From mail at michaelbarton.me.uk  Sat Feb  2 16:34:30 2013
From: mail at michaelbarton.me.uk (Michael Barton)
Date: Sat, 2 Feb 2013 16:34:30 -0500
Subject: [BioRuby] Genomer: a ruby project to simplify genome finishing
Message-ID: <20130202213430.GA1168@bartonh-mbp-01>

Hi Everyone,

I've been working a sequencing microbial genomes during my current post doc
position. I've combined many of the ruby scripts I was using into a single tool
called "genomer" which might be of interest to other bioinformaticians working
in the same area.

I used this tool to simplify the smaller, mundane tasks associated with a
genome. For instance moving contigs and associated annotations around,
generating the required files to submit to GenBank, and generating summaries of
the genome scaffold.

I created a small screencast for anyone who is interested in finding out more:
http://youtu.be/HfsdJOELFjs?hd=1

I wrote this tool to satisfy my own needs and use genomer extensively for the
microbial genome projects in our lab. My GNU Makefile (http://bit.ly/WMKlCZ)
from a P. fluorescens project illustrates how genomer combined with GenBank's
tbl2asn can be used to build the all files required for genome submission.

Hopefully genomer may be useful to other bioinformaticians and simplify the
steps required to finish and submit a genome.

Thanks

Michael Barton

From francesco.strozzi at gmail.com  Mon Feb  4 05:51:28 2013
From: francesco.strozzi at gmail.com (Francesco Strozzi)
Date: Mon, 4 Feb 2013 11:51:28 +0100
Subject: [BioRuby] Genomer: a ruby project to simplify genome finishing
In-Reply-To: <20130202213430.GA1168@bartonh-mbp-01>
References: <20130202213430.GA1168@bartonh-mbp-01>
Message-ID: <CACtet2Tfqpbmo7vg_hKYqc1q7_qWSbh0ds3xUr_Kzc5sdHSwcg@mail.gmail.com>

Hi Michael,
thanks for that! I am working on genome assembly as well from time to
time so I will try Genomer.
Anyway cool idea to create a screen cast!

Cheers

On Sat, Feb 2, 2013 at 10:34 PM, Michael Barton
<mail at michaelbarton.me.uk> wrote:
> Hi Everyone,
>
> I've been working a sequencing microbial genomes during my current post doc
> position. I've combined many of the ruby scripts I was using into a single tool
> called "genomer" which might be of interest to other bioinformaticians working
> in the same area.
>
> I used this tool to simplify the smaller, mundane tasks associated with a
> genome. For instance moving contigs and associated annotations around,
> generating the required files to submit to GenBank, and generating summaries of
> the genome scaffold.
>
> I created a small screencast for anyone who is interested in finding out more:
> http://youtu.be/HfsdJOELFjs?hd=1
>
> I wrote this tool to satisfy my own needs and use genomer extensively for the
> microbial genome projects in our lab. My GNU Makefile (http://bit.ly/WMKlCZ)
> from a P. fluorescens project illustrates how genomer combined with GenBank's
> tbl2asn can be used to build the all files required for genome submission.
>
> Hopefully genomer may be useful to other bioinformaticians and simplify the
> steps required to finish and submit a genome.
>
> Thanks
>
> Michael Barton
>
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>



-- 

Francesco

From ngoto at gen-info.osaka-u.ac.jp  Mon Feb  4 06:35:18 2013
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Mon, 4 Feb 2013 20:35:18 +0900
Subject: [BioRuby] Fw: Can any one help me in installing BIORUBY on Rails
Message-ID: <201302041144.r14BiCaK010462@portal.open-bio.org>

Hi all,

I've recieved the following email, but I'm not familiar with Rails.
Please could someone anwser the question?
Thanks,
Naohisa Goto
ng at bioruby.org

Begin forwarded message:

From: <************@gmail.com>
To: staff at bioruby.org
Subject: Can any one help me in installing BIORUBY on Rails


Dear Staffs,
Please provide me information on step by step installation of Bioruby on
Rails
Im using Windows PC
Ruby,BioRuby and Rails installed.
Kindly please reply.

From mail at michaelbarton.me.uk  Mon Feb  4 10:26:46 2013
From: mail at michaelbarton.me.uk (Michael Barton)
Date: Mon, 4 Feb 2013 10:26:46 -0500
Subject: [BioRuby] Genomer: a ruby project to simplify genome finishing
In-Reply-To: <20130202213430.GA1168@bartonh-mbp-01>
References: <20130202213430.GA1168@bartonh-mbp-01>
Message-ID: <20130204152646.GD5528@bartonh-mbp-01.uanet.edu>

I have created an additional screencast to follow up. This provides a more
concrete example of using genomer to generate the files required to submit a
genome project to GenBank.

http://www.youtube.com/watch?v=jVn62pMnIRA&hd=1

Thanks

Mike

On Sat, Feb 02, 2013 at 04:34:30PM -0500, Michael Barton wrote:

> Hi Everyone,
>
> I've been working a sequencing microbial genomes during my current
> post doc position. I've combined many of the ruby scripts I was using
> into a single tool called "genomer" which might be of interest to
> other bioinformaticians working in the same area.
>
> I used this tool to simplify the smaller, mundane tasks associated
> with a genome. For instance moving contigs and associated annotations
> around, generating the required files to submit to GenBank, and
> generating summaries of the genome scaffold.
>
> I created a small screencast for anyone who is interested in finding
> out more: http://youtu.be/HfsdJOELFjs?hd=1
>
> I wrote this tool to satisfy my own needs and use genomer extensively
> for the microbial genome projects in our lab. My GNU Makefile
> (http://bit.ly/WMKlCZ) from a P. fluorescens project illustrates how
> genomer combined with GenBank's tbl2asn can be used to build the all
> files required for genome submission.
>
> Hopefully genomer may be useful to other bioinformaticians and
> simplify the steps required to finish and submit a genome.
>
> Thanks
>
> Michael Barton



From pjotr.public14 at thebird.nl  Tue Feb  5 02:22:14 2013
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Tue, 5 Feb 2013 08:22:14 +0100
Subject: [BioRuby] biogems
Message-ID: <20130205072214.GB3105@thebird.nl>

rubygems are working again :)

From ngoto at gen-info.osaka-u.ac.jp  Tue Feb  5 04:48:51 2013
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Tue, 5 Feb 2013 18:48:51 +0900
Subject: [BioRuby] Fw: books to learn Ruby
Message-ID: <201302050948.r159mrEc032068@portal.open-bio.org>

Hi all,

I just find that I've recieved the following mail in may mailer's
spam folder. Sorry for responsing too late.

Unfortunately, I know little about books written in English about
learning Ruby. Could someone please recommend some books?

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

Begin forwarded message:

Date: Sun, 20 Jan 2013 13:31:29 +0530
From: <**********@gmail.com>
To: staff at bioruby.org
Subject: Please Help


Dear Ruby Admin,
I love to learn RUBY..I'm novice,
Basically from a Bioinformatics Background.

I wanted to know few things on Ruby..
1.How should I start learning RUBY, Any basic books you can suggest me?
2.How do I install BioRuby in my Windows PC ?

Please help me !
Thanks
---------------------------------------------------

From john.woods at marcottelab.org  Tue Feb  5 08:50:39 2013
From: john.woods at marcottelab.org (John Woods)
Date: Tue, 5 Feb 2013 07:50:39 -0600
Subject: [BioRuby] Fw: books to learn Ruby
In-Reply-To: <201302050948.r159mrEc032068@portal.open-bio.org>
References: <201302050948.r159mrEc032068@portal.open-bio.org>
Message-ID: <CAPkCRRvJaS4O8JEWU-mLdufOR7tvaNi9ybFW9LRUZeXOserJQw@mail.gmail.com>

Well, the author appears not to be a native English speaker, but normally
I advocate Why's Poignant Guide. The feedback I've gotten from
international students, however, suggests that this book is complicated for
people who aren't native speakers.

In that case, probably the O'Reilly stuff.

John
SciRuby Project

On Tuesday, February 5, 2013, Naohisa GOTO wrote:

> Hi all,
>
> I just find that I've recieved the following mail in may mailer's
> spam folder. Sorry for responsing too late.
>
> Unfortunately, I know little about books written in English about
> learning Ruby. Could someone please recommend some books?
>
> Naohisa Goto
> ng at bioruby.org <javascript:;> / ngoto at gen-info.osaka-u.ac.jp<javascript:;>
>
> Begin forwarded message:
>
> Date: Sun, 20 Jan 2013 13:31:29 +0530
> From: <**********@gmail.com>
> To: staff at bioruby.org <javascript:;>
> Subject: Please Help
>
>
> Dear Ruby Admin,
> I love to learn RUBY..I'm novice,
> Basically from a Bioinformatics Background.
>
> I wanted to know few things on Ruby..
> 1.How should I start learning RUBY, Any basic books you can suggest me?
> 2.How do I install BioRuby in my Windows PC ?
>
> Please help me !
> Thanks
> ---------------------------------------------------
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org <javascript:;>
> http://lists.open-bio.org/mailman/listinfo/bioruby
>

From rob.syme at gmail.com  Tue Feb  5 08:58:41 2013
From: rob.syme at gmail.com (Rob Syme)
Date: Tue, 5 Feb 2013 21:58:41 +0800
Subject: [BioRuby] Fw: books to learn Ruby
In-Reply-To: <201302050948.r159mrEc032068@portal.open-bio.org>
References: <201302050948.r159mrEc032068@portal.open-bio.org>
Message-ID: <CAEf4xgcJOhyscGE5oVvUzEpYr4r2MW3f8CrjwoTgUoDjM1LSOw@mail.gmail.com>

There is an good list of (free) books up at
http://stackoverflow.com/questions/194812/list-of-freely-available-programming-books

The ruby section includes two that I would recommend,
http://ruby.learncodethehardway.org/book/
and of course _why's poignant guide, which as John points out, might not be
as helpful in this instance
http://mislav.uniqpath.com/poignant-guide/

I'm sure there is enough there to get the student started.

-r

Hi all,

I just find that I've recieved the following mail in may mailer's
spam folder. Sorry for responsing too late.

Unfortunately, I know little about books written in English about
learning Ruby. Could someone please recommend some books?

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

Begin forwarded message:

Date: Sun, 20 Jan 2013 13:31:29 +0530
From: <**********@gmail.com>
To: staff at bioruby.org
Subject: Please Help

Dear Ruby Admin,
I love to learn RUBY..I'm novice,
Basically from a Bioinformatics Background.

I wanted to know few things on Ruby..
1.How should I start learning RUBY, Any basic books you can suggest me?
2.How do I install BioRuby in my Windows PC ?

Please help me !
Thanks
---------------------------------------------------
_______________________________________________
BioRuby Project - http://www.bioruby.org/
BioRuby mailing list
BioRuby at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioruby

From marian.povolny at gmail.com  Tue Feb  5 09:46:05 2013
From: marian.povolny at gmail.com (Marjan Povolni)
Date: Tue, 5 Feb 2013 15:46:05 +0100
Subject: [BioRuby] Fw: books to learn Ruby
In-Reply-To: <201302050948.r159mrEc032068@portal.open-bio.org>
References: <201302050948.r159mrEc032068@portal.open-bio.org>
Message-ID: <CADKP5Ck+LZdpTySKso5Bnxb4orie3fwKTjGicVSbKUTzf0Xc0w@mail.gmail.com>

Hi,

I used "The Well-Grounded Rubyist" by David A. Black. I don't remember
anymore why I liked it, but I did. Starting with a tutorial from this site
might be also a good idea, depends on the person:
http://www.ruby-lang.org/en/documentation/

To me, the Ruby Koans (http://rubykoans.com/windows) provided a nice
introduction to the language in a short time. There are also instructions
on how to install Ruby on windows on that website.

--
Marjan

On Tue, Feb 5, 2013 at 10:48 AM, Naohisa GOTO
<ngoto at gen-info.osaka-u.ac.jp>wrote:

> Hi all,
>
> I just find that I've recieved the following mail in may mailer's
> spam folder. Sorry for responsing too late.
>
> Unfortunately, I know little about books written in English about
> learning Ruby. Could someone please recommend some books?
>
> Naohisa Goto
> ng at bioruby.org / ngoto at gen-info.osaka-u.ac.jp
>
> Begin forwarded message:
>
> Date: Sun, 20 Jan 2013 13:31:29 +0530
> From: <**********@gmail.com>
> To: staff at bioruby.org
> Subject: Please Help
>
>
> Dear Ruby Admin,
> I love to learn RUBY..I'm novice,
> Basically from a Bioinformatics Background.
>
> I wanted to know few things on Ruby..
> 1.How should I start learning RUBY, Any basic books you can suggest me?
> 2.How do I install BioRuby in my Windows PC ?
>
> Please help me !
> Thanks
> ---------------------------------------------------
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>

From mphoeppner at gmail.com  Tue Feb  5 09:48:46 2013
From: mphoeppner at gmail.com (Marc Hoeppner)
Date: Tue, 05 Feb 2013 15:48:46 +0100
Subject: [BioRuby] Fwd: Re:  Fw: books to learn Ruby
Message-ID: <51111BCE.2070901@gmail.com>

Hi,

http://www.amazon.com/Programming-Ruby-1-9-Pragmatic-Programmers/dp/1934356085/ref=sr_1_1?ie=UTF8&qid=1360057937&sr=8-1&keywords=ruby+pragmatic

The pragmatic programmers guide, I think, is one of the better
introductions, as they also deal with a lot of general things about
writing good code. Then there is a load of decent-to-excellent tutorials
on the ruby website at http://www.ruby-lang.org/en/documentation/ . One
that I found useful to get started was this one:
http://pine.fm/LearnToProgram/

And the question about how to install Bioruby should be self-explanatory
once the basics about Ruby have been learned, I would think. Short
answer: It's a gem (a library, essentially), so googling for 'Ruby gems'
would be a good start.

Best,

/Marc
> Hi all,
>
> I just find that I've recieved the following mail in may mailer's
> spam folder. Sorry for responsing too late.
>
> Unfortunately, I know little about books written in English about
> learning Ruby. Could someone please recommend some books?
>
> Naohisa Goto
> ng at bioruby.org / ngoto at gen-info.osaka-u.ac.jp
>
> Begin forwarded message:
>
> Date: Sun, 20 Jan 2013 13:31:29 +0530
> From: <**********@gmail.com>
> To: staff at bioruby.org
> Subject: Please Help
>
>
> Dear Ruby Admin,
> I love to learn RUBY..I'm novice,
> Basically from a Bioinformatics Background.
>
> I wanted to know few things on Ruby..
> 1.How should I start learning RUBY, Any basic books you can suggest me?
> 2.How do I install BioRuby in my Windows PC ?
>
> Please help me !
> Thanks
> ---------------------------------------------------
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby


From jan.aerts at esat.kuleuven.be  Tue Feb  5 09:57:50 2013
From: jan.aerts at esat.kuleuven.be (Jan Aerts)
Date: Tue, 5 Feb 2013 15:57:50 +0100
Subject: [BioRuby] Fw: books to learn Ruby
In-Reply-To: <CADKP5Ck+LZdpTySKso5Bnxb4orie3fwKTjGicVSbKUTzf0Xc0w@mail.gmail.com>
References: <201302050948.r159mrEc032068@portal.open-bio.org>
	<CADKP5Ck+LZdpTySKso5Bnxb4orie3fwKTjGicVSbKUTzf0Xc0w@mail.gmail.com>
Message-ID: <CAErBFCyYRyGV3=i10=k8ZX9kRwK1TZhydN+TuXBKmD=MotfsAQ@mail.gmail.com>

I learned Ruby by reading a part-comic book over a Christmas holiday: why's
(poignant) guide to ruby. You can find it at
http://mislav.uniqpath.com/poignant-guide/book/

jan.


================================
Dr Jan Aerts
Assistant Professor
Faculty of Engineering - ESAT/SCD
University of Leuven
Kasteelpark Arenberg 10 bus 2446
3001 Leuven-Heverlee
ORCID: http://orcid.org/0000-0002-6416-2717
Tel: +32 16 321053
Fax: +32 16 321970


On 5 February 2013 15:46, Marjan Povolni <marian.povolny at gmail.com> wrote:

> Hi,
>
> I used "The Well-Grounded Rubyist" by David A. Black. I don't remember
> anymore why I liked it, but I did. Starting with a tutorial from this site
> might be also a good idea, depends on the person:
> http://www.ruby-lang.org/en/documentation/
>
> To me, the Ruby Koans (http://rubykoans.com/windows) provided a nice
> introduction to the language in a short time. There are also instructions
> on how to install Ruby on windows on that website.
>
> --
> Marjan
>
> On Tue, Feb 5, 2013 at 10:48 AM, Naohisa GOTO
> <ngoto at gen-info.osaka-u.ac.jp>wrote:
>
> > Hi all,
> >
> > I just find that I've recieved the following mail in may mailer's
> > spam folder. Sorry for responsing too late.
> >
> > Unfortunately, I know little about books written in English about
> > learning Ruby. Could someone please recommend some books?
> >
> > Naohisa Goto
> > ng at bioruby.org / ngoto at gen-info.osaka-u.ac.jp
> >
> > Begin forwarded message:
> >
> > Date: Sun, 20 Jan 2013 13:31:29 +0530
> > From: <**********@gmail.com>
> > To: staff at bioruby.org
> > Subject: Please Help
> >
> >
> > Dear Ruby Admin,
> > I love to learn RUBY..I'm novice,
> > Basically from a Bioinformatics Background.
> >
> > I wanted to know few things on Ruby..
> > 1.How should I start learning RUBY, Any basic books you can suggest me?
> > 2.How do I install BioRuby in my Windows PC ?
> >
> > Please help me !
> > Thanks
> > ---------------------------------------------------
> > _______________________________________________
> > BioRuby Project - http://www.bioruby.org/
> > BioRuby mailing list
> > BioRuby at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioruby
> >
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>

From pjotr.public14 at thebird.nl  Tue Feb  5 11:33:57 2013
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Tue, 5 Feb 2013 17:33:57 +0100
Subject: [BioRuby] Fw: books to learn Ruby
In-Reply-To: <CAErBFCyYRyGV3=i10=k8ZX9kRwK1TZhydN+TuXBKmD=MotfsAQ@mail.gmail.com>
References: <201302050948.r159mrEc032068@portal.open-bio.org>
	<CADKP5Ck+LZdpTySKso5Bnxb4orie3fwKTjGicVSbKUTzf0Xc0w@mail.gmail.com>
	<CAErBFCyYRyGV3=i10=k8ZX9kRwK1TZhydN+TuXBKmD=MotfsAQ@mail.gmail.com>
Message-ID: <20130205163357.GA5487@thebird.nl>

On Tue, Feb 05, 2013 at 03:57:50PM +0100, Jan Aerts wrote:
> I learned Ruby by reading a part-comic book over a Christmas holiday: why's
> (poignant) guide to ruby. You can find it at
> http://mislav.uniqpath.com/poignant-guide/book/


= Ruby just came to me =

Ruby just came to me
Like a sweet lover
She fits me
Even when unfaithful
I long for her

Behaviour driven, predictable, short and sweet
My Ruby, Ruby, Ruby

Ruby is not perfect
And I am not on Rails
Her dynamic typing can bite
But I love her for her Smalltalk message passing OOP
And I love her for her functional programming

Behaviour driven, predictable, short and sweet
My Ruby, Ruby, Ruby

I always come back to Ruby
And now on the JVM
She dances with Java, Scala, Clojure and soon node.jar
Ruby is still faithful to me
Always domain specific

Behaviour driven, predictable, short and sweet
My Ruby, Ruby, Ruby

Pj.


From pjotr.public14 at thebird.nl  Tue Feb  5 13:39:33 2013
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Tue, 5 Feb 2013 19:39:33 +0100
Subject: [BioRuby] JRuby and JS node.jar
Message-ID: <20130205183933.GA5880@thebird.nl>

I was wondering whether is any interest in combining Javascript with
BioRuby/BioJAVA on the JVM. There are two JS interpreters for the JVM
now, and am starting to lean the way of using Javascript for education
as JS is now a common language and it may be a way of getting (young)
people to try stuff in bioinformatics. I really like

  http://eloquentjavascript.net/

Writing a new BioJS may not be necessary with the good stuff we
already have.

Any thoughts?

Pj.

From pjotr.public14 at thebird.nl  Tue Feb  5 13:45:00 2013
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Tue, 5 Feb 2013 19:45:00 +0100
Subject: [BioRuby] Are the Bio* projects dying?
In-Reply-To: <CAKVJ-_6+baFosxGh94V3FpbARKG+mNjqm=deQptYRK6Qk=p8eQ@mail.gmail.com>
References: <20130129084011.GA15860@thebird.nl>
	<CAKVJ-_4m75g5-2+ZgNhA3QBm1YpPnW8nYCZSkyPYaz+xvtWjhg@mail.gmail.com>
	<20130129145921.GA16743@thebird.nl>
	<CAKVJ-_6TTidSkZ_ymTcfUR-QM_iysPOb=dChR=BrcdVL44P4TQ@mail.gmail.com>
	<20130129151548.GA16829@thebird.nl>
	<CAKVJ-_6+baFosxGh94V3FpbARKG+mNjqm=deQptYRK6Qk=p8eQ@mail.gmail.com>
Message-ID: <20130205184500.GA5909@thebird.nl>

On Tue, Jan 29, 2013 at 03:27:01PM +0000, Peter Cock wrote:
> https://github.com/biopython/biopython/graphs/commit-activity
> https://github.com/bioperl/bioperl-live/graphs/commit-activity
> https://github.com/bioruby/bioruby/graphs/commit-activity
> 
> (Not directly comparable as BioRuby has most commits outside
> the core in the BioGems, BioPerl likewise is splitting out code into
> smaller focused repositories, while Biopython is for now
> monolithic)

These are interesting statistics. They show Biopython is getting more
commits than I had found. I find it interesting to see how large the
communities are, especially for BioPerl.

Maybe the death of the Bio* projects is exaggerated, indeed.

I still would like to see more deep contributions, but maybe the lack
of deep diffs just shows the maturity of the core projects ;)

Pj.

From balkiprasanna1984 at gmail.com  Tue Feb 12 11:51:27 2013
From: balkiprasanna1984 at gmail.com (Prasanna Bala)
Date: Tue, 12 Feb 2013 22:21:27 +0530
Subject: [BioRuby] Machine Algorithm in Bioruby.
Message-ID: <CAMaJPdh8Wcf2K7dHfLxgQHEdYaNgnHVw=VqY_8HFOK8oo5t7_w@mail.gmail.com>

Hi,

I am working in Machine Learning algorithms related problems for more than
5 years. Yet I am fairly skeptical about my knowledge. I am also beginner
in Bio Ruby programming. I would like to know if there any implementation
in Bio Ruby for hard core machine learning problems related to
Bioinformatics. Very specifically using Naive Bayesian, HMM, SVD, SVM. We
know there are some good tools like WEKA, Mahout, Rapid miner present for
this. However I found them to be in predominantly in Java and not specific
for Bioinformatics. What is the role and development of Ruby specifically
in Bio Ruby in ML algorithms and Big Data analytics.

Regards,
Prasanna

From iainspeed at gmail.com  Sat Feb 16 10:55:39 2013
From: iainspeed at gmail.com (Iain Barnett)
Date: Sat, 16 Feb 2013 15:55:39 +0000
Subject: [BioRuby] Bio::Sequence::Common#randomize with a block
Message-ID: <05D649C2-1D3C-4CBC-8B6C-975FEA383304@gmail.com>

Hi,

I was looking at the Bio::Sequence::Common mixin, and specifically at the block form of `randomize`

https://github.com/bioruby/bioruby/blob/master/lib/bio/sequence/common.rb#L264

It returns an empty sequence, afaics to keep the return type the same, but wouldn't it be better to either return the randomised sequence e.g. `return seq` or yield the entire randomised sequence to the block, e.g. `yield seq` (and remove the `each`) as then you have more flexibility in what you can do with the sequence? Currently you can call `randomize` with a block and the only access you'll get to that is character by character. Personally, I'd prefer to get the randomised sequence returned, it seems strange not to.

I was just wondering. Any insight will be much appreciated.

Regards,
Iain

From mail at michaelbarton.me.uk  Sat Feb  2 21:34:30 2013
From: mail at michaelbarton.me.uk (Michael Barton)
Date: Sat, 2 Feb 2013 16:34:30 -0500
Subject: [BioRuby] Genomer: a ruby project to simplify genome finishing
Message-ID: <20130202213430.GA1168@bartonh-mbp-01>

Hi Everyone,

I've been working a sequencing microbial genomes during my current post doc
position. I've combined many of the ruby scripts I was using into a single tool
called "genomer" which might be of interest to other bioinformaticians working
in the same area.

I used this tool to simplify the smaller, mundane tasks associated with a
genome. For instance moving contigs and associated annotations around,
generating the required files to submit to GenBank, and generating summaries of
the genome scaffold.

I created a small screencast for anyone who is interested in finding out more:
http://youtu.be/HfsdJOELFjs?hd=1

I wrote this tool to satisfy my own needs and use genomer extensively for the
microbial genome projects in our lab. My GNU Makefile (http://bit.ly/WMKlCZ)
from a P. fluorescens project illustrates how genomer combined with GenBank's
tbl2asn can be used to build the all files required for genome submission.

Hopefully genomer may be useful to other bioinformaticians and simplify the
steps required to finish and submit a genome.

Thanks

Michael Barton

From francesco.strozzi at gmail.com  Mon Feb  4 10:51:28 2013
From: francesco.strozzi at gmail.com (Francesco Strozzi)
Date: Mon, 4 Feb 2013 11:51:28 +0100
Subject: [BioRuby] Genomer: a ruby project to simplify genome finishing
In-Reply-To: <20130202213430.GA1168@bartonh-mbp-01>
References: <20130202213430.GA1168@bartonh-mbp-01>
Message-ID: <CACtet2Tfqpbmo7vg_hKYqc1q7_qWSbh0ds3xUr_Kzc5sdHSwcg@mail.gmail.com>

Hi Michael,
thanks for that! I am working on genome assembly as well from time to
time so I will try Genomer.
Anyway cool idea to create a screen cast!

Cheers

On Sat, Feb 2, 2013 at 10:34 PM, Michael Barton
<mail at michaelbarton.me.uk> wrote:
> Hi Everyone,
>
> I've been working a sequencing microbial genomes during my current post doc
> position. I've combined many of the ruby scripts I was using into a single tool
> called "genomer" which might be of interest to other bioinformaticians working
> in the same area.
>
> I used this tool to simplify the smaller, mundane tasks associated with a
> genome. For instance moving contigs and associated annotations around,
> generating the required files to submit to GenBank, and generating summaries of
> the genome scaffold.
>
> I created a small screencast for anyone who is interested in finding out more:
> http://youtu.be/HfsdJOELFjs?hd=1
>
> I wrote this tool to satisfy my own needs and use genomer extensively for the
> microbial genome projects in our lab. My GNU Makefile (http://bit.ly/WMKlCZ)
> from a P. fluorescens project illustrates how genomer combined with GenBank's
> tbl2asn can be used to build the all files required for genome submission.
>
> Hopefully genomer may be useful to other bioinformaticians and simplify the
> steps required to finish and submit a genome.
>
> Thanks
>
> Michael Barton
>
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>



-- 

Francesco


From ngoto at gen-info.osaka-u.ac.jp  Mon Feb  4 11:35:18 2013
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Mon, 4 Feb 2013 20:35:18 +0900
Subject: [BioRuby] Fw: Can any one help me in installing BIORUBY on Rails
Message-ID: <201302041144.r14BiCaK010462@portal.open-bio.org>

Hi all,

I've recieved the following email, but I'm not familiar with Rails.
Please could someone anwser the question?
Thanks,
Naohisa Goto
ng at bioruby.org

Begin forwarded message:

From: <************@gmail.com>
To: staff at bioruby.org
Subject: Can any one help me in installing BIORUBY on Rails


Dear Staffs,
Please provide me information on step by step installation of Bioruby on
Rails
Im using Windows PC
Ruby,BioRuby and Rails installed.
Kindly please reply.


From mail at michaelbarton.me.uk  Mon Feb  4 15:26:46 2013
From: mail at michaelbarton.me.uk (Michael Barton)
Date: Mon, 4 Feb 2013 10:26:46 -0500
Subject: [BioRuby] Genomer: a ruby project to simplify genome finishing
In-Reply-To: <20130202213430.GA1168@bartonh-mbp-01>
References: <20130202213430.GA1168@bartonh-mbp-01>
Message-ID: <20130204152646.GD5528@bartonh-mbp-01.uanet.edu>

I have created an additional screencast to follow up. This provides a more
concrete example of using genomer to generate the files required to submit a
genome project to GenBank.

http://www.youtube.com/watch?v=jVn62pMnIRA&hd=1

Thanks

Mike

On Sat, Feb 02, 2013 at 04:34:30PM -0500, Michael Barton wrote:

> Hi Everyone,
>
> I've been working a sequencing microbial genomes during my current
> post doc position. I've combined many of the ruby scripts I was using
> into a single tool called "genomer" which might be of interest to
> other bioinformaticians working in the same area.
>
> I used this tool to simplify the smaller, mundane tasks associated
> with a genome. For instance moving contigs and associated annotations
> around, generating the required files to submit to GenBank, and
> generating summaries of the genome scaffold.
>
> I created a small screencast for anyone who is interested in finding
> out more: http://youtu.be/HfsdJOELFjs?hd=1
>
> I wrote this tool to satisfy my own needs and use genomer extensively
> for the microbial genome projects in our lab. My GNU Makefile
> (http://bit.ly/WMKlCZ) from a P. fluorescens project illustrates how
> genomer combined with GenBank's tbl2asn can be used to build the all
> files required for genome submission.
>
> Hopefully genomer may be useful to other bioinformaticians and
> simplify the steps required to finish and submit a genome.
>
> Thanks
>
> Michael Barton



From pjotr.public14 at thebird.nl  Tue Feb  5 07:22:14 2013
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Tue, 5 Feb 2013 08:22:14 +0100
Subject: [BioRuby] biogems
Message-ID: <20130205072214.GB3105@thebird.nl>

rubygems are working again :)


From ngoto at gen-info.osaka-u.ac.jp  Tue Feb  5 09:48:51 2013
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Tue, 5 Feb 2013 18:48:51 +0900
Subject: [BioRuby] Fw: books to learn Ruby
Message-ID: <201302050948.r159mrEc032068@portal.open-bio.org>

Hi all,

I just find that I've recieved the following mail in may mailer's
spam folder. Sorry for responsing too late.

Unfortunately, I know little about books written in English about
learning Ruby. Could someone please recommend some books?

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

Begin forwarded message:

Date: Sun, 20 Jan 2013 13:31:29 +0530
From: <**********@gmail.com>
To: staff at bioruby.org
Subject: Please Help


Dear Ruby Admin,
I love to learn RUBY..I'm novice,
Basically from a Bioinformatics Background.

I wanted to know few things on Ruby..
1.How should I start learning RUBY, Any basic books you can suggest me?
2.How do I install BioRuby in my Windows PC ?

Please help me !
Thanks
---------------------------------------------------


From john.woods at marcottelab.org  Tue Feb  5 13:50:39 2013
From: john.woods at marcottelab.org (John Woods)
Date: Tue, 5 Feb 2013 07:50:39 -0600
Subject: [BioRuby] Fw: books to learn Ruby
In-Reply-To: <201302050948.r159mrEc032068@portal.open-bio.org>
References: <201302050948.r159mrEc032068@portal.open-bio.org>
Message-ID: <CAPkCRRvJaS4O8JEWU-mLdufOR7tvaNi9ybFW9LRUZeXOserJQw@mail.gmail.com>

Well, the author appears not to be a native English speaker, but normally
I advocate Why's Poignant Guide. The feedback I've gotten from
international students, however, suggests that this book is complicated for
people who aren't native speakers.

In that case, probably the O'Reilly stuff.

John
SciRuby Project

On Tuesday, February 5, 2013, Naohisa GOTO wrote:

> Hi all,
>
> I just find that I've recieved the following mail in may mailer's
> spam folder. Sorry for responsing too late.
>
> Unfortunately, I know little about books written in English about
> learning Ruby. Could someone please recommend some books?
>
> Naohisa Goto
> ng at bioruby.org <javascript:;> / ngoto at gen-info.osaka-u.ac.jp<javascript:;>
>
> Begin forwarded message:
>
> Date: Sun, 20 Jan 2013 13:31:29 +0530
> From: <**********@gmail.com>
> To: staff at bioruby.org <javascript:;>
> Subject: Please Help
>
>
> Dear Ruby Admin,
> I love to learn RUBY..I'm novice,
> Basically from a Bioinformatics Background.
>
> I wanted to know few things on Ruby..
> 1.How should I start learning RUBY, Any basic books you can suggest me?
> 2.How do I install BioRuby in my Windows PC ?
>
> Please help me !
> Thanks
> ---------------------------------------------------
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org <javascript:;>
> http://lists.open-bio.org/mailman/listinfo/bioruby
>


From rob.syme at gmail.com  Tue Feb  5 13:58:41 2013
From: rob.syme at gmail.com (Rob Syme)
Date: Tue, 5 Feb 2013 21:58:41 +0800
Subject: [BioRuby] Fw: books to learn Ruby
In-Reply-To: <201302050948.r159mrEc032068@portal.open-bio.org>
References: <201302050948.r159mrEc032068@portal.open-bio.org>
Message-ID: <CAEf4xgcJOhyscGE5oVvUzEpYr4r2MW3f8CrjwoTgUoDjM1LSOw@mail.gmail.com>

There is an good list of (free) books up at
http://stackoverflow.com/questions/194812/list-of-freely-available-programming-books

The ruby section includes two that I would recommend,
http://ruby.learncodethehardway.org/book/
and of course _why's poignant guide, which as John points out, might not be
as helpful in this instance
http://mislav.uniqpath.com/poignant-guide/

I'm sure there is enough there to get the student started.

-r

Hi all,

I just find that I've recieved the following mail in may mailer's
spam folder. Sorry for responsing too late.

Unfortunately, I know little about books written in English about
learning Ruby. Could someone please recommend some books?

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

Begin forwarded message:

Date: Sun, 20 Jan 2013 13:31:29 +0530
From: <**********@gmail.com>
To: staff at bioruby.org
Subject: Please Help

Dear Ruby Admin,
I love to learn RUBY..I'm novice,
Basically from a Bioinformatics Background.

I wanted to know few things on Ruby..
1.How should I start learning RUBY, Any basic books you can suggest me?
2.How do I install BioRuby in my Windows PC ?

Please help me !
Thanks
---------------------------------------------------
_______________________________________________
BioRuby Project - http://www.bioruby.org/
BioRuby mailing list
BioRuby at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioruby


From marian.povolny at gmail.com  Tue Feb  5 14:46:05 2013
From: marian.povolny at gmail.com (Marjan Povolni)
Date: Tue, 5 Feb 2013 15:46:05 +0100
Subject: [BioRuby] Fw: books to learn Ruby
In-Reply-To: <201302050948.r159mrEc032068@portal.open-bio.org>
References: <201302050948.r159mrEc032068@portal.open-bio.org>
Message-ID: <CADKP5Ck+LZdpTySKso5Bnxb4orie3fwKTjGicVSbKUTzf0Xc0w@mail.gmail.com>

Hi,

I used "The Well-Grounded Rubyist" by David A. Black. I don't remember
anymore why I liked it, but I did. Starting with a tutorial from this site
might be also a good idea, depends on the person:
http://www.ruby-lang.org/en/documentation/

To me, the Ruby Koans (http://rubykoans.com/windows) provided a nice
introduction to the language in a short time. There are also instructions
on how to install Ruby on windows on that website.

--
Marjan

On Tue, Feb 5, 2013 at 10:48 AM, Naohisa GOTO
<ngoto at gen-info.osaka-u.ac.jp>wrote:

> Hi all,
>
> I just find that I've recieved the following mail in may mailer's
> spam folder. Sorry for responsing too late.
>
> Unfortunately, I know little about books written in English about
> learning Ruby. Could someone please recommend some books?
>
> Naohisa Goto
> ng at bioruby.org / ngoto at gen-info.osaka-u.ac.jp
>
> Begin forwarded message:
>
> Date: Sun, 20 Jan 2013 13:31:29 +0530
> From: <**********@gmail.com>
> To: staff at bioruby.org
> Subject: Please Help
>
>
> Dear Ruby Admin,
> I love to learn RUBY..I'm novice,
> Basically from a Bioinformatics Background.
>
> I wanted to know few things on Ruby..
> 1.How should I start learning RUBY, Any basic books you can suggest me?
> 2.How do I install BioRuby in my Windows PC ?
>
> Please help me !
> Thanks
> ---------------------------------------------------
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>


From mphoeppner at gmail.com  Tue Feb  5 14:48:46 2013
From: mphoeppner at gmail.com (Marc Hoeppner)
Date: Tue, 05 Feb 2013 15:48:46 +0100
Subject: [BioRuby] Fwd: Re:  Fw: books to learn Ruby
Message-ID: <51111BCE.2070901@gmail.com>

Hi,

http://www.amazon.com/Programming-Ruby-1-9-Pragmatic-Programmers/dp/1934356085/ref=sr_1_1?ie=UTF8&qid=1360057937&sr=8-1&keywords=ruby+pragmatic

The pragmatic programmers guide, I think, is one of the better
introductions, as they also deal with a lot of general things about
writing good code. Then there is a load of decent-to-excellent tutorials
on the ruby website at http://www.ruby-lang.org/en/documentation/ . One
that I found useful to get started was this one:
http://pine.fm/LearnToProgram/

And the question about how to install Bioruby should be self-explanatory
once the basics about Ruby have been learned, I would think. Short
answer: It's a gem (a library, essentially), so googling for 'Ruby gems'
would be a good start.

Best,

/Marc
> Hi all,
>
> I just find that I've recieved the following mail in may mailer's
> spam folder. Sorry for responsing too late.
>
> Unfortunately, I know little about books written in English about
> learning Ruby. Could someone please recommend some books?
>
> Naohisa Goto
> ng at bioruby.org / ngoto at gen-info.osaka-u.ac.jp
>
> Begin forwarded message:
>
> Date: Sun, 20 Jan 2013 13:31:29 +0530
> From: <**********@gmail.com>
> To: staff at bioruby.org
> Subject: Please Help
>
>
> Dear Ruby Admin,
> I love to learn RUBY..I'm novice,
> Basically from a Bioinformatics Background.
>
> I wanted to know few things on Ruby..
> 1.How should I start learning RUBY, Any basic books you can suggest me?
> 2.How do I install BioRuby in my Windows PC ?
>
> Please help me !
> Thanks
> ---------------------------------------------------
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby



From jan.aerts at esat.kuleuven.be  Tue Feb  5 14:57:50 2013
From: jan.aerts at esat.kuleuven.be (Jan Aerts)
Date: Tue, 5 Feb 2013 15:57:50 +0100
Subject: [BioRuby] Fw: books to learn Ruby
In-Reply-To: <CADKP5Ck+LZdpTySKso5Bnxb4orie3fwKTjGicVSbKUTzf0Xc0w@mail.gmail.com>
References: <201302050948.r159mrEc032068@portal.open-bio.org>
	<CADKP5Ck+LZdpTySKso5Bnxb4orie3fwKTjGicVSbKUTzf0Xc0w@mail.gmail.com>
Message-ID: <CAErBFCyYRyGV3=i10=k8ZX9kRwK1TZhydN+TuXBKmD=MotfsAQ@mail.gmail.com>

I learned Ruby by reading a part-comic book over a Christmas holiday: why's
(poignant) guide to ruby. You can find it at
http://mislav.uniqpath.com/poignant-guide/book/

jan.


================================
Dr Jan Aerts
Assistant Professor
Faculty of Engineering - ESAT/SCD
University of Leuven
Kasteelpark Arenberg 10 bus 2446
3001 Leuven-Heverlee
ORCID: http://orcid.org/0000-0002-6416-2717
Tel: +32 16 321053
Fax: +32 16 321970


On 5 February 2013 15:46, Marjan Povolni <marian.povolny at gmail.com> wrote:

> Hi,
>
> I used "The Well-Grounded Rubyist" by David A. Black. I don't remember
> anymore why I liked it, but I did. Starting with a tutorial from this site
> might be also a good idea, depends on the person:
> http://www.ruby-lang.org/en/documentation/
>
> To me, the Ruby Koans (http://rubykoans.com/windows) provided a nice
> introduction to the language in a short time. There are also instructions
> on how to install Ruby on windows on that website.
>
> --
> Marjan
>
> On Tue, Feb 5, 2013 at 10:48 AM, Naohisa GOTO
> <ngoto at gen-info.osaka-u.ac.jp>wrote:
>
> > Hi all,
> >
> > I just find that I've recieved the following mail in may mailer's
> > spam folder. Sorry for responsing too late.
> >
> > Unfortunately, I know little about books written in English about
> > learning Ruby. Could someone please recommend some books?
> >
> > Naohisa Goto
> > ng at bioruby.org / ngoto at gen-info.osaka-u.ac.jp
> >
> > Begin forwarded message:
> >
> > Date: Sun, 20 Jan 2013 13:31:29 +0530
> > From: <**********@gmail.com>
> > To: staff at bioruby.org
> > Subject: Please Help
> >
> >
> > Dear Ruby Admin,
> > I love to learn RUBY..I'm novice,
> > Basically from a Bioinformatics Background.
> >
> > I wanted to know few things on Ruby..
> > 1.How should I start learning RUBY, Any basic books you can suggest me?
> > 2.How do I install BioRuby in my Windows PC ?
> >
> > Please help me !
> > Thanks
> > ---------------------------------------------------
> > _______________________________________________
> > BioRuby Project - http://www.bioruby.org/
> > BioRuby mailing list
> > BioRuby at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioruby
> >
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>


From pjotr.public14 at thebird.nl  Tue Feb  5 16:33:57 2013
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Tue, 5 Feb 2013 17:33:57 +0100
Subject: [BioRuby] Fw: books to learn Ruby
In-Reply-To: <CAErBFCyYRyGV3=i10=k8ZX9kRwK1TZhydN+TuXBKmD=MotfsAQ@mail.gmail.com>
References: <201302050948.r159mrEc032068@portal.open-bio.org>
	<CADKP5Ck+LZdpTySKso5Bnxb4orie3fwKTjGicVSbKUTzf0Xc0w@mail.gmail.com>
	<CAErBFCyYRyGV3=i10=k8ZX9kRwK1TZhydN+TuXBKmD=MotfsAQ@mail.gmail.com>
Message-ID: <20130205163357.GA5487@thebird.nl>

On Tue, Feb 05, 2013 at 03:57:50PM +0100, Jan Aerts wrote:
> I learned Ruby by reading a part-comic book over a Christmas holiday: why's
> (poignant) guide to ruby. You can find it at
> http://mislav.uniqpath.com/poignant-guide/book/


= Ruby just came to me =

Ruby just came to me
Like a sweet lover
She fits me
Even when unfaithful
I long for her

Behaviour driven, predictable, short and sweet
My Ruby, Ruby, Ruby

Ruby is not perfect
And I am not on Rails
Her dynamic typing can bite
But I love her for her Smalltalk message passing OOP
And I love her for her functional programming

Behaviour driven, predictable, short and sweet
My Ruby, Ruby, Ruby

I always come back to Ruby
And now on the JVM
She dances with Java, Scala, Clojure and soon node.jar
Ruby is still faithful to me
Always domain specific

Behaviour driven, predictable, short and sweet
My Ruby, Ruby, Ruby

Pj.



From pjotr.public14 at thebird.nl  Tue Feb  5 18:39:33 2013
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Tue, 5 Feb 2013 19:39:33 +0100
Subject: [BioRuby] JRuby and JS node.jar
Message-ID: <20130205183933.GA5880@thebird.nl>

I was wondering whether is any interest in combining Javascript with
BioRuby/BioJAVA on the JVM. There are two JS interpreters for the JVM
now, and am starting to lean the way of using Javascript for education
as JS is now a common language and it may be a way of getting (young)
people to try stuff in bioinformatics. I really like

  http://eloquentjavascript.net/

Writing a new BioJS may not be necessary with the good stuff we
already have.

Any thoughts?

Pj.


From pjotr.public14 at thebird.nl  Tue Feb  5 18:45:00 2013
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Tue, 5 Feb 2013 19:45:00 +0100
Subject: [BioRuby] Are the Bio* projects dying?
In-Reply-To: <CAKVJ-_6+baFosxGh94V3FpbARKG+mNjqm=deQptYRK6Qk=p8eQ@mail.gmail.com>
References: <20130129084011.GA15860@thebird.nl>
	<CAKVJ-_4m75g5-2+ZgNhA3QBm1YpPnW8nYCZSkyPYaz+xvtWjhg@mail.gmail.com>
	<20130129145921.GA16743@thebird.nl>
	<CAKVJ-_6TTidSkZ_ymTcfUR-QM_iysPOb=dChR=BrcdVL44P4TQ@mail.gmail.com>
	<20130129151548.GA16829@thebird.nl>
	<CAKVJ-_6+baFosxGh94V3FpbARKG+mNjqm=deQptYRK6Qk=p8eQ@mail.gmail.com>
Message-ID: <20130205184500.GA5909@thebird.nl>

On Tue, Jan 29, 2013 at 03:27:01PM +0000, Peter Cock wrote:
> https://github.com/biopython/biopython/graphs/commit-activity
> https://github.com/bioperl/bioperl-live/graphs/commit-activity
> https://github.com/bioruby/bioruby/graphs/commit-activity
> 
> (Not directly comparable as BioRuby has most commits outside
> the core in the BioGems, BioPerl likewise is splitting out code into
> smaller focused repositories, while Biopython is for now
> monolithic)

These are interesting statistics. They show Biopython is getting more
commits than I had found. I find it interesting to see how large the
communities are, especially for BioPerl.

Maybe the death of the Bio* projects is exaggerated, indeed.

I still would like to see more deep contributions, but maybe the lack
of deep diffs just shows the maturity of the core projects ;)

Pj.


From balkiprasanna1984 at gmail.com  Tue Feb 12 16:51:27 2013
From: balkiprasanna1984 at gmail.com (Prasanna Bala)
Date: Tue, 12 Feb 2013 22:21:27 +0530
Subject: [BioRuby] Machine Algorithm in Bioruby.
Message-ID: <CAMaJPdh8Wcf2K7dHfLxgQHEdYaNgnHVw=VqY_8HFOK8oo5t7_w@mail.gmail.com>

Hi,

I am working in Machine Learning algorithms related problems for more than
5 years. Yet I am fairly skeptical about my knowledge. I am also beginner
in Bio Ruby programming. I would like to know if there any implementation
in Bio Ruby for hard core machine learning problems related to
Bioinformatics. Very specifically using Naive Bayesian, HMM, SVD, SVM. We
know there are some good tools like WEKA, Mahout, Rapid miner present for
this. However I found them to be in predominantly in Java and not specific
for Bioinformatics. What is the role and development of Ruby specifically
in Bio Ruby in ML algorithms and Big Data analytics.

Regards,
Prasanna


From iainspeed at gmail.com  Sat Feb 16 15:55:39 2013
From: iainspeed at gmail.com (Iain Barnett)
Date: Sat, 16 Feb 2013 15:55:39 +0000
Subject: [BioRuby] Bio::Sequence::Common#randomize with a block
Message-ID: <05D649C2-1D3C-4CBC-8B6C-975FEA383304@gmail.com>

Hi,

I was looking at the Bio::Sequence::Common mixin, and specifically at the block form of `randomize`

https://github.com/bioruby/bioruby/blob/master/lib/bio/sequence/common.rb#L264

It returns an empty sequence, afaics to keep the return type the same, but wouldn't it be better to either return the randomised sequence e.g. `return seq` or yield the entire randomised sequence to the block, e.g. `yield seq` (and remove the `each`) as then you have more flexibility in what you can do with the sequence? Currently you can call `randomize` with a block and the only access you'll get to that is character by character. Personally, I'd prefer to get the randomised sequence returned, it seems strange not to.

I was just wondering. Any insight will be much appreciated.

Regards,
Iain