From ngoto at gen-info.osaka-u.ac.jp  Thu Oct  8 09:58:45 2009
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Thu, 8 Oct 2009 22:58:45 +0900
Subject: [BioRuby] Status of bioruby with Debian packages
In-Reply-To: <b9140daa0904140230h3182f6b0l34b112350f5ac185@mail.gmail.com>
References: <b9140daa0904140230h3182f6b0l34b112350f5ac185@mail.gmail.com>
Message-ID: <20091008135848.C28FC1CBC565@idnmail.gen-info.osaka-u.ac.jp>

Hi,

Thanks to Debian Med Packaging Team, new version of Debian package
of BioRuby 1.3.1 is now uploaded to Debian unstable.

http://packages.debian.org/ja/sid/libbio-ruby
http://packages.debian.org/ja/sid/libbio-ruby1.8

Please test the package, and report any bugs, problems, or requests.
They would be included in the next Debian release, if no problems found.

In addition, if interested, please see the message
   http://lists.debian.org/debian-med/2009/10/msg00058.html
and, if possible, install the "popularity-contest" package,
to know how many users uses the libbio-ruby1.8 package.

Thanks,

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

From georgkam at gmail.com  Fri Oct 16 00:29:35 2009
From: georgkam at gmail.com (George Githinji)
Date: Fri, 16 Oct 2009 07:29:35 +0300
Subject: [BioRuby] matching against a zillion patterns
Message-ID: <55915f820910152129j3e40f7a7l50bdc368464e12dd@mail.gmail.com>

Recently had this discussion on the Ruby mailing list. Any ideas or
solutions

http://www.ruby-forum.com/topic/197365#new

-- 
---------------
Sincerely
George

Skype: george_g2
Blog: http://biorelated.wordpress.com/

From jan.aerts at gmail.com  Fri Oct 16 09:51:42 2009
From: jan.aerts at gmail.com (Jan Aerts)
Date: Fri, 16 Oct 2009 09:51:42 -0400
Subject: [BioRuby] matching against a zillion patterns
In-Reply-To: <55915f820910152129j3e40f7a7l50bdc368464e12dd@mail.gmail.com>
References: <55915f820910152129j3e40f7a7l50bdc368464e12dd@mail.gmail.com>
Message-ID: <4c7507a70910160651t3dbf7e81m580262d7e407edee@mail.gmail.com>

Hey George,
So if I understand correctly you've got a huge number of aminoacid sequences
(how many?) and about 400 regular expressions. And for each of the aminoacid
sequences: if they match just one of the regular expressions they are put in
box A and if they match none of the regexps, they go into box B. Correct?

It just happens that something very similar was the subject of Jim Tisdall's
(from Beginning Perl for Bioinformatics fame) talk at the bioinformatics
course we're teaching at the moment :-)

First thing: avoid loops. You don't want to take loop over all regexps for
each AA sequences, or the other way around.

Are all regexps of the same length? Would be nice if they are, but not
critical. My approach would be to go over the data just once. So suppose the
regexps all are of the same length.

A. Prepare your data:
  a. "Decode" the regexps into literal strings: e.g. /A[BC]D/ become "ABD"
and "ACD".
  b. Create a hash that contains all those things as keys.
  c. Concatenate all AA sequences together, joined with a non-AA, let's say
a semicolon ";". E.g. CAARGNDLYSKNIG;GGARGNDLYSKNIG;KKARGNDLYSKNIG

B. Do the actual search
  a. If the length of the strings to match (what used to be the regexps, and
are now the keys in the hash) is 5: take the first 5 characters of your
concatenated AA string and check if that substring exists as a key in the
hash. If so: you know that the AA sequence between the surrounding ";"
characters should go in box A.
  b. Advance 1 position: take AAs 2 to 6.
  c. Go back to a.

You might have to tweak this approach to exactly fit your requirements, but
if your code used to take a very long time, this might speed things up
immensely.

(George: can you forward this to the ruby mailing list it was discussed on
initially? Cheers)

Good luck,
jan.


2009/10/16 George Githinji <georgkam at gmail.com>

> Recently had this discussion on the Ruby mailing list. Any ideas or
> solutions
>
> http://www.ruby-forum.com/topic/197365#new
>
> --
> ---------------
> Sincerely
> George
>
> Skype: george_g2
> Blog: http://biorelated.wordpress.com/
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>

From georgkam at gmail.com  Sun Oct 18 03:01:41 2009
From: georgkam at gmail.com (George Githinji)
Date: Sun, 18 Oct 2009 10:01:41 +0300
Subject: [BioRuby] matching against a zillion patterns
In-Reply-To: <4c7507a70910160651t3dbf7e81m580262d7e407edee@mail.gmail.com>
References: <55915f820910152129j3e40f7a7l50bdc368464e12dd@mail.gmail.com> 
	<4c7507a70910160651t3dbf7e81m580262d7e407edee@mail.gmail.com>
Message-ID: <55915f820910180001r23b551e2nea9c1a9d1c46defd@mail.gmail.com>

Thank you for the approach.
The initial list of sequences was 2000.(i.e the ones that need to be
classified) and the numbers of patterns was 570. All of then are of the same
size(14 amino acids long). Using Robert's approach i was able to create a
single very loong regular expression for matching. It seems to work but i
will do some benchmarks and diagnostics tests.

I can twitch this approach so as to do a single pass for all the sequences
while doing the search.

Thank you so much!!

On Fri, Oct 16, 2009 at 4:51 PM, Jan Aerts <jan.aerts at gmail.com> wrote:

> Hey George,
> So if I understand correctly you've got a huge number of aminoacid
> sequences (how many?) and about 400 regular expressions. And for each of the
> aminoacid sequences: if they match just one of the regular expressions they
> are put in box A and if they match none of the regexps, they go into box B.
> Correct?
>
> It just happens that something very similar was the subject of Jim
> Tisdall's (from Beginning Perl for Bioinformatics fame) talk at the
> bioinformatics course we're teaching at the moment :-)
>
> First thing: avoid loops. You don't want to take loop over all regexps for
> each AA sequences, or the other way around.
>
> Are all regexps of the same length? Would be nice if they are, but not
> critical. My approach would be to go over the data just once. So suppose the
> regexps all are of the same length.
>
> A. Prepare your data:
>   a. "Decode" the regexps into literal strings: e.g. /A[BC]D/ become "ABD"
> and "ACD".
>   b. Create a hash that contains all those things as keys.
>   c. Concatenate all AA sequences together, joined with a non-AA, let's say
> a semicolon ";". E.g. CAARGNDLYSKNIG;GGARGNDLYSKNIG;KKARGNDLYSKNIG
>
> B. Do the actual search
>   a. If the length of the strings to match (what used to be the regexps,
> and are now the keys in the hash) is 5: take the first 5 characters of your
> concatenated AA string and check if that substring exists as a key in the
> hash. If so: you know that the AA sequence between the surrounding ";"
> characters should go in box A.
>   b. Advance 1 position: take AAs 2 to 6.
>   c. Go back to a.
>
> You might have to tweak this approach to exactly fit your requirements, but
> if your code used to take a very long time, this might speed things up
> immensely.
>
> (George: can you forward this to the ruby mailing list it was discussed on
> initially? Cheers)
>
> Good luck,
> jan.
>
>
> 2009/10/16 George Githinji <georgkam at gmail.com>
>
>> Recently had this discussion on the Ruby mailing list. Any ideas or
>>
>> solutions
>>
>> http://www.ruby-forum.com/topic/197365#new
>>
>> --
>> ---------------
>> Sincerely
>> George
>>
>> Skype: george_g2
>> Blog: http://biorelated.wordpress.com/
>> _______________________________________________
>> BioRuby mailing list
>> BioRuby at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioruby
>>
>
>


-- 
---------------
Sincerely
George

Skype: george_g2
Blog: http://biorelated.wordpress.com/

From jan.aerts at gmail.com  Tue Oct 20 14:37:37 2009
From: jan.aerts at gmail.com (Jan Aerts)
Date: Tue, 20 Oct 2009 14:37:37 -0400
Subject: [BioRuby] samtools
Message-ID: <4c7507a70910201137h39abcbedv4bb50d7d27f85eb3@mail.gmail.com>

Is anyone working on a ruby-wrapper for the SAM/BAM alignment format for
next-gen sequencing data (http://samtools.sourceforge.net)?
jan.

From kenglish at gmail.com  Wed Oct 21 13:59:13 2009
From: kenglish at gmail.com (Kevin English)
Date: Wed, 21 Oct 2009 07:59:13 -1000
Subject: [BioRuby] Batch Blasting sequences against NR-NT database
Message-ID: <d82e7f560910211059r3dd34cc1gab76cefad846f48b@mail.gmail.com>

Hi,
? I am developeing a program where users want to blast 1000's of
sequences against NCBI-NR database. I'm looking for advice on the best
way to implement this. The 2 options that I see available are:
1) Use Bio::Blast::Remote library in the bio-ruby API.
2) Download the NR database from here: ftp://ftp.ncbi.nih.gov/blast/db
and run blast locally.

Can anyone tell me, looking at this page:

http://blast.ncbi.nlm.nih.gov/blast_overview.shtml

Is the Bio::Blast::Remote using the Blastcl3 program or BLAST URL API?
and what are the trade offs?

My project is avaible on github although I haven't finished all the
documentation yet.

http://github.com/kenglishhi/biococonutisland

Thanks,

Kevin


From pjotr.public14 at thebird.nl  Wed Oct 21 16:40:48 2009
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Wed, 21 Oct 2009 22:40:48 +0200
Subject: [BioRuby] Batch Blasting sequences against NR-NT database
In-Reply-To: <d82e7f560910211059r3dd34cc1gab76cefad846f48b@mail.gmail.com>
References: <d82e7f560910211059r3dd34cc1gab76cefad846f48b@mail.gmail.com>
Message-ID: <20091021204048.GB12568@thebird.nl>

Hi Kevin,

I am doing something like that in a pipe line. Do want to provide a
web interface, or is it batch based? What is the user interface you
envision?

Pj.

On Wed, Oct 21, 2009 at 07:59:13AM -1000, Kevin English wrote:
> Hi,
> ? I am developeing a program where users want to blast 1000's of
> sequences against NCBI-NR database. I'm looking for advice on the best
> way to implement this. The 2 options that I see available are:
> 1) Use Bio::Blast::Remote library in the bio-ruby API.
> 2) Download the NR database from here: ftp://ftp.ncbi.nih.gov/blast/db
> and run blast locally.
> 
> Can anyone tell me, looking at this page:
> 
> http://blast.ncbi.nlm.nih.gov/blast_overview.shtml
> 
> Is the Bio::Blast::Remote using the Blastcl3 program or BLAST URL API?
> and what are the trade offs?
> 
> My project is avaible on github although I haven't finished all the
> documentation yet.
> 
> http://github.com/kenglishhi/biococonutisland
> 
> Thanks,
> 
> Kevin
> 
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby

From kenglish at gmail.com  Wed Oct 21 17:23:17 2009
From: kenglish at gmail.com (Kevin English)
Date: Wed, 21 Oct 2009 11:23:17 -1000
Subject: [BioRuby] Batch Blasting sequences against NR-NT database
In-Reply-To: <20091021204048.GB12568@thebird.nl>
References: <d82e7f560910211059r3dd34cc1gab76cefad846f48b@mail.gmail.com>
	<20091021204048.GB12568@thebird.nl>
Message-ID: <d82e7f560910211423h21f24901s82345ad126362c30@mail.gmail.com>

This will runs a batch job. I have ruby on rails web interface but all
my blasting is handled using the DelayedJob plugin.

What do you mean by "in a pipe line"?


Kevin

On Wed, Oct 21, 2009 at 10:40 AM, Pjotr Prins <pjotr.public14 at thebird.nl> wrote:
> Hi Kevin,
>
> I am doing something like that in a pipe line. Do want to provide a
> web interface, or is it batch based? What is the user interface you
> envision?
>
> Pj.
>
> On Wed, Oct 21, 2009 at 07:59:13AM -1000, Kevin English wrote:
>> Hi,
>> ? I am developeing a program where users want to blast 1000's of
>> sequences against NCBI-NR database. I'm looking for advice on the best
>> way to implement this. The 2 options that I see available are:
>> 1) Use Bio::Blast::Remote library in the bio-ruby API.
>> 2) Download the NR database from here: ftp://ftp.ncbi.nih.gov/blast/db
>> and run blast locally.
>>
>> Can anyone tell me, looking at this page:
>>
>> http://blast.ncbi.nlm.nih.gov/blast_overview.shtml
>>
>> Is the Bio::Blast::Remote using the Blastcl3 program or BLAST URL API?
>> and what are the trade offs?
>>
>> My project is avaible on github although I haven't finished all the
>> documentation yet.
>>
>> http://github.com/kenglishhi/biococonutisland
>>
>> Thanks,
>>
>> Kevin
>>
>> _______________________________________________
>> BioRuby mailing list
>> BioRuby at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioruby
>


From pjotr.public14 at thebird.nl  Thu Oct 22 09:14:54 2009
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Thu, 22 Oct 2009 15:14:54 +0200
Subject: [BioRuby] Batch Blasting sequences against NR-NT database
In-Reply-To: <d82e7f560910211423h21f24901s82345ad126362c30@mail.gmail.com>
References: <d82e7f560910211059r3dd34cc1gab76cefad846f48b@mail.gmail.com>
	<20091021204048.GB12568@thebird.nl>
	<d82e7f560910211423h21f24901s82345ad126362c30@mail.gmail.com>
Message-ID: <20091022131454.GC17287@thebird.nl>

On Wed, Oct 21, 2009 at 11:23:17AM -1000, Kevin English wrote:
> This will runs a batch job. I have ruby on rails web interface but all
> my blasting is handled using the DelayedJob plugin.

OK, this means you could benefit from an XML BLAST parser? Right?
Execute BLAST with XML output, parse that, and convert to some
representation online. Or do you want to use HTML output and embed
that in your tool?

> What do you mean by "in a pipe line"?

A pipeline for parallel computing:

http://en.wikipedia.org/wiki/Parallel_computing

Pj.

From ngoto at gen-info.osaka-u.ac.jp  Thu Oct  8 13:58:45 2009
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Thu, 8 Oct 2009 22:58:45 +0900
Subject: [BioRuby] Status of bioruby with Debian packages
In-Reply-To: <b9140daa0904140230h3182f6b0l34b112350f5ac185@mail.gmail.com>
References: <b9140daa0904140230h3182f6b0l34b112350f5ac185@mail.gmail.com>
Message-ID: <20091008135848.C28FC1CBC565@idnmail.gen-info.osaka-u.ac.jp>

Hi,

Thanks to Debian Med Packaging Team, new version of Debian package
of BioRuby 1.3.1 is now uploaded to Debian unstable.

http://packages.debian.org/ja/sid/libbio-ruby
http://packages.debian.org/ja/sid/libbio-ruby1.8

Please test the package, and report any bugs, problems, or requests.
They would be included in the next Debian release, if no problems found.

In addition, if interested, please see the message
   http://lists.debian.org/debian-med/2009/10/msg00058.html
and, if possible, install the "popularity-contest" package,
to know how many users uses the libbio-ruby1.8 package.

Thanks,

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


From georgkam at gmail.com  Fri Oct 16 04:29:35 2009
From: georgkam at gmail.com (George Githinji)
Date: Fri, 16 Oct 2009 07:29:35 +0300
Subject: [BioRuby] matching against a zillion patterns
Message-ID: <55915f820910152129j3e40f7a7l50bdc368464e12dd@mail.gmail.com>

Recently had this discussion on the Ruby mailing list. Any ideas or
solutions

http://www.ruby-forum.com/topic/197365#new

-- 
---------------
Sincerely
George

Skype: george_g2
Blog: http://biorelated.wordpress.com/


From jan.aerts at gmail.com  Fri Oct 16 13:51:42 2009
From: jan.aerts at gmail.com (Jan Aerts)
Date: Fri, 16 Oct 2009 09:51:42 -0400
Subject: [BioRuby] matching against a zillion patterns
In-Reply-To: <55915f820910152129j3e40f7a7l50bdc368464e12dd@mail.gmail.com>
References: <55915f820910152129j3e40f7a7l50bdc368464e12dd@mail.gmail.com>
Message-ID: <4c7507a70910160651t3dbf7e81m580262d7e407edee@mail.gmail.com>

Hey George,
So if I understand correctly you've got a huge number of aminoacid sequences
(how many?) and about 400 regular expressions. And for each of the aminoacid
sequences: if they match just one of the regular expressions they are put in
box A and if they match none of the regexps, they go into box B. Correct?

It just happens that something very similar was the subject of Jim Tisdall's
(from Beginning Perl for Bioinformatics fame) talk at the bioinformatics
course we're teaching at the moment :-)

First thing: avoid loops. You don't want to take loop over all regexps for
each AA sequences, or the other way around.

Are all regexps of the same length? Would be nice if they are, but not
critical. My approach would be to go over the data just once. So suppose the
regexps all are of the same length.

A. Prepare your data:
  a. "Decode" the regexps into literal strings: e.g. /A[BC]D/ become "ABD"
and "ACD".
  b. Create a hash that contains all those things as keys.
  c. Concatenate all AA sequences together, joined with a non-AA, let's say
a semicolon ";". E.g. CAARGNDLYSKNIG;GGARGNDLYSKNIG;KKARGNDLYSKNIG

B. Do the actual search
  a. If the length of the strings to match (what used to be the regexps, and
are now the keys in the hash) is 5: take the first 5 characters of your
concatenated AA string and check if that substring exists as a key in the
hash. If so: you know that the AA sequence between the surrounding ";"
characters should go in box A.
  b. Advance 1 position: take AAs 2 to 6.
  c. Go back to a.

You might have to tweak this approach to exactly fit your requirements, but
if your code used to take a very long time, this might speed things up
immensely.

(George: can you forward this to the ruby mailing list it was discussed on
initially? Cheers)

Good luck,
jan.


2009/10/16 George Githinji <georgkam at gmail.com>

> Recently had this discussion on the Ruby mailing list. Any ideas or
> solutions
>
> http://www.ruby-forum.com/topic/197365#new
>
> --
> ---------------
> Sincerely
> George
>
> Skype: george_g2
> Blog: http://biorelated.wordpress.com/
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>


From georgkam at gmail.com  Sun Oct 18 07:01:41 2009
From: georgkam at gmail.com (George Githinji)
Date: Sun, 18 Oct 2009 10:01:41 +0300
Subject: [BioRuby] matching against a zillion patterns
In-Reply-To: <4c7507a70910160651t3dbf7e81m580262d7e407edee@mail.gmail.com>
References: <55915f820910152129j3e40f7a7l50bdc368464e12dd@mail.gmail.com> 
	<4c7507a70910160651t3dbf7e81m580262d7e407edee@mail.gmail.com>
Message-ID: <55915f820910180001r23b551e2nea9c1a9d1c46defd@mail.gmail.com>

Thank you for the approach.
The initial list of sequences was 2000.(i.e the ones that need to be
classified) and the numbers of patterns was 570. All of then are of the same
size(14 amino acids long). Using Robert's approach i was able to create a
single very loong regular expression for matching. It seems to work but i
will do some benchmarks and diagnostics tests.

I can twitch this approach so as to do a single pass for all the sequences
while doing the search.

Thank you so much!!

On Fri, Oct 16, 2009 at 4:51 PM, Jan Aerts <jan.aerts at gmail.com> wrote:

> Hey George,
> So if I understand correctly you've got a huge number of aminoacid
> sequences (how many?) and about 400 regular expressions. And for each of the
> aminoacid sequences: if they match just one of the regular expressions they
> are put in box A and if they match none of the regexps, they go into box B.
> Correct?
>
> It just happens that something very similar was the subject of Jim
> Tisdall's (from Beginning Perl for Bioinformatics fame) talk at the
> bioinformatics course we're teaching at the moment :-)
>
> First thing: avoid loops. You don't want to take loop over all regexps for
> each AA sequences, or the other way around.
>
> Are all regexps of the same length? Would be nice if they are, but not
> critical. My approach would be to go over the data just once. So suppose the
> regexps all are of the same length.
>
> A. Prepare your data:
>   a. "Decode" the regexps into literal strings: e.g. /A[BC]D/ become "ABD"
> and "ACD".
>   b. Create a hash that contains all those things as keys.
>   c. Concatenate all AA sequences together, joined with a non-AA, let's say
> a semicolon ";". E.g. CAARGNDLYSKNIG;GGARGNDLYSKNIG;KKARGNDLYSKNIG
>
> B. Do the actual search
>   a. If the length of the strings to match (what used to be the regexps,
> and are now the keys in the hash) is 5: take the first 5 characters of your
> concatenated AA string and check if that substring exists as a key in the
> hash. If so: you know that the AA sequence between the surrounding ";"
> characters should go in box A.
>   b. Advance 1 position: take AAs 2 to 6.
>   c. Go back to a.
>
> You might have to tweak this approach to exactly fit your requirements, but
> if your code used to take a very long time, this might speed things up
> immensely.
>
> (George: can you forward this to the ruby mailing list it was discussed on
> initially? Cheers)
>
> Good luck,
> jan.
>
>
> 2009/10/16 George Githinji <georgkam at gmail.com>
>
>> Recently had this discussion on the Ruby mailing list. Any ideas or
>>
>> solutions
>>
>> http://www.ruby-forum.com/topic/197365#new
>>
>> --
>> ---------------
>> Sincerely
>> George
>>
>> Skype: george_g2
>> Blog: http://biorelated.wordpress.com/
>> _______________________________________________
>> BioRuby mailing list
>> BioRuby at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioruby
>>
>
>


-- 
---------------
Sincerely
George

Skype: george_g2
Blog: http://biorelated.wordpress.com/


From jan.aerts at gmail.com  Tue Oct 20 18:37:37 2009
From: jan.aerts at gmail.com (Jan Aerts)
Date: Tue, 20 Oct 2009 14:37:37 -0400
Subject: [BioRuby] samtools
Message-ID: <4c7507a70910201137h39abcbedv4bb50d7d27f85eb3@mail.gmail.com>

Is anyone working on a ruby-wrapper for the SAM/BAM alignment format for
next-gen sequencing data (http://samtools.sourceforge.net)?
jan.


From kenglish at gmail.com  Wed Oct 21 17:59:13 2009
From: kenglish at gmail.com (Kevin English)
Date: Wed, 21 Oct 2009 07:59:13 -1000
Subject: [BioRuby] Batch Blasting sequences against NR-NT database
Message-ID: <d82e7f560910211059r3dd34cc1gab76cefad846f48b@mail.gmail.com>

Hi,
? I am developeing a program where users want to blast 1000's of
sequences against NCBI-NR database. I'm looking for advice on the best
way to implement this. The 2 options that I see available are:
1) Use Bio::Blast::Remote library in the bio-ruby API.
2) Download the NR database from here: ftp://ftp.ncbi.nih.gov/blast/db
and run blast locally.

Can anyone tell me, looking at this page:

http://blast.ncbi.nlm.nih.gov/blast_overview.shtml

Is the Bio::Blast::Remote using the Blastcl3 program or BLAST URL API?
and what are the trade offs?

My project is avaible on github although I haven't finished all the
documentation yet.

http://github.com/kenglishhi/biococonutisland

Thanks,

Kevin



From pjotr.public14 at thebird.nl  Wed Oct 21 20:40:48 2009
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Wed, 21 Oct 2009 22:40:48 +0200
Subject: [BioRuby] Batch Blasting sequences against NR-NT database
In-Reply-To: <d82e7f560910211059r3dd34cc1gab76cefad846f48b@mail.gmail.com>
References: <d82e7f560910211059r3dd34cc1gab76cefad846f48b@mail.gmail.com>
Message-ID: <20091021204048.GB12568@thebird.nl>

Hi Kevin,

I am doing something like that in a pipe line. Do want to provide a
web interface, or is it batch based? What is the user interface you
envision?

Pj.

On Wed, Oct 21, 2009 at 07:59:13AM -1000, Kevin English wrote:
> Hi,
> ? I am developeing a program where users want to blast 1000's of
> sequences against NCBI-NR database. I'm looking for advice on the best
> way to implement this. The 2 options that I see available are:
> 1) Use Bio::Blast::Remote library in the bio-ruby API.
> 2) Download the NR database from here: ftp://ftp.ncbi.nih.gov/blast/db
> and run blast locally.
> 
> Can anyone tell me, looking at this page:
> 
> http://blast.ncbi.nlm.nih.gov/blast_overview.shtml
> 
> Is the Bio::Blast::Remote using the Blastcl3 program or BLAST URL API?
> and what are the trade offs?
> 
> My project is avaible on github although I haven't finished all the
> documentation yet.
> 
> http://github.com/kenglishhi/biococonutisland
> 
> Thanks,
> 
> Kevin
> 
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby


From kenglish at gmail.com  Wed Oct 21 21:23:17 2009
From: kenglish at gmail.com (Kevin English)
Date: Wed, 21 Oct 2009 11:23:17 -1000
Subject: [BioRuby] Batch Blasting sequences against NR-NT database
In-Reply-To: <20091021204048.GB12568@thebird.nl>
References: <d82e7f560910211059r3dd34cc1gab76cefad846f48b@mail.gmail.com>
	<20091021204048.GB12568@thebird.nl>
Message-ID: <d82e7f560910211423h21f24901s82345ad126362c30@mail.gmail.com>

This will runs a batch job. I have ruby on rails web interface but all
my blasting is handled using the DelayedJob plugin.

What do you mean by "in a pipe line"?


Kevin

On Wed, Oct 21, 2009 at 10:40 AM, Pjotr Prins <pjotr.public14 at thebird.nl> wrote:
> Hi Kevin,
>
> I am doing something like that in a pipe line. Do want to provide a
> web interface, or is it batch based? What is the user interface you
> envision?
>
> Pj.
>
> On Wed, Oct 21, 2009 at 07:59:13AM -1000, Kevin English wrote:
>> Hi,
>> ? I am developeing a program where users want to blast 1000's of
>> sequences against NCBI-NR database. I'm looking for advice on the best
>> way to implement this. The 2 options that I see available are:
>> 1) Use Bio::Blast::Remote library in the bio-ruby API.
>> 2) Download the NR database from here: ftp://ftp.ncbi.nih.gov/blast/db
>> and run blast locally.
>>
>> Can anyone tell me, looking at this page:
>>
>> http://blast.ncbi.nlm.nih.gov/blast_overview.shtml
>>
>> Is the Bio::Blast::Remote using the Blastcl3 program or BLAST URL API?
>> and what are the trade offs?
>>
>> My project is avaible on github although I haven't finished all the
>> documentation yet.
>>
>> http://github.com/kenglishhi/biococonutisland
>>
>> Thanks,
>>
>> Kevin
>>
>> _______________________________________________
>> BioRuby mailing list
>> BioRuby at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioruby
>



From pjotr.public14 at thebird.nl  Thu Oct 22 13:14:54 2009
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Thu, 22 Oct 2009 15:14:54 +0200
Subject: [BioRuby] Batch Blasting sequences against NR-NT database
In-Reply-To: <d82e7f560910211423h21f24901s82345ad126362c30@mail.gmail.com>
References: <d82e7f560910211059r3dd34cc1gab76cefad846f48b@mail.gmail.com>
	<20091021204048.GB12568@thebird.nl>
	<d82e7f560910211423h21f24901s82345ad126362c30@mail.gmail.com>
Message-ID: <20091022131454.GC17287@thebird.nl>

On Wed, Oct 21, 2009 at 11:23:17AM -1000, Kevin English wrote:
> This will runs a batch job. I have ruby on rails web interface but all
> my blasting is handled using the DelayedJob plugin.

OK, this means you could benefit from an XML BLAST parser? Right?
Execute BLAST with XML output, parse that, and convert to some
representation online. Or do you want to use HTML output and embed
that in your tool?

> What do you mean by "in a pipe line"?

A pipeline for parallel computing:

http://en.wikipedia.org/wiki/Parallel_computing

Pj.