From pjotr2006 at thebird.nl  Mon Jul  3 16:07:17 2006
From: pjotr2006 at thebird.nl (Pjotr Prins)
Date: Mon, 3 Jul 2006 22:07:17 +0200
Subject: [BioRuby] [OBF-developers] Call For Birds of a Feather
	Suggestions
In-Reply-To: <44A9107D.2050304@duke.edu>
References: <44A9107D.2050304@duke.edu>
Message-ID: <20060703200717.GA14558@thebird.nl>

Hi Daren,

Assuming either Toshiaka or I make it - it appears the majority of
flights is still going with Varig - we'll do a BoF on '(Bio)Ruby in
Science'.

Pj.

On Mon, Jul 03, 2006 at 08:41:33AM -0400, Darin London wrote:
> The BOSC organizing comittee is currently seeking suggestions for Birds
> of a Feather meeting ideas. Birds of a Feather meetings are one of the
> more popular activities at BOSC, occurring at the end of each days
> session. These are free-form meetings organized by the attendees
> themselves to discuss one or a few topics of interest in greater detail.
> BOF?s have been formed to allow developers and users of individual OBF
> software to meet each other face-to-face to discuss the project, or to
> discuss completely new ideas, and even start new software development
> projects. These meetings offer a unique opportunity for individuals to
> explore more about the activities of the various Open Source Projects,
> and, in some cases, even take an active role influencing the future of
> Open Source Software development. If you would like to create a BOF,
> just sign up for a wiki account, login, and edit the <a
> href="http://www.open-bio.org/wiki/BOSC_2006/Birds-of-a-Feather">BOSC
> 2006 Birds of a Feather page</a>.
> _______________________________________________
> obf-developers mailing list
> obf-developers at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/obf-developers

From daniel.amelang at gmail.com  Thu Jul  6 06:11:20 2006
From: daniel.amelang at gmail.com (Daniel Amelang)
Date: Thu, 6 Jul 2006 03:11:20 -0700
Subject: [BioRuby] Bio::Tree::Newick class
Message-ID: <a65ae5c90607060311j7ac47575n142fb82b1a715cff@mail.gmail.com>

I'm attaching a zipped tar file with a Bio::Tree::Newick class I wrote
a year and half ago (I hope the attachment goes through). It provides
a newick tree parser, a simple API for manipulating trees, and a
newick tree output generator. It could easily be refactored into a
more general tree library, if the need arose. I've documented the code
quite a bit (although it doesn't have a users manual) and it comes
with a test/unit fixture.

Sense the time I wrote this, I've left the field of bioinformatics and
no longer have any use for it or desire to maintain it. I'm hoping it
might come in handy for someone here. I don't have the time to do the
work to fully integrate it into bioruby, although someone interested
in doing so has contacted me, so hopefully that will happen someday.

- Dan Amelang


Here are some quick examples of it's use:

# parse returns an array of tree objects from a filename or IO object
trees = Bio::Tree::Newick::parse("trees.newick")
tree = trees.first
puts tree.children.size
tree.each_child do |child|
  puts child.distance
end
tree.each_leaf do |leaf|
  ...
end
tree.leaves
node = tree[2][1]
node.is_root?
node.children
node.descendents
node.ancestors[1]
node[3][2].sequence_name

# create a whole new tree
tree = Bio::Tree::Newick.new
tree << Bio::Tree::Newick::LeafNode("turtle")
tree << Bio::Tree::Newick::InnerNode
tree[1].distance = 0.12
tree[1] << Bio::Tree::Newick::LeafNode("panda", nil, 0.02)

# write out the tree (using the to_s method)
puts tree

#produces:

(
  turtle,
  (
    panda:0.02,
  ):0.12
);

From ngoto at gen-info.osaka-u.ac.jp  Sun Jul  9 01:54:55 2006
From: ngoto at gen-info.osaka-u.ac.jp (GOTO Naohisa)
Date: Sun, 9 Jul 2006 14:54:55 +0900
Subject: [BioRuby] Bio::Tree::Newick class
In-Reply-To: <a65ae5c90607060311j7ac47575n142fb82b1a715cff@mail.gmail.com>
References: <a65ae5c90607060311j7ac47575n142fb82b1a715cff@mail.gmail.com>
Message-ID: <200607090555.k695t3uQ017488@idns103.gen-info.osaka-u.ac.jp>

Dear Dan,

On Thu, 6 Jul 2006 03:11:20 -0700
"Daniel Amelang" <daniel.amelang at gmail.com> wrote:

> I'm attaching a zipped tar file with a Bio::Tree::Newick class I wrote
> a year and half ago (I hope the attachment goes through). It provides
> a newick tree parser, a simple API for manipulating trees, and a
> newick tree output generator. It could easily be refactored into a
> more general tree library, if the need arose. I've documented the code
> quite a bit (although it doesn't have a users manual) and it comes
> with a test/unit fixture.

I'm interested in your works, but, unfortunately, the attached file
is lost. Would you please resend to staff at bioruby.org ?

Sincerely,

-- 
Naohisa GOTO
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
Department of Genome Informatics, Genome Information Research Center,
Research Institute for Microbial Diseases, Osaka University, Japan

From pjotr2006 at thebird.nl  Sun Jul 23 06:02:14 2006
From: pjotr2006 at thebird.nl (Pjotr Prins)
Date: Sun, 23 Jul 2006 12:02:14 +0200
Subject: [BioRuby] Bio-projects comparison
Message-ID: <20060723100214.GA21384@thebird.nl>

Hi,

I have started a comparison of BioRuby, Bioperl, Biopython and
Bioconductor at:

http://sciruby.codeforpeople.com/sr.cgi/BioProjects

If you are aware of functional differences between these tool sets
please send me an E-mail. I hope it becomes a valuable resource for
bio-informaticians looking to solve a problem.

Pj.

From mmhohman at northwestern.edu  Sun Jul 23 10:47:08 2006
From: mmhohman at northwestern.edu (Moses M. Hohman)
Date: Sun, 23 Jul 2006 09:47:08 -0500
Subject: [BioRuby] Bio-projects comparison
In-Reply-To: <20060723100214.GA21384@thebird.nl>
References: <20060723100214.GA21384@thebird.nl>
Message-ID: <665D5052-80BE-4963-B425-F664B6FD2967@northwestern.edu>

Hi Pjotr,

That sounds like a good plan. Along these lines . . . I had an idea  
the other day, and I'm not sure how exactly it would work, but I  
thought I'd throw it out there. One thing that bothers me about the  
open bio software libraries is that they are all or nothing. That is,  
you can download and install all of the pieces of bioperl or bioruby,  
or install none of them.

If I just needed sequence manipulation, I would still have to install  
the parts of bioruby that handle graphs, parsing pubmed entries, etc.  
This becomes problematic mostly because I might want some parts of a  
given open bio project and not others. I might want the sequence  
manipulation stuff, but might want to be able to have a choice among  
various restriction site computation libraries (as a random example).  
Even more tricky, I might be happy with the bioruby restriction site  
library but want different sequence manipulation functionality.  
However, for all of the open bio projects, it seems like whatever  
happens to be the first acceptable solution to a problem remains part  
of the software forever.

It would be much nicer if I could just install the sequence  
manipulation bioruby gem, and then install my restriction site gem of  
choice, or vice versa. And because rubygems can declare their  
dependencies, all I would have to know is that I wanted to install a  
particular restriction site library, and the basic sequence  
manipulation stuff it depended on would be autoinstalled. The  
opposite direction would be more complicated, but I'm pretty sure we  
could figure this out, and I think Ruby offers us particular power  
and flexibility for doing this over other dynamic languages. I think  
this kind of approach could eventually make bioruby a much more  
useful tool.

I don't know, what do folks think? Worth it/not worth it? Too complex?

Moses

On Jul 23, 2006, at 5:02 AM, Pjotr Prins wrote:

> Hi,
>
> I have started a comparison of BioRuby, Bioperl, Biopython and
> Bioconductor at:
>
> http://sciruby.codeforpeople.com/sr.cgi/BioProjects
>
> If you are aware of functional differences between these tool sets
> please send me an E-mail. I hope it becomes a valuable resource for
> bio-informaticians looking to solve a problem.
>
> Pj.
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>


From pjotr2006 at thebird.nl  Mon Jul  3 20:07:17 2006
From: pjotr2006 at thebird.nl (Pjotr Prins)
Date: Mon, 3 Jul 2006 22:07:17 +0200
Subject: [BioRuby] [OBF-developers] Call For Birds of a Feather
	Suggestions
In-Reply-To: <44A9107D.2050304@duke.edu>
References: <44A9107D.2050304@duke.edu>
Message-ID: <20060703200717.GA14558@thebird.nl>

Hi Daren,

Assuming either Toshiaka or I make it - it appears the majority of
flights is still going with Varig - we'll do a BoF on '(Bio)Ruby in
Science'.

Pj.

On Mon, Jul 03, 2006 at 08:41:33AM -0400, Darin London wrote:
> The BOSC organizing comittee is currently seeking suggestions for Birds
> of a Feather meeting ideas. Birds of a Feather meetings are one of the
> more popular activities at BOSC, occurring at the end of each days
> session. These are free-form meetings organized by the attendees
> themselves to discuss one or a few topics of interest in greater detail.
> BOF?s have been formed to allow developers and users of individual OBF
> software to meet each other face-to-face to discuss the project, or to
> discuss completely new ideas, and even start new software development
> projects. These meetings offer a unique opportunity for individuals to
> explore more about the activities of the various Open Source Projects,
> and, in some cases, even take an active role influencing the future of
> Open Source Software development. If you would like to create a BOF,
> just sign up for a wiki account, login, and edit the <a
> href="http://www.open-bio.org/wiki/BOSC_2006/Birds-of-a-Feather">BOSC
> 2006 Birds of a Feather page</a>.
> _______________________________________________
> obf-developers mailing list
> obf-developers at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/obf-developers


From daniel.amelang at gmail.com  Thu Jul  6 10:11:20 2006
From: daniel.amelang at gmail.com (Daniel Amelang)
Date: Thu, 6 Jul 2006 03:11:20 -0700
Subject: [BioRuby] Bio::Tree::Newick class
Message-ID: <a65ae5c90607060311j7ac47575n142fb82b1a715cff@mail.gmail.com>

I'm attaching a zipped tar file with a Bio::Tree::Newick class I wrote
a year and half ago (I hope the attachment goes through). It provides
a newick tree parser, a simple API for manipulating trees, and a
newick tree output generator. It could easily be refactored into a
more general tree library, if the need arose. I've documented the code
quite a bit (although it doesn't have a users manual) and it comes
with a test/unit fixture.

Sense the time I wrote this, I've left the field of bioinformatics and
no longer have any use for it or desire to maintain it. I'm hoping it
might come in handy for someone here. I don't have the time to do the
work to fully integrate it into bioruby, although someone interested
in doing so has contacted me, so hopefully that will happen someday.

- Dan Amelang


Here are some quick examples of it's use:

# parse returns an array of tree objects from a filename or IO object
trees = Bio::Tree::Newick::parse("trees.newick")
tree = trees.first
puts tree.children.size
tree.each_child do |child|
  puts child.distance
end
tree.each_leaf do |leaf|
  ...
end
tree.leaves
node = tree[2][1]
node.is_root?
node.children
node.descendents
node.ancestors[1]
node[3][2].sequence_name

# create a whole new tree
tree = Bio::Tree::Newick.new
tree << Bio::Tree::Newick::LeafNode("turtle")
tree << Bio::Tree::Newick::InnerNode
tree[1].distance = 0.12
tree[1] << Bio::Tree::Newick::LeafNode("panda", nil, 0.02)

# write out the tree (using the to_s method)
puts tree

#produces:

(
  turtle,
  (
    panda:0.02,
  ):0.12
);

From ngoto at gen-info.osaka-u.ac.jp  Sun Jul  9 05:54:55 2006
From: ngoto at gen-info.osaka-u.ac.jp (GOTO Naohisa)
Date: Sun, 9 Jul 2006 14:54:55 +0900
Subject: [BioRuby] Bio::Tree::Newick class
In-Reply-To: <a65ae5c90607060311j7ac47575n142fb82b1a715cff@mail.gmail.com>
References: <a65ae5c90607060311j7ac47575n142fb82b1a715cff@mail.gmail.com>
Message-ID: <200607090555.k695t3uQ017488@idns103.gen-info.osaka-u.ac.jp>

Dear Dan,

On Thu, 6 Jul 2006 03:11:20 -0700
"Daniel Amelang" <daniel.amelang at gmail.com> wrote:

> I'm attaching a zipped tar file with a Bio::Tree::Newick class I wrote
> a year and half ago (I hope the attachment goes through). It provides
> a newick tree parser, a simple API for manipulating trees, and a
> newick tree output generator. It could easily be refactored into a
> more general tree library, if the need arose. I've documented the code
> quite a bit (although it doesn't have a users manual) and it comes
> with a test/unit fixture.

I'm interested in your works, but, unfortunately, the attached file
is lost. Would you please resend to staff at bioruby.org ?

Sincerely,

-- 
Naohisa GOTO
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
Department of Genome Informatics, Genome Information Research Center,
Research Institute for Microbial Diseases, Osaka University, Japan


From pjotr2006 at thebird.nl  Sun Jul 23 10:02:14 2006
From: pjotr2006 at thebird.nl (Pjotr Prins)
Date: Sun, 23 Jul 2006 12:02:14 +0200
Subject: [BioRuby] Bio-projects comparison
Message-ID: <20060723100214.GA21384@thebird.nl>

Hi,

I have started a comparison of BioRuby, Bioperl, Biopython and
Bioconductor at:

http://sciruby.codeforpeople.com/sr.cgi/BioProjects

If you are aware of functional differences between these tool sets
please send me an E-mail. I hope it becomes a valuable resource for
bio-informaticians looking to solve a problem.

Pj.


From mmhohman at northwestern.edu  Sun Jul 23 14:47:08 2006
From: mmhohman at northwestern.edu (Moses M. Hohman)
Date: Sun, 23 Jul 2006 09:47:08 -0500
Subject: [BioRuby] Bio-projects comparison
In-Reply-To: <20060723100214.GA21384@thebird.nl>
References: <20060723100214.GA21384@thebird.nl>
Message-ID: <665D5052-80BE-4963-B425-F664B6FD2967@northwestern.edu>

Hi Pjotr,

That sounds like a good plan. Along these lines . . . I had an idea  
the other day, and I'm not sure how exactly it would work, but I  
thought I'd throw it out there. One thing that bothers me about the  
open bio software libraries is that they are all or nothing. That is,  
you can download and install all of the pieces of bioperl or bioruby,  
or install none of them.

If I just needed sequence manipulation, I would still have to install  
the parts of bioruby that handle graphs, parsing pubmed entries, etc.  
This becomes problematic mostly because I might want some parts of a  
given open bio project and not others. I might want the sequence  
manipulation stuff, but might want to be able to have a choice among  
various restriction site computation libraries (as a random example).  
Even more tricky, I might be happy with the bioruby restriction site  
library but want different sequence manipulation functionality.  
However, for all of the open bio projects, it seems like whatever  
happens to be the first acceptable solution to a problem remains part  
of the software forever.

It would be much nicer if I could just install the sequence  
manipulation bioruby gem, and then install my restriction site gem of  
choice, or vice versa. And because rubygems can declare their  
dependencies, all I would have to know is that I wanted to install a  
particular restriction site library, and the basic sequence  
manipulation stuff it depended on would be autoinstalled. The  
opposite direction would be more complicated, but I'm pretty sure we  
could figure this out, and I think Ruby offers us particular power  
and flexibility for doing this over other dynamic languages. I think  
this kind of approach could eventually make bioruby a much more  
useful tool.

I don't know, what do folks think? Worth it/not worth it? Too complex?

Moses

On Jul 23, 2006, at 5:02 AM, Pjotr Prins wrote:

> Hi,
>
> I have started a comparison of BioRuby, Bioperl, Biopython and
> Bioconductor at:
>
> http://sciruby.codeforpeople.com/sr.cgi/BioProjects
>
> If you are aware of functional differences between these tool sets
> please send me an E-mail. I hope it becomes a valuable resource for
> bio-informaticians looking to solve a problem.
>
> Pj.
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>