-1 Takara-machi,
> Kanazawa, 920-0934, Japan
>
>
>
> On 2009/01/22, at 8:11, K. Patil wrote:
>
>  Hi,
>>
>> I was trying some simple methods for the Newick tree. I did the following,
>>
>>  t = Bio::Newick.new("(A,(B,C),D)")
>>> t.tree.nodes
>>>
>> =>[(Node:43c98a8), (Node:"A"), (Node:"B"), (Node:"D"), (Node:43c91f0),
>> (Node:"C")]
>>
>>> t.tree.number_of_nodes
>>>
>> => 6
>>
>> Am I doing something wrong? I am using bioruby version 1.2.1 in ruby 1.8.
>> Any suggestions are welcome.
>>
>> Cheers,
>> Kaustubh
>>
>>
>>
>> _______________________________________________
>> BioRuby mailing list
>> BioRuby at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioruby
>>
>>
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>



-- 
FYI: My email addresses at unimelb, uq and gmail all redirect to the same
place.

From ngoto at gen-info.osaka-u.ac.jp  Wed Jan 21 23:56:18 2009
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Thu, 22 Jan 2009 13:56:18 +0900
Subject: [BioRuby] newick tree
In-Reply-To: <bb2b67d00901211839w3dda10fev63854fd1e5ee72bd@mail.gmail.com>
References: <27715.84.58.197.42.1232579513.squirrel@webmail.science.uva.nl>
	<F70C4471-5F9C-4756-85F1-D48698F24F18@kenroku.kanazawa-u.ac.jp>
	<bb2b67d00901211839w3dda10fev63854fd1e5ee72bd@mail.gmail.com>
Message-ID: <20090122045618.E8CF01CBC4FD@idnmail.gen-info.osaka-u.ac.jp>

Hi,

If you want only leaf nodes (= OTUs in normal phylogenetic tree),

  t = Bio::Newick.new("(A,(B,C),D)")
  tree = t.tree
  tree.leaves
  # => [(Node:"B"), (Node:"D"), (Node:"C"), (Node:"A")]

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org

On Thu, 22 Jan 2009 12:39:50 +1000
Ben Woodcroft <donttrustben at gmail.com> wrote:

> I had the same problem - managed to solve it, but it wasn't the best. It
> used something like this:
> 
> count = 0
> tree.each_node do |node|
>   #I get internal nodes here - not sure how else to skip
>   next if node.name.nil? or node.name.length == 0
> 
>   count += 1
> end
> count
> 
> 2009/1/22 Tomoaki NISHIYAMA <tomoakin at kenroku.kanazawa-u.ac.jp>
> 
> > Hi,
> >
> > I have not used the Newick feature of bioruby but the behavior
> > you showed seems doing quite right.
> > What is your expectation? Or, what do you want?
> >
> > (A,(B,C),D)
> > represents the following tree, which have 4 terminal and 2 internal nodes.
> >
> > +------A
> > |
> > |   +---B
> > |   |
> > +---+
> > |   |
> > |   +---C
> > |
> > +-----D
> >
> > The two internal nodes have no label and referred as (Node:43c98a8)
> > (Node:43c91f0) in the representation.
> >
> > --
> > Tomoaki NISHIYAMA
> >
> > Advanced Science Research Center,
> > Kanazawa University,
> > 13-1 Takara-machi,
> > Kanazawa, 920-0934, Japan
> >
> >
> >
> > On 2009/01/22, at 8:11, K. Patil wrote:
> >
> >  Hi,
> >>
> >> I was trying some simple methods for the Newick tree. I did the following,
> >>
> >>  t = Bio::Newick.new("(A,(B,C),D)")
> >>> t.tree.nodes
> >>>
> >> =>[(Node:43c98a8), (Node:"A"), (Node:"B"), (Node:"D"), (Node:43c91f0),
> >> (Node:"C")]
> >>
> >>> t.tree.number_of_nodes
> >>>
> >> => 6
> >>
> >> Am I doing something wrong? I am using bioruby version 1.2.1 in ruby 1.8.
> >> Any suggestions are welcome.
> >>
> >> Cheers,
> >> Kaustubh
> >>
> >>
> >>
> >> _______________________________________________
> >> BioRuby mailing list
> >> BioRuby at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioruby
> >>
> >>
> > _______________________________________________
> > BioRuby mailing list
> > BioRuby at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioruby
> >
> 
> 
> 
> -- 
> FYI: My email addresses at unimelb, uq and gmail all redirect to the same
> place.
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby



From pjotr.public14 at thebird.nl  Fri Jan 30 06:21:57 2009
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Fri, 30 Jan 2009 12:21:57 +0100
Subject: [BioRuby] FOSDEM
Message-ID: <20090130112157.GA15524@thebird.nl>

Anyone coming to FOSDEM, Brussels 7+8 Feb? There is a nice Ruby track.

Pj.

From ngoto at gen-info.osaka-u.ac.jp  Fri Jan 30 11:00:16 2009
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Sat, 31 Jan 2009 01:00:16 +0900
Subject: [BioRuby] BioRuby 1.3.0 will soon be released
Message-ID: <20090130160016.739601CBC443@idnmail.gen-info.osaka-u.ac.jp>

Hi all,

I will release BioRuby 1.3.0 soon. The release of 1.3.0 have been
decided by three BioRuby developers in Japan (Toshiaki Katayama,
Mitsuteru Nakao, and me).

Now, It's time for a code freeze, except bug fix and documentation.

You can download preview version from the Github repository.
Please try it out and report any problems.

http://github.com/bioruby/bioruby/tree/master

Gem is also available from Github (but currenlty a little bit older
than git head).

Thanks,

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org

From andrew.j.grimm at gmail.com  Fri Jan 30 17:41:35 2009
From: andrew.j.grimm at gmail.com (Andrew Grimm)
Date: Sat, 31 Jan 2009 09:41:35 +1100
Subject: [BioRuby] Bioruby home page
Message-ID: <b9140daa0901301441x7acd3643t7dbab13a73178ff6@mail.gmail.com>

For the next bioruby release, is the documentation going to say that the
home web site is bioruby.org, or bioruby.open-bio.org?

Andrew

From kpatil at science.uva.nl  Wed Jan  7 13:32:52 2009
From: kpatil at science.uva.nl (K. Patil)
Date: Wed, 7 Jan 2009 14:32:52 +0100 (CET)
Subject: [BioRuby] error with big fasta files
Message-ID: <37628.139.19.75.1.1231335172.squirrel@webmail.science.uva.nl>

Hi,

I am trying to process some big fasta files. I get the following error;

/XXX/rubygems/bioruby-1.2.1/lib/bio/db/fasta.rb:156:in `initialize':
private method `sub' called for nil:NilClass (NoMethodError)

The corresponding file contains only one sequence with 3200227952
characters (there are no new lines in the file except the one after the
header).

Any clues?

Cheers,
Kaustubh





From ngoto at gen-info.osaka-u.ac.jp  Thu Jan  8 02:33:49 2009
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Thu, 8 Jan 2009 11:33:49 +0900
Subject: [BioRuby] error with big fasta files
In-Reply-To: <37628.139.19.75.1.1231335172.squirrel@webmail.science.uva.nl>
References: <37628.139.19.75.1.1231335172.squirrel@webmail.science.uva.nl>
Message-ID: <20090108023351.3088F1CBC4CF@idnmail.gen-info.osaka-u.ac.jp>

On Wed, 7 Jan 2009 14:32:52 +0100 (CET)
"K. Patil" <kpatil at science.uva.nl> wrote:

> Hi,
> 
> I am trying to process some big fasta files. I get the following error;
> 
> /XXX/rubygems/bioruby-1.2.1/lib/bio/db/fasta.rb:156:in `initialize':
> private method `sub' called for nil:NilClass (NoMethodError)
> 
> The corresponding file contains only one sequence with 3200227952
> characters (there are no new lines in the file except the one after the
> header).
> 
> Any clues?
> 
> Cheers,
> Kaustubh

The FastaFormat parser first reads all data into memory.
So, it seems memory exhaust.

In addition, in normal 32-bit OS, maximum memory size given
to an application is about 3GB, and it is possible that the
error might also be caused by a limitation of 32-bit.

Please try again by using 64-bit OS with abundant memory and
running 64-bit compiled Ruby (the newest version is strongly
recommended).

Naohisa Goto
ng at bioruby.org / ngoto at gen-info.osaka-u.ac.jp


From kpatil at science.uva.nl  Wed Jan 21 23:11:53 2009
From: kpatil at science.uva.nl (K. Patil)
Date: Thu, 22 Jan 2009 00:11:53 +0100 (CET)
Subject: [BioRuby] newick tree
Message-ID: <27715.84.58.197.42.1232579513.squirrel@webmail.science.uva.nl>

Hi,

I was trying some simple methods for the Newick tree. I did the following,

>t = Bio::Newick.new("(A,(B,C),D)")
>t.tree.nodes
=>[(Node:43c98a8), (Node:"A"), (Node:"B"), (Node:"D"), (Node:43c91f0),
(Node:"C")]
> t.tree.number_of_nodes
=> 6

Am I doing something wrong? I am using bioruby version 1.2.1 in ruby 1.8.
Any suggestions are welcome.

Cheers,
Kaustubh





From tomoakin at kenroku.kanazawa-u.ac.jp  Thu Jan 22 00:12:00 2009
From: tomoakin at kenroku.kanazawa-u.ac.jp (Tomoaki NISHIYAMA)
Date: Thu, 22 Jan 2009 09:12:00 +0900
Subject: [BioRuby] newick tree
In-Reply-To: <27715.84.58.197.42.1232579513.squirrel@webmail.science.uva.nl>
References: <27715.84.58.197.42.1232579513.squirrel@webmail.science.uva.nl>
Message-ID: <F70C4471-5F9C-4756-85F1-D48698F24F18@kenroku.kanazawa-u.ac.jp>

Hi,

I have not used the Newick feature of bioruby but the behavior
you showed seems doing quite right.
What is your expectation? Or, what do you want?

(A,(B,C),D)
represents the following tree, which have 4 terminal and 2 internal  
nodes.

+------A
|
|   +---B
|   |
+---+
|   |
|   +---C
|
+-----D

The two internal nodes have no label and referred as (Node:43c98a8)
(Node:43c91f0) in the representation.

-- 
Tomoaki NISHIYAMA

Advanced Science Research Center,
Kanazawa University,
13-1 Takara-machi,
Kanazawa, 920-0934, Japan


On 2009/01/22, at 8:11, K. Patil wrote:

> Hi,
>
> I was trying some simple methods for the Newick tree. I did the  
> following,
>
>> t = Bio::Newick.new("(A,(B,C),D)")
>> t.tree.nodes
> =>[(Node:43c98a8), (Node:"A"), (Node:"B"), (Node:"D"), (Node:43c91f0),
> (Node:"C")]
>> t.tree.number_of_nodes
> => 6
>
> Am I doing something wrong? I am using bioruby version 1.2.1 in  
> ruby 1.8.
> Any suggestions are welcome.
>
> Cheers,
> Kaustubh
>
>
>
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>



From donttrustben at gmail.com  Thu Jan 22 02:39:50 2009
From: donttrustben at gmail.com (Ben Woodcroft)
Date: Thu, 22 Jan 2009 12:39:50 +1000
Subject: [BioRuby] newick tree
In-Reply-To: <F70C4471-5F9C-4756-85F1-D48698F24F18@kenroku.kanazawa-u.ac.jp>
References: <27715.84.58.197.42.1232579513.squirrel@webmail.science.uva.nl>
	<F70C4471-5F9C-4756-85F1-D48698F24F18@kenroku.kanazawa-u.ac.jp>
Message-ID: <bb2b67d00901211839w3dda10fev63854fd1e5ee72bd@mail.gmail.com>

I had the same problem - managed to solve it, but it wasn't the best. It
used something like this:

count = 0
tree.each_node do |node|
  #I get internal nodes here - not sure how else to skip
  next if node.name.nil? or node.name.length == 0

  count += 1
end
count

2009/1/22 Tomoaki NISHIYAMA <tomoakin at kenroku.kanazawa-u.ac.jp>

> Hi,
>
> I have not used the Newick feature of bioruby but the behavior
> you showed seems doing quite right.
> What is your expectation? Or, what do you want?
>
> (A,(B,C),D)
> represents the following tree, which have 4 terminal and 2 internal nodes.
>
> +------A
> |
> |   +---B
> |   |
> +---+
> |   |
> |   +---C
> |
> +-----D
>
> The two internal nodes have no label and referred as (Node:43c98a8)
> (Node:43c91f0) in the representation.
>
> --
> Tomoaki NISHIYAMA
>
> Advanced Science Research Center,
> Kanazawa University,
> 13-1 Takara-machi,
> Kanazawa, 920-0934, Japan
>
>
>
> On 2009/01/22, at 8:11, K. Patil wrote:
>
>  Hi,
>>
>> I was trying some simple methods for the Newick tree. I did the following,
>>
>>  t = Bio::Newick.new("(A,(B,C),D)")
>>> t.tree.nodes
>>>
>> =>[(Node:43c98a8), (Node:"A"), (Node:"B"), (Node:"D"), (Node:43c91f0),
>> (Node:"C")]
>>
>>> t.tree.number_of_nodes
>>>
>> => 6
>>
>> Am I doing something wrong? I am using bioruby version 1.2.1 in ruby 1.8.
>> Any suggestions are welcome.
>>
>> Cheers,
>> Kaustubh
>>
>>
>>
>> _______________________________________________
>> BioRuby mailing list
>> BioRuby at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioruby
>>
>>
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>



-- 
FYI: My email addresses at unimelb, uq and gmail all redirect to the same
place.


From ngoto at gen-info.osaka-u.ac.jp  Thu Jan 22 04:56:18 2009
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Thu, 22 Jan 2009 13:56:18 +0900
Subject: [BioRuby] newick tree
In-Reply-To: <bb2b67d00901211839w3dda10fev63854fd1e5ee72bd@mail.gmail.com>
References: <27715.84.58.197.42.1232579513.squirrel@webmail.science.uva.nl>
	<F70C4471-5F9C-4756-85F1-D48698F24F18@kenroku.kanazawa-u.ac.jp>
	<bb2b67d00901211839w3dda10fev63854fd1e5ee72bd@mail.gmail.com>
Message-ID: <20090122045618.E8CF01CBC4FD@idnmail.gen-info.osaka-u.ac.jp>

Hi,

If you want only leaf nodes (= OTUs in normal phylogenetic tree),

  t = Bio::Newick.new("(A,(B,C),D)")
  tree = t.tree
  tree.leaves
  # => [(Node:"B"), (Node:"D"), (Node:"C"), (Node:"A")]

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org

On Thu, 22 Jan 2009 12:39:50 +1000
Ben Woodcroft <donttrustben at gmail.com> wrote:

> I had the same problem - managed to solve it, but it wasn't the best. It
> used something like this:
> 
> count = 0
> tree.each_node do |node|
>   #I get internal nodes here - not sure how else to skip
>   next if node.name.nil? or node.name.length == 0
> 
>   count += 1
> end
> count
> 
> 2009/1/22 Tomoaki NISHIYAMA <tomoakin at kenroku.kanazawa-u.ac.jp>
> 
> > Hi,
> >
> > I have not used the Newick feature of bioruby but the behavior
> > you showed seems doing quite right.
> > What is your expectation? Or, what do you want?
> >
> > (A,(B,C),D)
> > represents the following tree, which have 4 terminal and 2 internal nodes.
> >
> > +------A
> > |
> > |   +---B
> > |   |
> > +---+
> > |   |
> > |   +---C
> > |
> > +-----D
> >
> > The two internal nodes have no label and referred as (Node:43c98a8)
> > (Node:43c91f0) in the representation.
> >
> > --
> > Tomoaki NISHIYAMA
> >
> > Advanced Science Research Center,
> > Kanazawa University,
> > 13-1 Takara-machi,
> > Kanazawa, 920-0934, Japan
> >
> >
> >
> > On 2009/01/22, at 8:11, K. Patil wrote:
> >
> >  Hi,
> >>
> >> I was trying some simple methods for the Newick tree. I did the following,
> >>
> >>  t = Bio::Newick.new("(A,(B,C),D)")
> >>> t.tree.nodes
> >>>
> >> =>[(Node:43c98a8), (Node:"A"), (Node:"B"), (Node:"D"), (Node:43c91f0),
> >> (Node:"C")]
> >>
> >>> t.tree.number_of_nodes
> >>>
> >> => 6
> >>
> >> Am I doing something wrong? I am using bioruby version 1.2.1 in ruby 1.8.
> >> Any suggestions are welcome.
> >>
> >> Cheers,
> >> Kaustubh
> >>
> >>
> >>
> >> _______________________________________________
> >> BioRuby mailing list
> >> BioRuby at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioruby
> >>
> >>
> > _______________________________________________
> > BioRuby mailing list
> > BioRuby at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioruby
> >
> 
> 
> 
> -- 
> FYI: My email addresses at unimelb, uq and gmail all redirect to the same
> place.
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby




From pjotr.public14 at thebird.nl  Fri Jan 30 11:21:57 2009
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Fri, 30 Jan 2009 12:21:57 +0100
Subject: [BioRuby] FOSDEM
Message-ID: <20090130112157.GA15524@thebird.nl>

Anyone coming to FOSDEM, Brussels 7+8 Feb? There is a nice Ruby track.

Pj.


From ngoto at gen-info.osaka-u.ac.jp  Fri Jan 30 16:00:16 2009
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Sat, 31 Jan 2009 01:00:16 +0900
Subject: [BioRuby] BioRuby 1.3.0 will soon be released
Message-ID: <20090130160016.739601CBC443@idnmail.gen-info.osaka-u.ac.jp>

Hi all,

I will release BioRuby 1.3.0 soon. The release of 1.3.0 have been
decided by three BioRuby developers in Japan (Toshiaki Katayama,
Mitsuteru Nakao, and me).

Now, It's time for a code freeze, except bug fix and documentation.

You can download preview version from the Github repository.
Please try it out and report any problems.

http://github.com/bioruby/bioruby/tree/master

Gem is also available from Github (but currenlty a little bit older
than git head).

Thanks,

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org


From andrew.j.grimm at gmail.com  Fri Jan 30 22:41:35 2009
From: andrew.j.grimm at gmail.com (Andrew Grimm)
Date: Sat, 31 Jan 2009 09:41:35 +1100
Subject: [BioRuby] Bioruby home page
Message-ID: <b9140daa0901301441x7acd3643t7dbab13a73178ff6@mail.gmail.com>

For the next bioruby release, is the documentation going to say that the
home web site is bioruby.org, or bioruby.open-bio.org?

Andrew