From pjotr.public14 at thebird.nl  Thu Mar  1 02:14:36 2012
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Thu, 1 Mar 2012 08:14:36 +0100
Subject: [BioRuby] IRC
Message-ID: <20120301071436.GA860@thebird.nl>

We will be on IRC, most of the day.

Pj.

From mictadlo at gmail.com  Fri Mar  2 04:11:35 2012
From: mictadlo at gmail.com (Mic)
Date: Fri, 2 Mar 2012 19:11:35 +1000
Subject: [BioRuby] Bio::Faster plugin
In-Reply-To: <CALf85+V1-a+i2dc0YKf95vgrEX1pipXSZ_gHayii2ayGs8m+4Q@mail.gmail.com>
References: <CACtet2TWTXMRkpgbai0=Fue7Cmn3v6EBbuXWd32cOa_xiD90AA@mail.gmail.com>
	<CB2A292C.747B%bonnal@ingm.org>
	<CALf85+V1-a+i2dc0YKf95vgrEX1pipXSZ_gHayii2ayGs8m+4Q@mail.gmail.com>
Message-ID: <CAOP6n=h3JcZ7=_bp51LRdX1nQDKnHY-o3eQo9_g9EZ4t4OZcuA@mail.gmail.com>

Did also compare the speed between biofaster and reading 4 lines (fastq)/2
lines (fasta) at the time?

Cheers,

On Thu, Jan 5, 2012 at 1:20 AM, George Githinji <georgkam at gmail.com> wrote:

> ++1 Sounds cool!
>
>
> On Wed, Jan 4, 2012 at 6:05 PM, Raoul Bonnal <bonnal at ingm.org> wrote:
> > Hi Francesco,
> > It's very cool!
> >
> > And you can access to the seq object/array also in this way:
> > Bio::Faster.parse(File.join(TEST_DATA,"sample.fastq")) do |id, comments,
> > sequence, quality|
> >  puts "#{id} #{comments} #{sequence} #{quality}"
> > end
> >
> > Obviously I like it more than using the raw array :-)
> > I suppose in case of no quality value you get a nil object
> >
> >
> > +1
> >
> >
> > On 04/01/12 10.50, "Francesco Strozzi" <francesco.strozzi at gmail.com>
> wrote:
> >
> >> Hi guys,
> >>
> >> I have created a BioRuby plugin called bio-faster, that implements a
> fast
> >> and simple parser for FastA and FastQ files. It's based on the C library
> >> Kseq written by Heng Li (author of Samtools and BWA). Compared to
> >> Bio::FastQ it is actually 4-5 times faster in parsing large FastQ files.
> >> The code will not create a Bio object for each sequence but it will
> return
> >> a simple array with sequence data and quality values for FastQ (it
> supports
> >> Sanger/Phred format only).
> >> Bio::Faster could be a good choice when you just need to parse huge
> files,
> >> for example to extract information or to store sequence data in a
> database,
> >> and you don't need to create an object for each sequence but you only
> want
> >> to parse the dataset easily and quickly.
> >>
> >> Here is the code: https://github.com/fstrozzi/bioruby-faster
> >> Here is the wiki for more details:
> >> https://github.com/fstrozzi/bioruby-faster/wiki
> >> To get the gem: gem install bio-faster
> >>
> >> Tested with Ruby 1.9 only.
> >>
> >> Any comment or feedback is much appreciated!
> >>
> >> Cheers
> >
> >
> > _______________________________________________
> > BioRuby Project - http://www.bioruby.org/
> > 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/
> Twitter: http://twitter.com/#!/george_l
>
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>

From p.j.a.cock at googlemail.com  Fri Mar  2 09:04:21 2012
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 2 Mar 2012 14:04:21 +0000
Subject: [BioRuby] Google Summer of Code project ideas
In-Reply-To: <CF39235E-DD8E-4B28-B2CE-5C1E9F80A54B@illinois.edu>
References: <4F355910.4060203@gmail.com>
	<CF39235E-DD8E-4B28-B2CE-5C1E9F80A54B@illinois.edu>
Message-ID: <CAKVJ-_5uKFqH_krSzEemCikVN-pDK1C9E0s4yfk=JGNbkqk=3g@mail.gmail.com>

On 10 Feb, Robert Buels wrote (posted by Chris Field):
> Hi all,
>
> I'm going to be OBF project admin again this year for Google Summer of
> code. ?OBF's application is due in a couple of weeks, and we need to update
> our project ideas on the OBF wiki page and on each project's individual wiki
> pages.
>
> So, for each of the OBF projects that wants to do GSoC again this year,
> please:
>
> a.) Update the list of project ideas on your project's GSoC page
> (BioPython, BioPerl, BioRuby, etc). ?Add new ones, remove ones that have
> already been done or no longer relevant, etc.
>
> b.) Update the list of project ideas on the main OBF GSoC page
> (http://www.open-bio.org/wiki/Google_Summer_of_Code) to match.
>
> c.) Let me know via email that you have done so and it's ready for Google
> to peruse.
>
> Please have the updates done, if possible, by this Friday (March 11). The
> number and quality of the project ideas are part of the evaluation process
> for whether OBF is accepted as a Summer of Code organization again this
> year, so let's come up with some good ones. ?:-)
>
> Rob
>
> ----
> Robert Buels

Hi BioRuby folk,

You seem to have been the most organized Bio* project for GSoC so far, and have
put together good set of GSoC project ideas by Rob's target date. Well done :)

Is the list here complete now?
http://bioruby.open-bio.org/wiki/Google_Summer_of_Code

    3.1.1 Write the world's fastest parallelized GFF3/GTF parser in D,
for Ruby FFI
    3.1.2 Extend bio-alignment plug-in with Multiple Alignment Format
-MAF- parser (FFI?)
    3.1.3 Testing framework for biogem plugins
    3.1.4 Adding social networking functionality to BioRuby.org
    3.1.5 Update bio-images a plugin to represent bio-object with cool images
    3.1.6 Update to the Ruby Ensembl API

I noticed "Testing framework for biogem plugins" was missing on the OBF
summary page, so I added it:
http://www.open-bio.org/wiki/Google_Summer_of_Code

Regards,

Peter


From mictadlo at gmail.com  Fri Mar  2 20:14:40 2012
From: mictadlo at gmail.com (Mic)
Date: Sat, 3 Mar 2012 11:14:40 +1000
Subject: [BioRuby] Google Summer of Code project ideas
In-Reply-To: <CAKVJ-_5uKFqH_krSzEemCikVN-pDK1C9E0s4yfk=JGNbkqk=3g@mail.gmail.com>
References: <4F355910.4060203@gmail.com>
	<CF39235E-DD8E-4B28-B2CE-5C1E9F80A54B@illinois.edu>
	<CAKVJ-_5uKFqH_krSzEemCikVN-pDK1C9E0s4yfk=JGNbkqk=3g@mail.gmail.com>
Message-ID: <CAOP6n=h8bWUaBra-N35AxqnZm2H6p8WH+akx5tB9q9fdhwgkfw@mail.gmail.com>

Howabout to include:
* Bedtools
* tabix


On Sat, Mar 3, 2012 at 12:04 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On 10 Feb, Robert Buels wrote (posted by Chris Field):
> > Hi all,
> >
> > I'm going to be OBF project admin again this year for Google Summer of
> > code.  OBF's application is due in a couple of weeks, and we need to
> update
> > our project ideas on the OBF wiki page and on each project's individual
> wiki
> > pages.
> >
> > So, for each of the OBF projects that wants to do GSoC again this year,
> > please:
> >
> > a.) Update the list of project ideas on your project's GSoC page
> > (BioPython, BioPerl, BioRuby, etc).  Add new ones, remove ones that have
> > already been done or no longer relevant, etc.
> >
> > b.) Update the list of project ideas on the main OBF GSoC page
> > (http://www.open-bio.org/wiki/Google_Summer_of_Code) to match.
> >
> > c.) Let me know via email that you have done so and it's ready for Google
> > to peruse.
> >
> > Please have the updates done, if possible, by this Friday (March 11). The
> > number and quality of the project ideas are part of the evaluation
> process
> > for whether OBF is accepted as a Summer of Code organization again this
> > year, so let's come up with some good ones.  :-)
> >
> > Rob
> >
> > ----
> > Robert Buels
>
> Hi BioRuby folk,
>
> You seem to have been the most organized Bio* project for GSoC so far, and
> have
> put together good set of GSoC project ideas by Rob's target date. Well
> done :)
>
> Is the list here complete now?
> http://bioruby.open-bio.org/wiki/Google_Summer_of_Code
>
>    3.1.1 Write the world's fastest parallelized GFF3/GTF parser in D,
> for Ruby FFI
>    3.1.2 Extend bio-alignment plug-in with Multiple Alignment Format
> -MAF- parser (FFI?)
>    3.1.3 Testing framework for biogem plugins
>    3.1.4 Adding social networking functionality to BioRuby.org
>    3.1.5 Update bio-images a plugin to represent bio-object with cool
> images
>    3.1.6 Update to the Ruby Ensembl API
>
> I noticed "Testing framework for biogem plugins" was missing on the OBF
> summary page, so I added it:
> http://www.open-bio.org/wiki/Google_Summer_of_Code
>
> Regards,
>
> Peter
>
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>

From francesco.strozzi at gmail.com  Sat Mar  3 02:38:54 2012
From: francesco.strozzi at gmail.com (Francesco Strozzi)
Date: Sat, 3 Mar 2012 08:38:54 +0100
Subject: [BioRuby] Bio::Faster plugin
In-Reply-To: <CAOP6n=h3JcZ7=_bp51LRdX1nQDKnHY-o3eQo9_g9EZ4t4OZcuA@mail.gmail.com>
References: <CACtet2TWTXMRkpgbai0=Fue7Cmn3v6EBbuXWd32cOa_xiD90AA@mail.gmail.com>
	<CB2A292C.747B%bonnal@ingm.org>
	<CALf85+V1-a+i2dc0YKf95vgrEX1pipXSZ_gHayii2ayGs8m+4Q@mail.gmail.com>
	<CAOP6n=h3JcZ7=_bp51LRdX1nQDKnHY-o3eQo9_g9EZ4t4OZcuA@mail.gmail.com>
Message-ID: <CACtet2T__UCO8Eq6WXkCHEQr+FFaO93_vm7p1dqt=iOZRFVB=Q@mail.gmail.com>

Hi,
I haven't done this comparison, but if you want to run it I will be happy
to put the outputs on the wiki.

Cheers

On Friday, March 2, 2012, Mic <mictadlo at gmail.com> wrote:
> Did also compare the speed between biofaster and reading 4 lines (fastq)/2
> lines (fasta) at the time?
>
> Cheers,
>
> On Thu, Jan 5, 2012 at 1:20 AM, George Githinji <georgkam at gmail.com>
wrote:
>
>> ++1 Sounds cool!
>>
>>
>> On Wed, Jan 4, 2012 at 6:05 PM, Raoul Bonnal <bonnal at ingm.org> wrote:
>> > Hi Francesco,
>> > It's very cool!
>> >
>> > And you can access to the seq object/array also in this way:
>> > Bio::Faster.parse(File.join(TEST_DATA,"sample.fastq")) do |id,
comments,
>> > sequence, quality|
>> >  puts "#{id} #{comments} #{sequence} #{quality}"
>> > end
>> >
>> > Obviously I like it more than using the raw array :-)
>> > I suppose in case of no quality value you get a nil object
>> >
>> >
>> > +1
>> >
>> >
>> > On 04/01/12 10.50, "Francesco Strozzi" <francesco.strozzi at gmail.com>
>> wrote:
>> >
>> >> Hi guys,
>> >>
>> >> I have created a BioRuby plugin called bio-faster, that implements a
>> fast
>> >> and simple parser for FastA and FastQ files. It's based on the C
library
>> >> Kseq written by Heng Li (author of Samtools and BWA). Compared to
>> >> Bio::FastQ it is actually 4-5 times faster in parsing large FastQ
files.
>> >> The code will not create a Bio object for each sequence but it will
>> return
>> >> a simple array with sequence data and quality values for FastQ (it
>> supports
>> >> Sanger/Phred format only).
>> >> Bio::Faster could be a good choice when you just need to parse huge
>> files,
>> >> for example to extract information or to store sequence data in a
>> database,
>> >> and you don't need to create an object for each sequence but you only
>> want
>> >> to parse the dataset easily and quickly.
>> >>
>> >> Here is the code: https://github.com/fstrozzi/bioruby-faster
>> >> Here is the wiki for more details:
>> >> https://github.com/fstrozzi/bioruby-faster/wiki
>> >> To get the gem: gem install bio-faster
>> >>
>> >> Tested with Ruby 1.9 only.
>> >>
>> >> Any comment or feedback is much appreciated!
>> >>
>> >> Cheers
>> >
>> >
>> > _______________________________________________
>> > BioRuby Project - http://www.bioruby.org/
>> > 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/
>> Twitter: http://twitter.com/#!/george_l
>>
>> _______________________________________________
>> 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
>

-- 

Francesco

From bonnal at ingm.org  Sat Mar  3 06:15:56 2012
From: bonnal at ingm.org (Raoul Bonnal)
Date: Sat, 03 Mar 2012 12:15:56 +0100
Subject: [BioRuby] Google Summer of Code project ideas
In-Reply-To: <CAOP6n=h8bWUaBra-N35AxqnZm2H6p8WH+akx5tB9q9fdhwgkfw@mail.gmail.com>
Message-ID: <CB77BBFC.84F8%bonnal@ingm.org>

What you mean ?

I would add "Extract BioSQL form BioRuby and create a biogem plug-in,
updating the library where needed."

Is there more time to add this project?


On 03/03/12 02.14, "Mic" <mictadlo at gmail.com> wrote:

> Howabout to include:
> * Bedtools
> * tabix
> 
> 
> On Sat, Mar 3, 2012 at 12:04 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:
> 
>> On 10 Feb, Robert Buels wrote (posted by Chris Field):
>>> Hi all,
>>> 
>>> I'm going to be OBF project admin again this year for Google Summer of
>>> code.  OBF's application is due in a couple of weeks, and we need to
>> update
>>> our project ideas on the OBF wiki page and on each project's individual
>> wiki
>>> pages.
>>> 
>>> So, for each of the OBF projects that wants to do GSoC again this year,
>>> please:
>>> 
>>> a.) Update the list of project ideas on your project's GSoC page
>>> (BioPython, BioPerl, BioRuby, etc).  Add new ones, remove ones that have
>>> already been done or no longer relevant, etc.
>>> 
>>> b.) Update the list of project ideas on the main OBF GSoC page
>>> (http://www.open-bio.org/wiki/Google_Summer_of_Code) to match.
>>> 
>>> c.) Let me know via email that you have done so and it's ready for Google
>>> to peruse.
>>> 
>>> Please have the updates done, if possible, by this Friday (March 11). The
>>> number and quality of the project ideas are part of the evaluation
>> process
>>> for whether OBF is accepted as a Summer of Code organization again this
>>> year, so let's come up with some good ones.  :-)
>>> 
>>> Rob
>>> 
>>> ----
>>> Robert Buels
>> 
>> Hi BioRuby folk,
>> 
>> You seem to have been the most organized Bio* project for GSoC so far, and
>> have
>> put together good set of GSoC project ideas by Rob's target date. Well
>> done :)
>> 
>> Is the list here complete now?
>> http://bioruby.open-bio.org/wiki/Google_Summer_of_Code
>> 
>>    3.1.1 Write the world's fastest parallelized GFF3/GTF parser in D,
>> for Ruby FFI
>>    3.1.2 Extend bio-alignment plug-in with Multiple Alignment Format
>> -MAF- parser (FFI?)
>>    3.1.3 Testing framework for biogem plugins
>>    3.1.4 Adding social networking functionality to BioRuby.org
>>    3.1.5 Update bio-images a plugin to represent bio-object with cool
>> images
>>    3.1.6 Update to the Ruby Ensembl API
>> 
>> I noticed "Testing framework for biogem plugins" was missing on the OBF
>> summary page, so I added it:
>> http://www.open-bio.org/wiki/Google_Summer_of_Code
>> 
>> Regards,
>> 
>> Peter
>> 
>> _______________________________________________
>> 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 bonnal at ingm.org  Sat Mar  3 06:15:57 2012
From: bonnal at ingm.org (Raoul Bonnal)
Date: Sat, 03 Mar 2012 12:15:57 +0100
Subject: [BioRuby] Google Summer of Code project ideas
In-Reply-To: <CAKVJ-_5uKFqH_krSzEemCikVN-pDK1C9E0s4yfk=JGNbkqk=3g@mail.gmail.com>
Message-ID: <CB77BBFD.84F8%bonnal@ingm.org>

Thanks !

Rob is aware that our page is ready to go.

Good job BioRubyGuys


On 02/03/12 15.04, "Peter Cock" <p.j.a.cock at googlemail.com> wrote:

> On 10 Feb, Robert Buels wrote (posted by Chris Field):
>> Hi all,
>> 
>> I'm going to be OBF project admin again this year for Google Summer of
>> code. ?OBF's application is due in a couple of weeks, and we need to update
>> our project ideas on the OBF wiki page and on each project's individual wiki
>> pages.
>> 
>> So, for each of the OBF projects that wants to do GSoC again this year,
>> please:
>> 
>> a.) Update the list of project ideas on your project's GSoC page
>> (BioPython, BioPerl, BioRuby, etc). ?Add new ones, remove ones that have
>> already been done or no longer relevant, etc.
>> 
>> b.) Update the list of project ideas on the main OBF GSoC page
>> (http://www.open-bio.org/wiki/Google_Summer_of_Code) to match.
>> 
>> c.) Let me know via email that you have done so and it's ready for Google
>> to peruse.
>> 
>> Please have the updates done, if possible, by this Friday (March 11). The
>> number and quality of the project ideas are part of the evaluation process
>> for whether OBF is accepted as a Summer of Code organization again this
>> year, so let's come up with some good ones. ?:-)
>> 
>> Rob
>> 
>> ----
>> Robert Buels
> 
> Hi BioRuby folk,
> 
> You seem to have been the most organized Bio* project for GSoC so far, and
> have
> put together good set of GSoC project ideas by Rob's target date. Well done :)
> 
> Is the list here complete now?
> http://bioruby.open-bio.org/wiki/Google_Summer_of_Code
> 
>     3.1.1 Write the world's fastest parallelized GFF3/GTF parser in D,
> for Ruby FFI
>     3.1.2 Extend bio-alignment plug-in with Multiple Alignment Format
> -MAF- parser (FFI?)
>     3.1.3 Testing framework for biogem plugins
>     3.1.4 Adding social networking functionality to BioRuby.org
>     3.1.5 Update bio-images a plugin to represent bio-object with cool images
>     3.1.6 Update to the Ruby Ensembl API
> 
> I noticed "Testing framework for biogem plugins" was missing on the OBF
> summary page, so I added it:
> http://www.open-bio.org/wiki/Google_Summer_of_Code
> 
> Regards,
> 
> Peter
> 
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby




From cjfields at illinois.edu  Sat Mar  3 08:44:40 2012
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Sat, 3 Mar 2012 13:44:40 +0000
Subject: [BioRuby] Bio::Faster plugin
In-Reply-To: <CACtet2T__UCO8Eq6WXkCHEQr+FFaO93_vm7p1dqt=iOZRFVB=Q@mail.gmail.com>
References: <CACtet2TWTXMRkpgbai0=Fue7Cmn3v6EBbuXWd32cOa_xiD90AA@mail.gmail.com>
	<CB2A292C.747B%bonnal@ingm.org>
	<CALf85+V1-a+i2dc0YKf95vgrEX1pipXSZ_gHayii2ayGs8m+4Q@mail.gmail.com>
	<CAOP6n=h3JcZ7=_bp51LRdX1nQDKnHY-o3eQo9_g9EZ4t4OZcuA@mail.gmail.com>
	<CACtet2T__UCO8Eq6WXkCHEQr+FFaO93_vm7p1dqt=iOZRFVB=Q@mail.gmail.com>
Message-ID: <F1BDB21F-8CEC-4880-B2F1-56AF003CCA44@illinois.edu>

I have a perl binding to the same C lib implementation (Heng Li's readfq), haven't benchmarked it against our low-level pure perl version but it does seem to be significantly faster.  Not to mention it covers both FASTQ and FASTA.

Not sure how it handles the FASTQ test suite we came up with, might be worth checking out.

chris

On Mar 3, 2012, at 1:38 AM, Francesco Strozzi wrote:

> Hi,
> I haven't done this comparison, but if you want to run it I will be happy
> to put the outputs on the wiki.
> 
> Cheers
> 
> On Friday, March 2, 2012, Mic <mictadlo at gmail.com> wrote:
>> Did also compare the speed between biofaster and reading 4 lines (fastq)/2
>> lines (fasta) at the time?
>> 
>> Cheers,
>> 
>> On Thu, Jan 5, 2012 at 1:20 AM, George Githinji <georgkam at gmail.com>
> wrote:
>> 
>>> ++1 Sounds cool!
>>> 
>>> 
>>> On Wed, Jan 4, 2012 at 6:05 PM, Raoul Bonnal <bonnal at ingm.org> wrote:
>>>> Hi Francesco,
>>>> It's very cool!
>>>> 
>>>> And you can access to the seq object/array also in this way:
>>>> Bio::Faster.parse(File.join(TEST_DATA,"sample.fastq")) do |id,
> comments,
>>>> sequence, quality|
>>>> puts "#{id} #{comments} #{sequence} #{quality}"
>>>> end
>>>> 
>>>> Obviously I like it more than using the raw array :-)
>>>> I suppose in case of no quality value you get a nil object
>>>> 
>>>> 
>>>> +1
>>>> 
>>>> 
>>>> On 04/01/12 10.50, "Francesco Strozzi" <francesco.strozzi at gmail.com>
>>> wrote:
>>>> 
>>>>> Hi guys,
>>>>> 
>>>>> I have created a BioRuby plugin called bio-faster, that implements a
>>> fast
>>>>> and simple parser for FastA and FastQ files. It's based on the C
> library
>>>>> Kseq written by Heng Li (author of Samtools and BWA). Compared to
>>>>> Bio::FastQ it is actually 4-5 times faster in parsing large FastQ
> files.
>>>>> The code will not create a Bio object for each sequence but it will
>>> return
>>>>> a simple array with sequence data and quality values for FastQ (it
>>> supports
>>>>> Sanger/Phred format only).
>>>>> Bio::Faster could be a good choice when you just need to parse huge
>>> files,
>>>>> for example to extract information or to store sequence data in a
>>> database,
>>>>> and you don't need to create an object for each sequence but you only
>>> want
>>>>> to parse the dataset easily and quickly.
>>>>> 
>>>>> Here is the code: https://github.com/fstrozzi/bioruby-faster
>>>>> Here is the wiki for more details:
>>>>> https://github.com/fstrozzi/bioruby-faster/wiki
>>>>> To get the gem: gem install bio-faster
>>>>> 
>>>>> Tested with Ruby 1.9 only.
>>>>> 
>>>>> Any comment or feedback is much appreciated!
>>>>> 
>>>>> Cheers
>>>> 
>>>> 
>>>> _______________________________________________
>>>> BioRuby Project - http://www.bioruby.org/
>>>> 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/
>>> Twitter: http://twitter.com/#!/george_l
>>> 
>>> _______________________________________________
>>> 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
>> 
> 
> -- 
> 
> Francesco
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby



From bonnal at ingm.org  Mon Mar  5 09:19:10 2012
From: bonnal at ingm.org (Raoul Bonnal)
Date: Mon, 05 Mar 2012 15:19:10 +0100
Subject: [BioRuby] RubyMine
Message-ID: <CB7A89EE.854F%bonnal@ingm.org>

Some time ago I asked JetBrains to support our project with their Open
Source License program.

So if you are interested in using RubyMine http://www.jetbrains.com/ruby/
drop me an e-mail and I?ll share the license code with you; the license is
one year from now.

I can not publish it and I invite you to not publish it on
webpages/site/forums/any social network.

--
Ra


From mictadlo at gmail.com  Wed Mar  7 01:58:00 2012
From: mictadlo at gmail.com (Mic)
Date: Wed, 7 Mar 2012 16:58:00 +1000
Subject: [BioRuby] Google Summer of Code project ideas
In-Reply-To: <CB7B84C5.8586%bonnal@ingm.org>
References: <CAOP6n=j=7cMp0B=G1MuYj0XvMbCW6sY++XV7OjALCKdinWhcHQ@mail.gmail.com>
	<CB7B84C5.8586%bonnal@ingm.org>
Message-ID: <CAOP6n=hcuH4cxQnkpxdumHYaXuQu-6dVWx54mRGY4+9YyiUUsw@mail.gmail.com>

HI Raoul,
Analogous to Samfile, a Tabixfile allows fast random access to compressed
and tabix indexed tab-separated file formats with genomic data:

*import pysam*
*tabixfile = pysam.Tabixfile( "example.gtf.gz" )*
*
*
*for gtf in tabixfile.fetch('chr1', 1000, 2000):*
*    print gtf.contig, gtf.start, gtf.end, gtf.gene_id*
*
*
*
*
I am not suitable for a mentor, because I have not used Ruby for years. I
just observe BioRuby and try give some ideas.

Cheers,

On Tue, Mar 6, 2012 at 6:09 PM, Raoul Bonnal <bonnal at ingm.org> wrote:

>  Hi Mic,
>
> >* a ruby version of
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232365/?tool=pubmed
> If you want to help us with GSoC please add it to the list and put
> yourself as a mentor ( later you?ll need to register yourself as a mentor),
> for us (the panel) any bioruby developer/user can be a mentor, it?s not
> much work and you?ll not be alone :)
>
>
> >a ruby interface for tabix ( http://samtools.sourceforge.net/tabix.shtml) see pysam
> http://code.google.com/p/pysam/source/browse/tests/tabix_test.py?r=2fff972c6b60390e4962d3f46f7c269acd9aa33e
>  Is it an interface to sam/bam ? Have you see this
> https://github.com/helios/bioruby-samtools project ? Can you evaluate the
> main differences between the two projects ?
>
> Please add them to GSoC (on our wik) in any case, we?ll keep there the
> list of desired things. If you do not have time to be a mentor just write
> the projects and maybe someone will lead it.
>
> Thanks a lot!
>
>
> On 06/03/12 02.18, "Mic" <mictadlo at gmail.com> wrote:
>
>
>    - a ruby version of
>    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232365/?tool=pubmed
>
>
>
>
> * a ruby interface for tabix ( http://samtools.sourceforge.net/tabix.shtml) see pysam
> http://code.google.com/p/pysam/source/browse/tests/tabix_test.py?r=2fff972c6b60390e4962d3f46f7c269acd9aa33e
>
>
> On Sat, Mar 3, 2012 at 9:15 PM, Raoul Bonnal <bonnal at ingm.org> wrote:
>
> Thanks !
>
> Rob is aware that our page is ready to go.
>
> Good job BioRubyGuys
>
>
> On 02/03/12 15.04, "Peter Cock" <p.j.a.cock at googlemail.com> wrote:
>
> > On 10 Feb, Robert Buels wrote (posted by Chris Field):
> >> Hi all,
> >>
> >> I'm going to be OBF project admin again this year for Google Summer of
> >> code.  OBF's application is due in a couple of weeks, and we need to
> update
> >> our project ideas on the OBF wiki page and on each project's individual
> wiki
> >> pages.
> >>
> >> So, for each of the OBF projects that wants to do GSoC again this year,
> >> please:
> >>
> >> a.) Update the list of project ideas on your project's GSoC page
> >> (BioPython, BioPerl, BioRuby, etc).  Add new ones, remove ones that have
> >> already been done or no longer relevant, etc.
> >>
> >> b.) Update the list of project ideas on the main OBF GSoC page
> >> (http://www.open-bio.org/wiki/Google_Summer_of_Code) to match.
> >>
> >> c.) Let me know via email that you have done so and it's ready for
> Google
> >> to peruse.
> >>
> >> Please have the updates done, if possible, by this Friday (March 11).
> The
> >> number and quality of the project ideas are part of the evaluation
> process
> >> for whether OBF is accepted as a Summer of Code organization again this
> >> year, so let's come up with some good ones.  :-)
> >>
> >> Rob
> >>
> >> ----
> >> Robert Buels
> >
> > Hi BioRuby folk,
> >
> > You seem to have been the most organized Bio* project for GSoC so far,
> and
> > have
> > put together good set of GSoC project ideas by Rob's target date. Well
> done :)
> >
> > Is the list here complete now?
> > http://bioruby.open-bio.org/wiki/Google_Summer_of_Code
> >
> >     3.1.1 Write the world's fastest parallelized GFF3/GTF parser in D,
> > for Ruby FFI
> >     3.1.2 Extend bio-alignment plug-in with Multiple Alignment Format
> > -MAF- parser (FFI?)
> >     3.1.3 Testing framework for biogem plugins
> >     3.1.4 Adding social networking functionality to BioRuby.org
> >     3.1.5 Update bio-images a plugin to represent bio-object with cool
> images
> >     3.1.6 Update to the Ruby Ensembl API
> >
> > I noticed "Testing framework for biogem plugins" was missing on the OBF
> > summary page, so I added it:
> > http://www.open-bio.org/wiki/Google_Summer_of_Code
> >
> > Regards,
> >
> > Peter
> >
> > _______________________________________________
> > 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 missy at be.to  Wed Mar  7 21:55:43 2012
From: missy at be.to (MISHIMA, Hiroyuki)
Date: Thu, 08 Mar 2012 11:55:43 +0900
Subject: [BioRuby] Ruby UCSC API v0.4.0 is released
Message-ID: <4F581FAF.8050005@be.to>

Hi all,

Ruby UCSC API, a BioGem to access the UCSC genome database using Ruby, 
is updated. The API is refined (simplified) with keeping backward 
compatibility. Rails/ActiveRecord v3.1 and later are supported.

GitHub:
https://github.com/misshie/bioruby-ucsc-api

RubyGems:
https://rubygems.org/gems/bio-ucsc-api

User feedback forum:
http://rubyucscapi.userecho.com/

Your comments and suggestions are *very* welcome!

Sincerely yours,
Hiro.
-- 
MISHIMA, Hiroyuki, DDS, Ph.D.
COE Research Fellow
Department of Human Genetics
Nagasaki University Graduate School of Biomedical Sciences

From pjotr.public14 at thebird.nl  Sun Mar 11 08:53:08 2012
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Sun, 11 Mar 2012 13:53:08 +0100
Subject: [BioRuby] BioRuby: newick parser
Message-ID: <20120311125308.GB4204@thebird.nl>

Hi Naohisa and others,

I am looking at the Newick/Nexux/PhyloXML parsers at the moment. The
BioRuby ones look rather complete, if not a tad overcomplicated. 

Are you happy with the state of affairs, or do you thing it could be
improved/simplified?  Also, for walking the tree, is the interface now
the one you would choose to implement?

I am asking, because I am looking for the most intuitive way of
parsing and traversing tree information. I see Christian has done a
lot of work in this area (mostly in Java), even to the point of
taking standards forward. Maybe I should ask him? It appears to me we
have solid parsers and data structures. Walking the trees, however,
is less straightforward, and documentation somewhat lacking.

Anyone happy to correct me?

Pj.

From ngoto at gen-info.osaka-u.ac.jp  Mon Mar 12 02:18:48 2012
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Mon, 12 Mar 2012 15:18:48 +0900
Subject: [BioRuby] BioRuby: newick parser
In-Reply-To: <20120311125308.GB4204@thebird.nl>
References: <20120311125308.GB4204@thebird.nl>
Message-ID: <201203120625.q2C6POXo013432@portal.open-bio.org>

Hi Pjotr,

They can be divided into several parts.

1. Newick/NHX parser and writer: 

1-1. Implementation: I think it is enough quiality. The implementation
complexity is due to the Newick specification (e.g. escaping of special
characters) and some undocumented conventions (e.g. bootstrap values).
For refactoring, using Racc (parser generator for Ruby) seems good,
but low priority.

1-2. Parser API: Parsing a string is simple. Reading from files is
depended on Bio::FlatFile system, which is enough for most cases.

1-3. Writer API: depending on Bio::Tree API.

2. Nexus parser and writer:

2-1: Implementation: I don't know details of current status,
but for trees, it only passes the data to Bio::Newick class.
Please ask Christian for details.

2-2: API: Nexus Parser API is complicated because the Nexus
specification is very complex.
It seems that Nexus writer is missing.

3: PhyloXML parser and writer:

3-1: Parser implementation and API: Enough quality. Its
complexity is mainly due to the on-demand partial reading of
XML files, which saves memory for a large tree file.

3-2: Writer implementation and API: Not enough. It can only
write PhyloXML data, and it is very hard to output Bio::Tree
as PhyloXML format.

3-3: Other topics: It uses libxml-ruby, but it seems that
Ruby XML parser de-facto standard is now Nokogiri, and
I think it may be rewritten by using Nokogiri in some days.

4. Bio::Tree data structure:

4-1. Implementation: It is based on BioRuby internal graph
library. It can be changed to use other graph library.

4-2. API: The API design is based on tree API of other
open-bio projects and generic graph library API.

When writing HOWTO based on BioPerl HOWTO:Trees,
(http://bioruby.open-bio.org/wiki/HOWTO:Trees but still incomplete)
I'm thinking to add/modify some API about speficying nodes/edges.


> I see Christian has done a lot of work in this area (mostly in Java),
> even to the point of taking standards forward. Maybe I should ask him?

I'd like to hear his advice, too.

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


On Sun, 11 Mar 2012 13:53:08 +0100
Pjotr Prins <pjotr.public14 at thebird.nl> wrote:

> Hi Naohisa and others,
> 
> I am looking at the Newick/Nexux/PhyloXML parsers at the moment. The
> BioRuby ones look rather complete, if not a tad overcomplicated. 
> 
> Are you happy with the state of affairs, or do you thing it could be
> improved/simplified?  Also, for walking the tree, is the interface now
> the one you would choose to implement?
> 
> I am asking, because I am looking for the most intuitive way of
> parsing and traversing tree information. I see Christian has done a
> lot of work in this area (mostly in Java), even to the point of
> taking standards forward. Maybe I should ask him? It appears to me we
> have solid parsers and data structures. Walking the trees, however,
> is less straightforward, and documentation somewhat lacking.
> 
> Anyone happy to correct me?
> 
> Pj.


From pjotr.public14 at thebird.nl  Mon Mar 12 06:08:41 2012
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Mon, 12 Mar 2012 11:08:41 +0100
Subject: [BioRuby] BioRuby: newick parser
References: <20120311125308.GB4204@thebird.nl>
Message-ID: <20120312100841.GA8543@thebird.nl>

Hi Naohisa,

Thanks for the quick reply. I think the Newick parser and Phyloxml
parser are the way to go. I guess it is partly due to me that the
latter is somewhat complex for not reading the DOM in RAM ;).

I'll start using the string based Newick parser for MSA, as it is so
common, and see if I can make it flow naturally :)

Pj.

On Mon, Mar 12, 2012 at 03:18:48PM +0900, Naohisa GOTO wrote:
> Hi Pjotr,
> 
> They can be divided into several parts.
> 
> 1. Newick/NHX parser and writer: 
> 
> 1-1. Implementation: I think it is enough quiality. The implementation
> complexity is due to the Newick specification (e.g. escaping of special
> characters) and some undocumented conventions (e.g. bootstrap values).
> For refactoring, using Racc (parser generator for Ruby) seems good,
> but low priority.
> 
> 1-2. Parser API: Parsing a string is simple. Reading from files is
> depended on Bio::FlatFile system, which is enough for most cases.
> 
> 1-3. Writer API: depending on Bio::Tree API.
> 
> 2. Nexus parser and writer:
> 
> 2-1: Implementation: I don't know details of current status,
> but for trees, it only passes the data to Bio::Newick class.
> Please ask Christian for details.
> 
> 2-2: API: Nexus Parser API is complicated because the Nexus
> specification is very complex.
> It seems that Nexus writer is missing.
> 
> 3: PhyloXML parser and writer:
> 
> 3-1: Parser implementation and API: Enough quality. Its
> complexity is mainly due to the on-demand partial reading of
> XML files, which saves memory for a large tree file.
> 
> 3-2: Writer implementation and API: Not enough. It can only
> write PhyloXML data, and it is very hard to output Bio::Tree
> as PhyloXML format.
> 
> 3-3: Other topics: It uses libxml-ruby, but it seems that
> Ruby XML parser de-facto standard is now Nokogiri, and
> I think it may be rewritten by using Nokogiri in some days.
> 
> 4. Bio::Tree data structure:
> 
> 4-1. Implementation: It is based on BioRuby internal graph
> library. It can be changed to use other graph library.
> 
> 4-2. API: The API design is based on tree API of other
> open-bio projects and generic graph library API.
> 
> When writing HOWTO based on BioPerl HOWTO:Trees,
> (http://bioruby.open-bio.org/wiki/HOWTO:Trees but still incomplete)
> I'm thinking to add/modify some API about speficying nodes/edges.
> 
> 
> > I see Christian has done a lot of work in this area (mostly in Java),
> > even to the point of taking standards forward. Maybe I should ask him?
> 
> I'd like to hear his advice, too.
> 
> Naohisa Goto
> ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
> 
> 
> On Sun, 11 Mar 2012 13:53:08 +0100
> Pjotr Prins <pjotr.public14 at thebird.nl> wrote:
> 
> > Hi Naohisa and others,
> > 
> > I am looking at the Newick/Nexux/PhyloXML parsers at the moment. The
> > BioRuby ones look rather complete, if not a tad overcomplicated. 
> > 
> > Are you happy with the state of affairs, or do you thing it could be
> > improved/simplified?  Also, for walking the tree, is the interface now
> > the one you would choose to implement?
> > 
> > I am asking, because I am looking for the most intuitive way of
> > parsing and traversing tree information. I see Christian has done a
> > lot of work in this area (mostly in Java), even to the point of
> > taking standards forward. Maybe I should ask him? It appears to me we
> > have solid parsers and data structures. Walking the trees, however,
> > is less straightforward, and documentation somewhat lacking.
> > 
> > Anyone happy to correct me?
> > 
> > Pj.
> 

From pjotr.public14 at thebird.nl  Mon Mar 12 12:24:38 2012
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Mon, 12 Mar 2012 17:24:38 +0100
Subject: [BioRuby] BioRuby: newick parser
References: <20120311125308.GB4204@thebird.nl>
Message-ID: <20120312162438.GA11131@thebird.nl>

On Mon, Mar 12, 2012 at 03:18:48PM +0900, Naohisa GOTO wrote:
> When writing HOWTO based on BioPerl HOWTO:Trees,
> (http://bioruby.open-bio.org/wiki/HOWTO:Trees but still incomplete)
> I'm thinking to add/modify some API about speficying nodes/edges.

After some trying I agree. The Bio::Tree::Node object should know
'more' about its state. I would like to do something like:

  root.leaf?.should == false
  node = root.childeren.first
  node.leaf?.should == false
  node2 == node.childeren.first
  node.leaf?.should == true
  node2.edge(node).distance.should == 1.34

now I need to do something like 

  tree = @tree
  node = tree.get_node_by_name('node')
  tree.get_edge(node, tree.parent(node)).distance.should == 1.34

which uses the tree state to get a node edge, and does not feel that
intuitive.

I'll try to extend Bio::Tree for bio-alignment, see what works.

Pj.

From pjotr.public14 at thebird.nl  Mon Mar 12 12:36:29 2012
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Mon, 12 Mar 2012 17:36:29 +0100
Subject: [BioRuby] RFC: the BioRuby panel
Message-ID: <20120312163629.GA11785@thebird.nl>

Please comment. We have come up with the following:

What is the BioRuby panel?

    The BioRuby panel is an elected body of volunteers out of the
    BioRuby community consisting of active code contributors to the
    BioRuby project.  BioRuby is defined in the widest sense here,
    i.e. the library, website, and biogems.

What is the goal of the BioRuby panel?

    The goal of the BioRuby panel is to represent the BioRuby project
    in terms of directing software and tool development and
    popularizing BioRuby. 

for more, see

    http://bioruby.open-bio.org/wiki/BioRuby_Panel



From pjotr.public14 at thebird.nl  Mon Mar 12 13:05:26 2012
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Mon, 12 Mar 2012 18:05:26 +0100
Subject: [BioRuby] BioRuby: newick parser
In-Reply-To: <20120312162438.GA11131@thebird.nl>
References: <20120311125308.GB4204@thebird.nl>
	<20120312162438.GA11131@thebird.nl>
Message-ID: <20120312170526.GA11997@thebird.nl>

OK, this works:

  @aln.link_tree(@tree)  # @tree contains a parsed Newick tree
  root = @aln.root # get the root of the tree
  root.leaf?.should == false
  children = root.children
  children.map { |n| n.name }.sort.should == ["","seq7"]
  seq7 = children.last
  seq7.name.should == 'seq7'
  seq7.leaf?.should == true
  seq7.parent.should == root

the added functionality for BioRuby's Bio::Tree::Node can be seen here

  https://github.com/pjotrp/bioruby-alignment/blob/development/lib/bio-alignment/tree.rb

basically I inject the @tree info into every existing Node object.
>From then on, I can use it to make the interface nicer. A monkey
patch, indeed.

Good enough for now.

Pj.

On Mon, Mar 12, 2012 at 05:24:38PM +0100, Pjotr Prins wrote:
> On Mon, Mar 12, 2012 at 03:18:48PM +0900, Naohisa GOTO wrote:
> > When writing HOWTO based on BioPerl HOWTO:Trees,
> > (http://bioruby.open-bio.org/wiki/HOWTO:Trees but still incomplete)
> > I'm thinking to add/modify some API about speficying nodes/edges.
> 
> After some trying I agree. The Bio::Tree::Node object should know
> 'more' about its state. I would like to do something like:
> 
>   root.leaf?.should == false
>   node = root.childeren.first
>   node.leaf?.should == false
>   node2 == node.childeren.first
>   node.leaf?.should == true
>   node2.edge(node).distance.should == 1.34
> 
> now I need to do something like 
> 
>   tree = @tree
>   node = tree.get_node_by_name('node')
>   tree.get_edge(node, tree.parent(node)).distance.should == 1.34
> 
> which uses the tree state to get a node edge, and does not feel that
> intuitive.
> 
> I'll try to extend Bio::Tree for bio-alignment, see what works.
> 
> Pj.
> 

From pjotr.public14 at thebird.nl  Mon Mar 12 16:11:59 2012
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Mon, 12 Mar 2012 21:11:59 +0100
Subject: [BioRuby] BioRuby: newick parser
In-Reply-To: <20120312170526.GA11997@thebird.nl>
References: <20120311125308.GB4204@thebird.nl>
	<20120312162438.GA11131@thebird.nl>
	<20120312170526.GA11997@thebird.nl>
Message-ID: <20120312201159.GA12553@thebird.nl>

Bio::Tree::distance(node1,node2)'s calculating the path distance is
pretty cool :)

http://bioruby.open-bio.org/rdoc/Bio/Pathway.html#method-i-breadth_first_search

  seq7.parent.should == root
  seq4 = tree.find("seq4")
  seq4.distance(seq7).should == 19.387756600000003 

Pj.

On Mon, Mar 12, 2012 at 06:05:26PM +0100, Pjotr Prins wrote:
> OK, this works:
> 
>   @aln.link_tree(@tree)  # @tree contains a parsed Newick tree
>   root = @aln.root # get the root of the tree
>   root.leaf?.should == false
>   children = root.children
>   children.map { |n| n.name }.sort.should == ["","seq7"]
>   seq7 = children.last
>   seq7.name.should == 'seq7'
>   seq7.leaf?.should == true
>   seq7.parent.should == root
> 
> the added functionality for BioRuby's Bio::Tree::Node can be seen here
> 
>   https://github.com/pjotrp/bioruby-alignment/blob/development/lib/bio-alignment/tree.rb
> 
> basically I inject the @tree info into every existing Node object.
> From then on, I can use it to make the interface nicer. A monkey
> patch, indeed.
> 
> Good enough for now.
> 
> Pj.
> 
> On Mon, Mar 12, 2012 at 05:24:38PM +0100, Pjotr Prins wrote:
> > On Mon, Mar 12, 2012 at 03:18:48PM +0900, Naohisa GOTO wrote:
> > > When writing HOWTO based on BioPerl HOWTO:Trees,
> > > (http://bioruby.open-bio.org/wiki/HOWTO:Trees but still incomplete)
> > > I'm thinking to add/modify some API about speficying nodes/edges.
> > 
> > After some trying I agree. The Bio::Tree::Node object should know
> > 'more' about its state. I would like to do something like:
> > 
> >   root.leaf?.should == false
> >   node = root.childeren.first
> >   node.leaf?.should == false
> >   node2 == node.childeren.first
> >   node.leaf?.should == true
> >   node2.edge(node).distance.should == 1.34
> > 
> > now I need to do something like 
> > 
> >   tree = @tree
> >   node = tree.get_node_by_name('node')
> >   tree.get_edge(node, tree.parent(node)).distance.should == 1.34
> > 
> > which uses the tree state to get a node edge, and does not feel that
> > intuitive.
> > 
> > I'll try to extend Bio::Tree for bio-alignment, see what works.
> > 
> > Pj.
> > 
> 

From rutgeraldo at gmail.com  Mon Mar 12 19:56:16 2012
From: rutgeraldo at gmail.com (Rutger Vos)
Date: Tue, 13 Mar 2012 00:56:16 +0100
Subject: [BioRuby] BioRuby: newick parser
In-Reply-To: <20120312201159.GA12553@thebird.nl>
References: <20120311125308.GB4204@thebird.nl>
	<20120312162438.GA11131@thebird.nl>
	<20120312170526.GA11997@thebird.nl>
	<20120312201159.GA12553@thebird.nl>
Message-ID: <CAC9cYqH60L=eE5scS9Fh26wUMFngeOZ476sA0u5PXULknUB46Q@mail.gmail.com>

I would be flattered if you would find something of interest or
inspiration about the API of  Bio::Phylo::Forest::Tree
(http://search.cpan.org/~rvosa/Bio-Phylo-0.46/lib/Bio/Phylo/Forest/Tree.pm)
and the node objects
(http://search.cpan.org/~rvosa/Bio-Phylo-0.46/lib/Bio/Phylo/Forest/Node.pm)

On Mon, Mar 12, 2012 at 9:11 PM, Pjotr Prins <pjotr.public14 at thebird.nl> wrote:
> Bio::Tree::distance(node1,node2)'s calculating the path distance is
> pretty cool :)
>
> http://bioruby.open-bio.org/rdoc/Bio/Pathway.html#method-i-breadth_first_search
>
> ?seq7.parent.should == root
> ?seq4 = tree.find("seq4")
> ?seq4.distance(seq7).should == 19.387756600000003
>
> Pj.
>
> On Mon, Mar 12, 2012 at 06:05:26PM +0100, Pjotr Prins wrote:
>> OK, this works:
>>
>> ? @aln.link_tree(@tree) ?# @tree contains a parsed Newick tree
>> ? root = @aln.root # get the root of the tree
>> ? root.leaf?.should == false
>> ? children = root.children
>> ? children.map { |n| n.name }.sort.should == ["","seq7"]
>> ? seq7 = children.last
>> ? seq7.name.should == 'seq7'
>> ? seq7.leaf?.should == true
>> ? seq7.parent.should == root
>>
>> the added functionality for BioRuby's Bio::Tree::Node can be seen here
>>
>> ? https://github.com/pjotrp/bioruby-alignment/blob/development/lib/bio-alignment/tree.rb
>>
>> basically I inject the @tree info into every existing Node object.
>> From then on, I can use it to make the interface nicer. A monkey
>> patch, indeed.
>>
>> Good enough for now.
>>
>> Pj.
>>
>> On Mon, Mar 12, 2012 at 05:24:38PM +0100, Pjotr Prins wrote:
>> > On Mon, Mar 12, 2012 at 03:18:48PM +0900, Naohisa GOTO wrote:
>> > > When writing HOWTO based on BioPerl HOWTO:Trees,
>> > > (http://bioruby.open-bio.org/wiki/HOWTO:Trees but still incomplete)
>> > > I'm thinking to add/modify some API about speficying nodes/edges.
>> >
>> > After some trying I agree. The Bio::Tree::Node object should know
>> > 'more' about its state. I would like to do something like:
>> >
>> > ? root.leaf?.should == false
>> > ? node = root.childeren.first
>> > ? node.leaf?.should == false
>> > ? node2 == node.childeren.first
>> > ? node.leaf?.should == true
>> > ? node2.edge(node).distance.should == 1.34
>> >
>> > now I need to do something like
>> >
>> > ? tree = @tree
>> > ? node = tree.get_node_by_name('node')
>> > ? tree.get_edge(node, tree.parent(node)).distance.should == 1.34
>> >
>> > which uses the tree state to get a node edge, and does not feel that
>> > intuitive.
>> >
>> > I'll try to extend Bio::Tree for bio-alignment, see what works.
>> >
>> > Pj.
>> >
>>
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby



-- 
Dr. Rutger A. Vos
Bioinformaticist
NCB Naturalis
Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the Netherlands
Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands
http://rutgervos.blogspot.com


From ngoto at gen-info.osaka-u.ac.jp  Tue Mar 13 10:23:26 2012
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Tue, 13 Mar 2012 23:23:26 +0900
Subject: [BioRuby] BioRuby: newick parser
In-Reply-To: <20120312162438.GA11131@thebird.nl>
References: <20120311125308.GB4204@thebird.nl>
	<20120312162438.GA11131@thebird.nl>
Message-ID: <201203131423.q2DENTd0021313@portal.open-bio.org>

Hi Pjotr,

The design of Bio::Tree that a nod has no tree information and
only tree object have node information was what I intended.
This makes easy to split a tree into subtrees, to build a tree
from scratch, to concatenate trees, to replace nodes and edges, etc.
However, as you described, for traversing a static tree,
indirect operations are needed which are sometimes annoying.

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


On Mon, 12 Mar 2012 17:24:38 +0100
Pjotr Prins <pjotr.public14 at thebird.nl> wrote:

> On Mon, Mar 12, 2012 at 03:18:48PM +0900, Naohisa GOTO wrote:
> > When writing HOWTO based on BioPerl HOWTO:Trees,
> > (http://bioruby.open-bio.org/wiki/HOWTO:Trees but still incomplete)
> > I'm thinking to add/modify some API about speficying nodes/edges.
> 
> After some trying I agree. The Bio::Tree::Node object should know
> 'more' about its state. I would like to do something like:
> 
>   root.leaf?.should == false
>   node = root.childeren.first
>   node.leaf?.should == false
>   node2 == node.childeren.first
>   node.leaf?.should == true
>   node2.edge(node).distance.should == 1.34
> 
> now I need to do something like 
> 
>   tree = @tree
>   node = tree.get_node_by_name('node')
>   tree.get_edge(node, tree.parent(node)).distance.should == 1.34
> 
> which uses the tree state to get a node edge, and does not feel that
> intuitive.
> 
> I'll try to extend Bio::Tree for bio-alignment, see what works.
> 
> Pj.


From ngoto at gen-info.osaka-u.ac.jp  Tue Mar 13 10:37:27 2012
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Tue, 13 Mar 2012 23:37:27 +0900
Subject: [BioRuby] BioRuby: newick parser
In-Reply-To: <20120312201159.GA12553@thebird.nl>
References: <20120311125308.GB4204@thebird.nl>
	<20120312162438.GA11131@thebird.nl>
	<20120312170526.GA11997@thebird.nl>
	<20120312201159.GA12553@thebird.nl>
Message-ID: <201203131437.q2DEbS6S021797@portal.open-bio.org>

Hi Pjotr,

On Mon, 12 Mar 2012 21:11:59 +0100
Pjotr Prins <pjotr.public14 at thebird.nl> wrote:

> Bio::Tree::distance(node1,node2)'s calculating the path distance is
> pretty cool :)
> 
> http://bioruby.open-bio.org/rdoc/Bio/Pathway.html#method-i-breadth_first_search
> 
>   seq7.parent.should == root
>   seq4 = tree.find("seq4")
>   seq4.distance(seq7).should == 19.387756600000003 

This is a problem of floating point numbers.
Calculating sum of floating point numbers frequently causes
accumulation of errors and/or loss of significant digits.

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

From pjotr.public14 at thebird.nl  Fri Mar 16 09:51:53 2012
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Fri, 16 Mar 2012 14:51:53 +0100
Subject: [BioRuby] Drawing a phylogeny ASCII tree
References: <20120311125308.GB4204@thebird.nl>
	<20120312162438.GA11131@thebird.nl>
Message-ID: <20120316135153.GA11119@thebird.nl>

Anyone interesting in a little coding challenge? I wrote a feature
for drawing a phylogeny ASCII tree:

When you have an alignment, with a Newick tree attached, as supported
by the bio-alignment gem, I would like to get the following ASCII 
drawings:

And draw the MSA with the tree
  """
  +--9.69----------------------------------------- seq7  ----------PTIIFSGCSKACSGK-----VCGIFHAVRSFM
  |                                   ,--1.19----- seq1  ----SNSFSRPTIIFSGCSTACSGK--SELVCGFRSFMLSDV
  |                          ,--1.79--|        ,-- seq2  SSIISNSFSRPTIIFSGCSTACSGK--SEQVCGFR---LSDV
  |                 ,--1.07--+        `--1.19--+-- seq3  SSIISNSFSRPTIIFSGCSTACSGKLTSEQVCGFR---LSDV
  |                 |        |--1.79--+--1.19----- seq5  ----------PTIIFSGCSKACSGKGLSELVCGFRSFMLSDV
  |        ,--1.31--|                 `--1.19----- seq8  --------PTIIFSGCSKACSGK--SELVCGFRSFMLSAV
  |--4.34--|        `--4.05----------------------- seq4  ----PKLFSRPTIIFSGCSTACSGK--SEPVCGFRSFMLSDV
           `--5.36-------------------------------- seq6  ----------PTIIFSGCSKACSGK-----FRSFRSFMLSAV
  """
Then draw MSA with the short tree
  """
  +----------------- seq7  ----------PTIIFSGCSKACSGK-----VCGIFHAVRSFM
  |           ,----- seq1  ----SNSFSRPTIIFSGCSTACSGK--SELVCGFRSFMLSDV
  |        ,--|  ,-- seq2  SSIISNSFSRPTIIFSGCSTACSGK--SEQVCGFR---LSDV
  |     ,--+  `--+-- seq3  SSIISNSFSRPTIIFSGCSTACSGKLTSEQVCGFR---LSDV
  |     |  |--+----- seq5  ----------PTIIFSGCSKACSGKGLSELVCGFRSFMLSDV
  |  ,--|     `----- seq8  --------PTIIFSGCSKACSGK--SELVCGFRSFMLSAV
  |--|  `----------- seq4  ----PKLFSRPTIIFSGCSTACSGK--SEPVCGFRSFMLSDV
     `-------------- seq6  ----------PTIIFSGCSKACSGK-----FRSFRSFMLSAV
  """

BioPerl has someting similar here, but less useful:

  http://doc.bioperl.org/releases/bioperl-1.4/Bio/TreeIO/tabtree.html

And there are some good Ruby examples trees at

  http://www.rubyquiz.com/quiz40.html

The full feature description is here, and the bio-alignment module
allows for loading and traversing trees. It is only a matter of
getting the algorithm right :) See

  https://github.com/pjotrp/bioruby-alignment/blob/master/features/tree.feature

and 

  https://github.com/pjotrp/bioruby-alignment/blob/master/features/tree-feature.rb

The same algorithm will be used for a HTML drawing.

Pj.

On Tue, Mar 13, 2012 at 11:23:26PM +0900, Naohisa GOTO wrote:
> Hi Pjotr,
> 
> The design of Bio::Tree that a nod has no tree information and
> only tree object have node information was what I intended.
> This makes easy to split a tree into subtrees, to build a tree
> from scratch, to concatenate trees, to replace nodes and edges, etc.
> However, as you described, for traversing a static tree,
> indirect operations are needed which are sometimes annoying.
> 
> Naohisa Goto
> ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
> 
> 
> On Mon, 12 Mar 2012 17:24:38 +0100
> Pjotr Prins <pjotr.public14 at thebird.nl> wrote:
> 
> > On Mon, Mar 12, 2012 at 03:18:48PM +0900, Naohisa GOTO wrote:
> > > When writing HOWTO based on BioPerl HOWTO:Trees,
> > > (http://bioruby.open-bio.org/wiki/HOWTO:Trees but still incomplete)
> > > I'm thinking to add/modify some API about speficying nodes/edges.
> > 
> > After some trying I agree. The Bio::Tree::Node object should know
> > 'more' about its state. I would like to do something like:
> > 
> >   root.leaf?.should == false
> >   node = root.childeren.first
> >   node.leaf?.should == false
> >   node2 == node.childeren.first
> >   node.leaf?.should == true
> >   node2.edge(node).distance.should == 1.34
> > 
> > now I need to do something like 
> > 
> >   tree = @tree
> >   node = tree.get_node_by_name('node')
> >   tree.get_edge(node, tree.parent(node)).distance.should == 1.34
> > 
> > which uses the tree state to get a node edge, and does not feel that
> > intuitive.
> > 
> > I'll try to extend Bio::Tree for bio-alignment, see what works.
> > 
> > Pj.
> 

From dafian90 at gmail.com  Fri Mar 16 14:30:55 2012
From: dafian90 at gmail.com (Filippo Andrea D'Angelo)
Date: Fri, 16 Mar 2012 19:30:55 +0100
Subject: [BioRuby] New Trainee. BioRuby: Bio-Images Project
Message-ID: <CAK8_7p2bs4=sP4NqvJ_NMCtCF16PKRthv2TSWQpHXtbAYbvo4w@mail.gmail.com>

Hi everybody, my name is Filippo Andrea D'Angelo and I'm a student in
University of Milano-Bicocca. I chose to do my university stage with Bonnal
Raoul helping him in the project "BioRuby: Bio-Images Project". I hope that
I will learn a lot from this experience and be able to contribute as much
as possibile during this time.

D'Angelo F. Andrea

From freeparis2 at gmail.com  Fri Mar 16 15:36:38 2012
From: freeparis2 at gmail.com (Kazuo Ishii)
Date: Sat, 17 Mar 2012 04:36:38 +0900
Subject: [BioRuby] New Trainee. BioRuby: Bio-Images Project
In-Reply-To: <CAK8_7p2bs4=sP4NqvJ_NMCtCF16PKRthv2TSWQpHXtbAYbvo4w@mail.gmail.com>
References: <CAK8_7p2bs4=sP4NqvJ_NMCtCF16PKRthv2TSWQpHXtbAYbvo4w@mail.gmail.com>
Message-ID: <CAJDOTrJRWL_ifhwGLdYuM4qqs6a354ECsmhGjV6_GZdK9-bSCw@mail.gmail.com>

You are very welcome and good luck.

2012/3/17, Filippo Andrea D'Angelo <dafian90 at gmail.com>:
> Hi everybody, my name is Filippo Andrea D'Angelo and I'm a student in
> University of Milano-Bicocca. I chose to do my university stage with Bonnal
> Raoul helping him in the project "BioRuby: Bio-Images Project". I hope that
> I will learn a lot from this experience and be able to contribute as much
> as possibile during this time.
>
> D'Angelo F. Andrea
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>


-- 
Kazuo Ishii, Ph.D., Professor of Genome Science,
Tokyo University of Agriculture and Technology
3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, JAPAN
Email: kishii at cc.tuat.ac.jp

From bonnal at ingm.org  Sat Mar 17 14:22:48 2012
From: bonnal at ingm.org (Raoul Bonnal)
Date: Sat, 17 Mar 2012 19:22:48 +0100
Subject: [BioRuby] New Trainee. BioRuby: Bio-Images Project
In-Reply-To: <CAJDOTrJRWL_ifhwGLdYuM4qqs6a354ECsmhGjV6_GZdK9-bSCw@mail.gmail.com>
Message-ID: <CB8A9508.8805%bonnal@ingm.org>

Welcome ;-)


On 16/03/12 20.36, "Kazuo Ishii" <freeparis2 at gmail.com> wrote:

> You are very welcome and good luck.
> 
> 2012/3/17, Filippo Andrea D'Angelo <dafian90 at gmail.com>:
>> Hi everybody, my name is Filippo Andrea D'Angelo and I'm a student in
>> University of Milano-Bicocca. I chose to do my university stage with Bonnal
>> Raoul helping him in the project "BioRuby: Bio-Images Project". I hope that
>> I will learn a lot from this experience and be able to contribute as much
>> as possibile during this time.
>> 
>> D'Angelo F. Andrea
>> _______________________________________________
>> BioRuby Project - http://www.bioruby.org/
>> BioRuby mailing list
>> BioRuby at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioruby
>> 
> 



From andrea.nodari91 at gmail.com  Sat Mar 17 15:29:52 2012
From: andrea.nodari91 at gmail.com (Andrea Nodari)
Date: Sat, 17 Mar 2012 20:29:52 +0100
Subject: [BioRuby] restyle of bioruby.org
Message-ID: <CA+FV2YYX2Sy98ed4vHzaK+hA4-DPng0nbM7-cV+VGyw_qqiwgw@mail.gmail.com>

Hi all,
I'm Andrea Nodari and I'm a student of CS @ University of Trento , Italy,
I'm working as web developer and I am stronlgy interested in the
project of GSoC about restyling bioruby.org.
I hope to learn and contribute as much as possible to this comunity :)

-- 
Andrea

From francesco.strozzi at gmail.com  Sat Mar 17 16:03:35 2012
From: francesco.strozzi at gmail.com (Francesco Strozzi)
Date: Sat, 17 Mar 2012 21:03:35 +0100
Subject: [BioRuby] restyle of bioruby.org
In-Reply-To: <CA+FV2YYX2Sy98ed4vHzaK+hA4-DPng0nbM7-cV+VGyw_qqiwgw@mail.gmail.com>
References: <CA+FV2YYX2Sy98ed4vHzaK+hA4-DPng0nbM7-cV+VGyw_qqiwgw@mail.gmail.com>
Message-ID: <CACtet2QmczOSdG07eUXV13k9qPi+k0LKZcHt0nAprLbLaR+nGQ@mail.gmail.com>

Hi Andrea and welcome!
The deadline for student proposals is April 6th. You can find below the
details of the GSoC and how to apply for OBF projects.

We are here to help you develop your work proposal on GSoC, so feel free to
write on the ML and/or directly to the mentors to receive advise and
feedbacks. As BioRuby we have an IRC channel #bioruby on irc.freenode.net.
You can reach us there, we also have a weekly IRC meeting on Thursday
afternoon at 16.00 CET but you can find us there almost every working day.

Cheers
Francesco


----------

GSoC is a Google-sponsored student internship program for open-source
projects, open to students from around the world (not just US
residents).   Students are paid a $5000 USD stipend to work as a
developer on an open-source project for the summer. For more on GSoC,
see GSoC 2012 FAQ at http://goo.gl/kNv48

Student applications are due April 6, 2012 at 19:00 UTC.  Students who
are interested in participating should look at the OBF's GSoC page at
http://open-bio.org/wiki/**Google_Summer_of_Code<http://open-bio.org/wiki/Google_Summer_of_Code>,
which lists project
ideas, and whom to contact about applying.

-----------

On Sat, Mar 17, 2012 at 20:29, Andrea Nodari <andrea.nodari91 at gmail.com>wrote:

> Hi all,
> I'm Andrea Nodari and I'm a student of CS @ University of Trento , Italy,
> I'm working as web developer and I am stronlgy interested in the
> project of GSoC about restyling bioruby.org.
> I hope to learn and contribute as much as possible to this comunity :)
>
> --
> Andrea
> _______________________________________________
> 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 bonnal at ingm.org  Sat Mar 17 16:20:06 2012
From: bonnal at ingm.org (Raoul Bonnal)
Date: Sat, 17 Mar 2012 21:20:06 +0100
Subject: [BioRuby] restyle of bioruby.org
In-Reply-To: <CACtet2QmczOSdG07eUXV13k9qPi+k0LKZcHt0nAprLbLaR+nGQ@mail.gmail.com>
Message-ID: <CB8AB086.880E%bonnal@ingm.org>

Hello Andrea,
I read your chat with Marjan on irc, I think now you have all the references
github and wiki links so ... Welcome.
As Francesco said, please feel free to contact us on the ml (which is the
preferred way for official GSoC communications -so that other mentors from
other project can follow the progresses).

Ciao! 


On 17/03/12 21.03, "Francesco Strozzi" <francesco.strozzi at gmail.com> wrote:

> Hi Andrea and welcome!
> The deadline for student proposals is April 6th. You can find below the
> details of the GSoC and how to apply for OBF projects.
> 
> We are here to help you develop your work proposal on GSoC, so feel free to
> write on the ML and/or directly to the mentors to receive advise and
> feedbacks. As BioRuby we have an IRC channel #bioruby on irc.freenode.net.
> You can reach us there, we also have a weekly IRC meeting on Thursday
> afternoon at 16.00 CET but you can find us there almost every working day.
> 
> Cheers
> Francesco
> 
> 
> ----------
> 
> GSoC is a Google-sponsored student internship program for open-source
> projects, open to students from around the world (not just US
> residents).   Students are paid a $5000 USD stipend to work as a
> developer on an open-source project for the summer. For more on GSoC,
> see GSoC 2012 FAQ at http://goo.gl/kNv48
> 
> Student applications are due April 6, 2012 at 19:00 UTC.  Students who
> are interested in participating should look at the OBF's GSoC page at
> http://open-bio.org/wiki/**Google_Summer_of_Code<http://open-bio.org/wiki/Goog
> le_Summer_of_Code>,
> which lists project
> ideas, and whom to contact about applying.
> 
> -----------
> 
> On Sat, Mar 17, 2012 at 20:29, Andrea Nodari <andrea.nodari91 at gmail.com>wrote:
> 
>> Hi all,
>> I'm Andrea Nodari and I'm a student of CS @ University of Trento , Italy,
>> I'm working as web developer and I am stronlgy interested in the
>> project of GSoC about restyling bioruby.org.
>> I hope to learn and contribute as much as possible to this comunity :)
>> 
>> --
>> Andrea
>> _______________________________________________
>> BioRuby Project - http://www.bioruby.org/
>> BioRuby mailing list
>> BioRuby at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioruby
>> 
> 
> 



From moduvyas at gmail.com  Sat Mar 17 22:54:06 2012
From: moduvyas at gmail.com (varun vyas)
Date: Sun, 18 Mar 2012 08:24:06 +0530
Subject: [BioRuby] Gsoc:Asking for suggestion and view for Bioruby project
Message-ID: <CAFjAtqLU0J94Sx45R=tSuLkHAzP-QN4Gii0abe6MNjPmvdL=Dw@mail.gmail.com>

Hi,
   This is Varun Vyas from DA-IICT,Gandhinagar,India, in last year of his
B.tech. I want to ask about project titled "Adding social networking
functionality to BioRuby.org".
I would like to know who will be the mentor for this project, so as to
contact him to discuss more about the same. If anyone can suggest me
correct approach to this project i.e. point that must be included in
proposal, any must prerequisites, What are the expectations for this
project,who will take design decision,will design be provided  or  any
design constraint for site.Any help or suggestion would be great.
I am doing my intership in a start-up, where i created its website with
Ruby-on-rails 3.2. Have intermediate knowledge of Ruby and
Javascript(Jquery), learned as much was needed for completing my project
will working on it.  Though i know only basics of Coffescript  and Haml,
but can quickly learn and apply them if needed.

Thanks for any advice.



Thanking you
varun vyas

From pjotr.public14 at thebird.nl  Sun Mar 18 05:18:46 2012
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Sun, 18 Mar 2012 10:18:46 +0100
Subject: [BioRuby] Gsoc:Asking for suggestion and view for Bioruby
 project
In-Reply-To: <CAFjAtqLU0J94Sx45R=tSuLkHAzP-QN4Gii0abe6MNjPmvdL=Dw@mail.gmail.com>
References: <CAFjAtqLU0J94Sx45R=tSuLkHAzP-QN4Gii0abe6MNjPmvdL=Dw@mail.gmail.com>
Message-ID: <20120318091846.GA23224@thebird.nl>

Hi Varun,

On Sun, Mar 18, 2012 at 08:24:06AM +0530, varun vyas wrote:
> Hi,
>    This is Varun Vyas from DA-IICT,Gandhinagar,India, in last year of his
> B.tech. I want to ask about project titled "Adding social networking
> functionality to BioRuby.org".

You are welcome :)

> I would like to know who will be the mentor for this project, so as to
> contact him to discuss more about the same. If anyone can suggest me
> correct approach to this project i.e. point that must be included in
> proposal, any must prerequisites, What are the expectations for this
> project,who will take design decision,will design be provided  or  any
> design constraint for site.Any help or suggestion would be great.
> I am doing my intership in a start-up, where i created its website with
> Ruby-on-rails 3.2. Have intermediate knowledge of Ruby and
> Javascript(Jquery), learned as much was needed for completing my project
> will working on it.  Though i know only basics of Coffescript  and Haml,
> but can quickly learn and apply them if needed.

Programming experience is actually not really a requirement for GSoC.
The idea is to get people into OSS projects and make them long-term
contributors to OSS. If this project proposal appeals to you, please
do apply. One of BioRuby's little successes is Kharagpur based Anurag
Priyam, who came in with GSoC and is a very active OSS contributor,
see https://github.com/yeban (kudos to Anurag, sukria/donobad, I
wanted an excuse to mention that!).

Most of your questions will be answered by reading the GSoC
instructions

  http://code.google.com/p/google-summer-of-code/wiki/AdviceforStudents

and the OBF pages. Our projects have *multiple* mentors, and the
BioRuby panel also monitors actively. If you frame your questions
right, you will get answers on the mailing list (ML) or IRC.

Another important point is that the application process of GSoC is
rather competitive. More students apply than get selected! The only
way to get in is to produce a good proposal. A good proposal shows
the motivation of the student. A mentor will help, once there is
something on the table. Don't expect mentors to put in time for
'free'.

Enjoy :)

Pj.

From pjotr.public14 at thebird.nl  Sun Mar 18 06:09:05 2012
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Sun, 18 Mar 2012 11:09:05 +0100
Subject: [BioRuby] Drawing a phylogeny ASCII tree
In-Reply-To: <20120316135153.GA11119@thebird.nl>
References: <20120311125308.GB4204@thebird.nl>
	<20120312162438.GA11131@thebird.nl>
	<20120316135153.GA11119@thebird.nl>
Message-ID: <20120318100905.GA24171@thebird.nl>

On Fri, Mar 16, 2012 at 02:51:53PM +0100, Pjotr Prins wrote:
> Anyone interesting in a little coding challenge? I wrote a feature
> for drawing a phylogeny ASCII tree:
> 
> (snip)
>
> Then draw MSA with the short tree
>   """
>   +----------------- seq7  ----------PTIIFSGCSKACSGK-----VCGIFHAVRSFM
>   |           ,----- seq1  ----SNSFSRPTIIFSGCSTACSGK--SELVCGFRSFMLSDV
>   |        ,--|  ,-- seq2  SSIISNSFSRPTIIFSGCSTACSGK--SEQVCGFR---LSDV
>   |     ,--+  `--+-- seq3  SSIISNSFSRPTIIFSGCSTACSGKLTSEQVCGFR---LSDV
>   |     |  |--+----- seq5  ----------PTIIFSGCSKACSGKGLSELVCGFRSFMLSDV
>   |  ,--|     `----- seq8  --------PTIIFSGCSKACSGK--SELVCGFRSFMLSAV
>   |--|  `----------- seq4  ----PKLFSRPTIIFSGCSTACSGK--SEPVCGFRSFMLSDV
>      `-------------- seq6  ----------PTIIFSGCSKACSGK-----FRSFRSFMLSAV
>      1  2  3  4  5
>   """

I have been thinking about this 'ASCII cladogram' algorithm, as it
would be very useful for testing code. Unfortunately I have found no
example that really appeals to me in the other Bio* projects (we are
talking text here, not graphics; the graphics ones are actually
nicer). 

The examples I have are

* BioPerl tabtree
* Ruby challenge http://blade.nagaokaut.ac.jp/cgi-bin/scat.rb/ruby/ruby-talk/149701
* BioPythons http://biopython.org/DIST/docs/api/Bio.Phylo._utils-pysrc.html#draw_ascii

I have mailed T. Mike Keesey, of
http://www.palaeos.org/Ascii_phylogenetic_tree, as he has some interesting
generator, but he has not responded, yet.

So, assuming I am on my own, I was thinking that the tree needs to be
drawn in a matrix of characters. The pseudo code I come up with is
based on 'matrix expansion' - every time a sequence gets added, we
add a line. If a tree goes left (up), e.g. the last node before seq2, 
we expand the matrix by injecting a new line and extending the
verticals. We extend the horizontals in the final step.

Assuming we know the tree with leafs and nodes:

step 1, start with the first leaf seq7 (R=root, L=Leaf, o=node, N=new node)

  R--L seq7

step 2, add seq1 (4 nodes)

  R--L seq7
  `--o--o--o--o--L seq1

step 3, add seq2 (5 nodes)

  R--L seq7
  |           ,--L seq1
  `--o--o--o--N--o--L seq2

Now what you see is that seq1 is on the branch of new seq2. So after
adding seq2, we wipe seq1 to the left of N and copy the verticals on
the left side of the new node (N). 

step 4, add seq 3


  R--L seq7
  |           ,--L seq1
  |           |  ,--L seq2
  `--o--o--o--|--N--L seq3

Same principle. After adding seq3, we find seq2 is connected and we
split seq2 - left side extend verticals, right side connect

step 5, add seq5 (4 nodes)

  R--L seq7
  |           ,--L seq1
  |           |  ,--L seq2
  |        ,--|--N--L seq3
  `--o--o--N--o--L seq5

Again, seq5 connects at the 3rd node. So we split the above

step 6, seq 8 (4 nodes)

  R--L seq7
  |           ,--L seq1
  |           |  ,--L seq2
  |        ,--|--N--L seq3
  |        |  ,--L seq5
  `--o--o--|--N--L seq8

Split on node 4. Expand verticals to the left of N.
Here the algorithm changed the original drawing a little.

step 7, seq 4 (2 nodes)

  R--L seq7
  |           ,--L seq1
  |           |  ,--L seq2
  |        ,--|--N--L seq3
  |        |  ,--L seq5
  |     ,--|--N--L seq8
  `--o--N--L seq4

step 8, seq6 (1 node)


  R--L seq7
  |           ,--L seq1
  |           |  ,--L seq2
  |        ,--|--N--L seq3
  |        |  ,--L seq5
  |     ,--|--N--L seq8
  |  ,--N--L seq4
  `--N--L seq6

step 9, we can expand horizontally


  R----------------- seq7
  |           ,----- seq1
  |           |  ,-- seq2
  |        ,--+--+-- seq3
  |        |  ,----- seq5
  |     ,--+--+----- seq8
  |  ,--+----------- seq4
  `--+-------------- seq6
     1  2  3  4  5

I think this is pretty much what Mike Keesey does on

  http://namesonnodes.org/texttree/

Anyone see a flaw in my reasoning?

Pj.

From yannick.wurm at unil.ch  Sun Mar 18 23:19:56 2012
From: yannick.wurm at unil.ch (Yannick Wurm)
Date: Mon, 19 Mar 2012 03:19:56 +0000
Subject: [BioRuby] Drawing a phylogeny ASCII tree
In-Reply-To: <mailman.5.1332086407.20174.bioruby@lists.open-bio.org>
References: <mailman.5.1332086407.20174.bioruby@lists.open-bio.org>
Message-ID: <50203D1A-A35A-40FF-96C9-34045977210E@unil.ch>

On 18 Mar 2012, at 16:00, bioruby-request at lists.open-bio.org wrote:

> I have found no
> example that really appeals to me in the other Bio* projects (we are
> talking text here, not graphics; the graphics ones are actually
> nicer). 


Here's another example 
http://cegg.unige.ch/newick_utils

The tool nw_display outputs your tree in the console in text format...

cheers,

yannick



Yannick Wurm
Ants, Genomes & Evolution ? y.wurm at qmul.ac.uk ? skype:yannickwurm ? +44 207 882 3049
5.03A Fogg ? School of Biological & Chemical Sciences ? Queen Mary, University of London ? Mile End Road ? E1 4NX London ? UK


From pjotr.public14 at thebird.nl  Mon Mar 19 03:03:04 2012
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Mon, 19 Mar 2012 08:03:04 +0100
Subject: [BioRuby] Drawing a phylogeny ASCII tree
In-Reply-To: <50203D1A-A35A-40FF-96C9-34045977210E@unil.ch>
References: <mailman.5.1332086407.20174.bioruby@lists.open-bio.org>
	<50203D1A-A35A-40FF-96C9-34045977210E@unil.ch>
Message-ID: <20120319070304.GC29236@thebird.nl>

On Mon, Mar 19, 2012 at 03:19:56AM +0000, Yannick Wurm wrote:
> On 18 Mar 2012, at 16:00, bioruby-request at lists.open-bio.org wrote:
> 
> > I have found no
> > example that really appeals to me in the other Bio* projects (we are
> > talking text here, not graphics; the graphics ones are actually
> > nicer). 
> 
> 
> Here's another example 
> http://cegg.unige.ch/newick_utils
> 
> The tool nw_display outputs your tree in the console in text format...

Excellent!

Also, Mike Keesey sent me his code:

  http://code.google.com/p/a3lbmonkeybrain-as3/source/browse/trunk/src/a3lbmonkeybrain/calculia/collections/graphs/exporters/TextCladogramExporter.as?spec=svn26&r=26

No need to fully reinvent the wheel then.

Pj.

From naliwajek at gmail.com  Mon Mar 19 12:29:24 2012
From: naliwajek at gmail.com (Jakub Naliwajek)
Date: Mon, 19 Mar 2012 17:29:24 +0100
Subject: [BioRuby] GSoC: Testing framework for biogem plugins
Message-ID: <CAO--zKeD34pqYry3UUoxhO-NShz++MEKkt4i1Rmrrabd_AFiJw@mail.gmail.com>

Hi,

My name's Jakub. I'm a CS student and a back-end RoR developer from Poland.

I just wanted to check if my reasoning of whole process of adding a new bio
gem is right:

1. New bio gem is created by someone on GitHub;
2. Then gem is added by him to RubyGems;
3. Then gem is added (by him and *accepted* by OBF?) to BioGems;
4. Then all three services are automatically linked together by a framework;
5. Tests (all tests across gem and its dependencies) run for a first time
(initial release);
6. After that tests run only:
   *** when manually triggered (BioGems link action somewhere) OR;
   *** labeled on GitHub OR;
   *** new release (check if pushed to BioGems [or RubyGems if they have
such event handler]) is out;

7. (Eventually) with person responsible about restyle of bioruby.org we
decide how (if any) those results are going to look at main
bioruby.orgsite (not dev-only BioGems.info)

(For already existing gems let's say we begin from point 5 treating current
release as an initial one)

Of course, besides testing each gem with its dependencies individually, we
include option to test different BioGems together (different setups) and
display results at BioGems.info too.

Test results are displayed not only with "failed/passed" statement but also
with error log so developer can see straight from BioGems site what is
wrong, right?

Is it okay or did I forget something?

Also, I lack CoffeeScript knowledge but I guess it's not that hard to learn.


Cheers,
-- 
Jakub Naliwajek

From pjotr.public14 at thebird.nl  Tue Mar 20 05:34:06 2012
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Tue, 20 Mar 2012 10:34:06 +0100
Subject: [BioRuby] GSoC: Testing framework for biogem plugins
In-Reply-To: <CAO--zKeD34pqYry3UUoxhO-NShz++MEKkt4i1Rmrrabd_AFiJw@mail.gmail.com>
References: <CAO--zKeD34pqYry3UUoxhO-NShz++MEKkt4i1Rmrrabd_AFiJw@mail.gmail.com>
Message-ID: <20120320093406.GA4581@thebird.nl>

Hi Jakub,

On Mon, Mar 19, 2012 at 05:29:24PM +0100, Jakub Naliwajek wrote:
> Hi,
> 
> My name's Jakub. I'm a CS student and a back-end RoR developer from Poland.
> 
> I just wanted to check if my reasoning of whole process of adding a new bio
> gem is right:
> 
> 1. New bio gem is created by someone on GitHub;
> 2. Then gem is added by him to RubyGems;
> 3. Then gem is added (by him and *accepted* by OBF?) to BioGems;

No, it is automatic. If you gem starts with bio- it will
automatically show up on http://biogems.info/

> 4. Then all three services are automatically linked together by a framework;
> 5. Tests (all tests across gem and its dependencies) run for a first time
> (initial release);

At the moment the tests are handled by travis-ci. You need to
register your project with them (two small steps!), and create a
.travis.yml file in your tree.

I like travis-ci, even when the service would disappear, it would be
reasonably easy to recreate ourselves (the source code is online).

> 6. After that tests run only:
>    *** when manually triggered (BioGems link action somewhere) OR;
>    *** labeled on GitHub OR;
>    *** new release (check if pushed to BioGems [or RubyGems if they have
> such event handler]) is out;

The default for travis is to run a test, every time you push to
github. There is also a manual override.

> 7. (Eventually) with person responsible about restyle of bioruby.org we
> decide how (if any) those results are going to look at main
> bioruby.orgsite (not dev-only BioGems.info)

Yes, both sites could be one site, but I agree biogems.info mostly
targets experienced developers. Design decisions are part of the
discussion on the ML. We created the BioRuby panel to ascertain we
find the best solution for the community.

> (For already existing gems let's say we begin from point 5 treating current
> release as an initial one)

That would be great.

> Of course, besides testing each gem with its dependencies individually, we
> include option to test different BioGems together (different setups) and
> display results at BioGems.info too.

Agree. 

Gems posted on rubygems.org have tagged releases on github. We can
test each release, with its dependencies. Travis-ci, btw, would also
allow us to run the test in dependent gems in one go(!)

> Test results are displayed not only with "failed/passed" statement but also
> with error log so developer can see straight from BioGems site what is
> wrong, right?
> 
> Is it okay or did I forget something?

Sounds right to me. I am glad you appreciate the importance of a
proper testing framework.

> Also, I lack CoffeeScript knowledge but I guess it's not that hard to learn.

Yes.

Pj.

From pjotr.public14 at thebird.nl  Tue Mar 20 05:41:55 2012
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Tue, 20 Mar 2012 10:41:55 +0100
Subject: [BioRuby] IRC
Message-ID: <20120320094155.GA6229@thebird.nl>

We'll be on IRC today.

From naliwajek at gmail.com  Thu Mar 22 11:27:15 2012
From: naliwajek at gmail.com (Jakub Naliwajek)
Date: Thu, 22 Mar 2012 16:27:15 +0100
Subject: [BioRuby] GSoC: Testing framework for biogem plugins
In-Reply-To: <20120320093406.GA4581@thebird.nl>
References: <CAO--zKeD34pqYry3UUoxhO-NShz++MEKkt4i1Rmrrabd_AFiJw@mail.gmail.com>
	<20120320093406.GA4581@thebird.nl>
Message-ID: <CAO--zKdJ5qiK_=HTeg_u1dLjsehwU=7v9d9X1_W44xTs33RJSg@mail.gmail.com>

Thanks for your response, Pjotr.

I was trying to plan project's timeline and here are 2 additional questions
I thought about:

1. Biogems.info is written in Ruby on Rails, right?

2. Travis-CI handles users via their GitHub accounts. Would we also like to
handle users that way, so they can hit "run my test" straight from
biogems.info? (and upload travis.yml file by/through our framwork, register
new gem in travis-ci straight from biogems.info etc.)

Cheers,
-- 
Jakub Naliwajek

From pjotr.public14 at thebird.nl  Thu Mar 22 11:37:30 2012
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Thu, 22 Mar 2012 16:37:30 +0100
Subject: [BioRuby] GSoC: Testing framework for biogem plugins
In-Reply-To: <CAO--zKdJ5qiK_=HTeg_u1dLjsehwU=7v9d9X1_W44xTs33RJSg@mail.gmail.com>
References: <CAO--zKeD34pqYry3UUoxhO-NShz++MEKkt4i1Rmrrabd_AFiJw@mail.gmail.com>
	<20120320093406.GA4581@thebird.nl>
	<CAO--zKdJ5qiK_=HTeg_u1dLjsehwU=7v9d9X1_W44xTs33RJSg@mail.gmail.com>
Message-ID: <20120322153730.GA24105@thebird.nl>

On Thu, Mar 22, 2012 at 04:27:15PM +0100, Jakub Naliwajek wrote:
> Thanks for your response, Pjotr.
> 
> I was trying to plan project's timeline and here are 2 additional questions
> I thought about:
> 
> 1. Biogems.info is written in Ruby on Rails, right?

Nope. staticmatic - see https://github.com/pjotrp/biogems.info

> 2. Travis-CI handles users via their GitHub accounts. Would we also like to
> handle users that way, so they can hit "run my test" straight from
> biogems.info? (and upload travis.yml file by/through our framwork, register
> new gem in travis-ci straight from biogems.info etc.)

I think Marjan has put github authentication in.

Pj.

From marian.povolny at gmail.com  Thu Mar 22 13:39:36 2012
From: marian.povolny at gmail.com (Marjan Povolni)
Date: Thu, 22 Mar 2012 18:39:36 +0100
Subject: [BioRuby] GSoC: Testing framework for biogem plugins
In-Reply-To: <20120322153730.GA24105@thebird.nl>
References: <CAO--zKeD34pqYry3UUoxhO-NShz++MEKkt4i1Rmrrabd_AFiJw@mail.gmail.com>
	<20120320093406.GA4581@thebird.nl>
	<CAO--zKdJ5qiK_=HTeg_u1dLjsehwU=7v9d9X1_W44xTs33RJSg@mail.gmail.com>
	<20120322153730.GA24105@thebird.nl>
Message-ID: <CADKP5C=NKabtbtoyo5M-XBtZR41zeEKcTrNuYtkoSbFWsn-hXQ@mail.gmail.com>

Hi,


> > 2. Travis-CI handles users via their GitHub accounts. Would we also like
> to
> > handle users that way, so they can hit "run my test" straight from
> > biogems.info? (and upload travis.yml file by/through our framwork,
> register
> > new gem in travis-ci straight from biogems.info etc.)
>
> I think Marjan has put github authentication in.
>
>
Yes, that's correct, users can sign into the new website using their GitHub
account. We're using OmniAuth gem to make this possible, the wiki page on
restyling bioruby.org has some additional details on this.

However, from reading GitHub API docs, I would say that it' not possible to
create a new commit to add travis.yml file to the repository in question
from the site. The site has only read access of all repositories which
belong to a user:

http://developer.github.com/v3/oauth/#scopes


--
Marjan

From pjotr.public14 at thebird.nl  Thu Mar 22 15:29:01 2012
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Thu, 22 Mar 2012 20:29:01 +0100
Subject: [BioRuby] GSoC: Testing framework for biogem plugins
In-Reply-To: <CADKP5C=NKabtbtoyo5M-XBtZR41zeEKcTrNuYtkoSbFWsn-hXQ@mail.gmail.com>
References: <CAO--zKeD34pqYry3UUoxhO-NShz++MEKkt4i1Rmrrabd_AFiJw@mail.gmail.com>
	<20120320093406.GA4581@thebird.nl>
	<CAO--zKdJ5qiK_=HTeg_u1dLjsehwU=7v9d9X1_W44xTs33RJSg@mail.gmail.com>
	<20120322153730.GA24105@thebird.nl>
	<CADKP5C=NKabtbtoyo5M-XBtZR41zeEKcTrNuYtkoSbFWsn-hXQ@mail.gmail.com>
Message-ID: <20120322192901.GA24808@thebird.nl>

On Thu, Mar 22, 2012 at 06:39:36PM +0100, Marjan Povolni wrote:
>    Hi,
> 
>      > 2. Travis-CI handles users via their GitHub accounts. Would we also
>      like to
>      > handle users that way, so they can hit "run my test" straight from
>      > [1]biogems.info? (and upload travis.yml file by/through our framwork,
>      register
>      > new gem in travis-ci straight from [2]biogems.info etc.)
> 
>      I think Marjan has put github authentication in.
> 
>    Yes, that's correct, users can sign into the new website using their
>    GitHub account. We're using OmniAuth gem to make this possible, the wiki
>    page on restyling [3]bioruby.org has some additional details on this.
>    However, from reading GitHub API docs, I would say that it' not possible
>    to create a new commit to add travis.yml file to the repository in
>    question from the site. The site has only read access of all repositories
>    which belong to a user:
>    [4]http://developer.github.com/v3/oauth/#scopes

Rightly so :).

biogem does generate the travis.yml file now, by default, on
generation of a new gem.

Pj.

From pjotr.public14 at thebird.nl  Thu Mar 22 15:51:39 2012
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Thu, 22 Mar 2012 20:51:39 +0100
Subject: [BioRuby] BioRuby.org website
In-Reply-To: <20120229172026.GA29664@thebird.nl>
References: <20120229090233.GB27695@thebird.nl>
	<CAKVJ-_4pgFXg9fMaKTV96MkmeBvuzmHHNbnfYQwVwW_vr00+tg@mail.gmail.com>
	<20120229145443.GA28775@thebird.nl>
	<CAKVJ-_5n3w5nVF4jCz9_Oh=eJwYWqwPHf=tyQWruKVwV-k0HzQ@mail.gmail.com>
	<098C48D9-F855-4E5A-B978-FE9B690B785D@illinois.edu>
	<20120229172026.GA29664@thebird.nl>
Message-ID: <20120322195139.GA25227@thebird.nl>

Feature: Create challenges for newbies using github issues

  We want to create a page that lists challenges for newbies. These
  challenges are harvested from github issues tagged with the 'newbie' 
  tag.

  Scenario: The coding challenges page
    Given a user visits the BioRuby challenges page
    When the page gets shown
    Then I want to show all known issues in all biogems that have been tagged 'newbie'
 
see also https://github.com/pjotrp/NA-BioRuby.org/tree/master/features

From gianluca at dellavedova.org  Fri Mar 23 01:27:51 2012
From: gianluca at dellavedova.org (Gianluca Della Vedova)
Date: Fri, 23 Mar 2012 06:27:51 +0100
Subject: [BioRuby] BioRuby.org website
In-Reply-To: <20120322195139.GA25227@thebird.nl>
References: <20120229090233.GB27695@thebird.nl>
	<CAKVJ-_4pgFXg9fMaKTV96MkmeBvuzmHHNbnfYQwVwW_vr00+tg@mail.gmail.com>
	<20120229145443.GA28775@thebird.nl>
	<CAKVJ-_5n3w5nVF4jCz9_Oh=eJwYWqwPHf=tyQWruKVwV-k0HzQ@mail.gmail.com>
	<098C48D9-F855-4E5A-B978-FE9B690B785D@illinois.edu>
	<20120229172026.GA29664@thebird.nl>
	<20120322195139.GA25227@thebird.nl>
Message-ID: <20120323052751.GA4749@dellavedova-E4310.dellavedova.org>

That's a great idea.
--
Gianluca Della Vedova
* Pjotr Prins <pjotr.public14 at thebird.nl> [2012-03-22 20:51:39 +0100]:

>Feature: Create challenges for newbies using github issues
>
>  We want to create a page that lists challenges for newbies. These
>  challenges are harvested from github issues tagged with the 'newbie'
>  tag.
>
>  Scenario: The coding challenges page
>    Given a user visits the BioRuby challenges page
>    When the page gets shown
>    Then I want to show all known issues in all biogems that have been tagged 'newbie'
>
>see also https://github.com/pjotrp/NA-BioRuby.org/tree/master/features
>_______________________________________________
>BioRuby Project - http://www.bioruby.org/
>BioRuby mailing list
>BioRuby at lists.open-bio.org
>http://lists.open-bio.org/mailman/listinfo/bioruby

From info at orbicule.com  Fri Mar 23 06:52:54 2012
From: info at orbicule.com (Peter Schols)
Date: Fri, 23 Mar 2012 11:52:54 +0100
Subject: [BioRuby] [STUDENT JOB] BioRuby summer job in human genomics
Message-ID: <07B2DC43-18F3-4C86-B03E-7C4023BF3A12@orbicule.com>

Dear list,

We are looking for a student who is passionate about bioinformatics and (Bio)Ruby to join our team this summer.
Candidates should have:

- some background in biology / genetics / bioinformatics
- good knowledge of Ruby 
- preferably some experience with BioRuby and bio gems
- experience with Rails is a plus

You will be working with our developers and designers on an exciting new project in the field of human genomics.
We can offer you:

- super flexible schedule
- highly motivated team
- the possibility to work from home
- the possibility to have your work seen by thousands of people worldwide, a great addition to your cv
- 1500 euro (about $1950) net monthly wage

Interested? Please send your resume to jobs at orbicule.com

Peter Schols
Orbicule

From cswh at umich.edu  Mon Mar 26 03:26:14 2012
From: cswh at umich.edu (Clayton Wheeler)
Date: Mon, 26 Mar 2012 03:26:14 -0400
Subject: [BioRuby] GSoC: MAF parser questions
Message-ID: <DEB9EA3D-4E72-4348-A02A-D701571D6ECF@umich.edu>

Hello,

I'm Clayton Wheeler, an undergraduate microbiology student at the University of Michigan. I'm particularly interested in molecular biology and microbial ecology, but in a previous life I was a programmer and system administrator for 11 years, so I'm very interested in applying that background to bioinformatics, also. The lab I've been working in uses bioinformatics tools and next-generation sequencing quite a bit, especially for studying hydrothermal plume communities; I've been working on the wet-lab side, but this is an area I'd like to learn more about. Moreover, I've been using Ruby for the last six years or so, and so I'd like to help develop it as a bioinformatics platform. The GSoC projects for BioRuby caught my eye, and I'd like to see if there's a good way I could contribute there.

The parser projects for MAF and GFF3 seem interesting and doable; I've been looking into the MAF parser project in particular, and I have a few questions about it. 

First, does the set of operations on MAF data described in Blankenberg et al (http://1.usa.gov/GQRYvX) cover the use cases that such a parser and indexing system should support?

Is https://github.com/polyatail/biopython the correct location of the BioPython MAF code described in http://biopython.org/wiki/Multiple_Alignment_Format? (It looks like it's been 11 months since the last commit.) 

Also, I've found a few existing tools for working with MAF files such as the scripts shipped with bx-python and PHAST, but not too many worked examples of how they'd be used in practice. Are there any more or less real-world examples available of MAF operations demonstrating the kinds of indexed access, large data sizes, etc. that should be supported in bio-alignment? 

Thanks,

Clayton Wheeler
cswh at umich.edu




From p.j.a.cock at googlemail.com  Mon Mar 26 05:09:50 2012
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 26 Mar 2012 10:09:50 +0100
Subject: [BioRuby] GSoC: MAF parser questions
In-Reply-To: <DEB9EA3D-4E72-4348-A02A-D701571D6ECF@umich.edu>
References: <DEB9EA3D-4E72-4348-A02A-D701571D6ECF@umich.edu>
Message-ID: <CAKVJ-_6=1ThQ4c27CBtS_fU2at_1CQHpwL7oBHFh2oz5eFPHYw@mail.gmail.com>

On Mon, Mar 26, 2012 at 8:26 AM, Clayton Wheeler <cswh at umich.edu> wrote:
> Is https://github.com/polyatail/biopython the correct location of the BioPython
> MAF code described in http://biopython.org/wiki/Multiple_Alignment_Format?
> (It looks like it's been 11 months since the last commit.)

Yes, specifically this
branch:https://github.com/polyatail/biopython/tree/alignio-maf

This is something we're going to be looking at merging for Biopython 1.60,
http://lists.open-bio.org/pipermail/biopython-dev/2012-February/009384.html

Peter

From saketkc at gmail.com  Mon Mar 26 11:32:40 2012
From: saketkc at gmail.com (Saket Choudhary)
Date: Mon, 26 Mar 2012 21:02:40 +0530
Subject: [BioRuby] [GSoC] [GSoC2012] BioRuby
In-Reply-To: <20120326133700.GA22488@thebird.nl>
References: <CAEDHeive9DOXSMMPXfjNEu1i6X0iqC0czqBtnAvrar1MUjb+yQ@mail.gmail.com>
	<20120326133700.GA22488@thebird.nl>
Message-ID: <CAEDHeisH+7cUPp2EsFNJ9yOevb4kDG78kL-3d-We8of0+7G+Rg@mail.gmail.com>

Hi Pjotr,

Thanks !

I have been using BioRuby and BioPython for 6 months now to solve the
"Protein Loop Closure" problem. I use it mainly to manipulate the atom
positions in a given PDB file, thus perturbing their positions.

I went through the discussion that happened on the mailing list last month:
Here are my notes about the same

1.http://lists.open-bio.org/pipermail/bioruby/2012-February/002087.html

Even I am a big fan of Jruby homepage. Here are my suggestiosn :
1. Ruby is simple, clear , intutitve and this makes Biouby intutive to
everyone. This needs to be emphasised the very first time a user comes to
the webpage : Instead of giving them examples on Wiki[
http://bioruby.open-bio.org/wiki/SampleCodes] to "read" through a tutorial
in the form of a short writeup/description about Ruby/BioRuby foolwed by a
challenge would be more appealing and intuitive to the user even though he
is being exposed to Ruby/BioRuby for the first time. Say some tutorial on
the lines of http://www.codecademy.com/ , a short tutorial followed by your
Scratchpad. !


2. Calendar/Tweet/Conference widget:

Something again on the lines of Jruby website.


3. Favicon missing ?

Though a very trivial issue , but just wanted to know why isn't there a
favicon for bioruby.org ?

These are the stuff I gathered , I am still digging the old threads, will
post here if something relevant comes up !


Saket Choudhary
IIT Bombay
github.com/saketkc



On 26 March 2012 19:07, Pjotr Prins <pjotr2012 at thebird.nl> wrote:

> Hi Saket,
>
> Welcome!
>
> It would be good if you also introduce yourself to the BioRuby ML, and
> post your ideas. We are working on the website (should I say
> web 'experience'), and I like what you propose. Also check out the ML
> archive of the last months, you'll find a lot of information.
>
> Pj.
>
> On Mon, Mar 26, 2012 at 02:10:51PM +0530, Saket Choudhary wrote:
> > Hi !
> >
> > I am Saket Choudhary, a third year undergraduate student at IIT Bombay,
> > India.
> >
> > Ruby has been my first love for programming. My last project[internship]
> > was at SlideShare <http://www.slideshare.net>, one of the biggest Ruby
> on
> > Rails website in the world. I had developed the Admin interface for
> > SlideShare which could enable suspending users, reconversion/deletion of
> > SlideShows , and user deletion/suspension.
> >
> > My hack at Yahoo! Open Hack India -2011 qualified among the Top 50 hacks
> ,
> > I built a Sinatra app for fetching a defined file from a Dropbox account
> > and sending it to a specified email address , just on a SMS.[
> > https://github.com/saketkc/dropbox_on_sms]
> >
> > I went through the GSoC idea page and "Adding social networking
> > functionality to BioRuby.org", is of my special interest. I have an
> > experience working on the Rails platform. My plans for making the website
> > more "Social" is as follows:
> >
> > 1. Provide an online 'Scratchpad' for Ruby/BioRuby enthusiasts that not
> > only allows them to run their codes online but also provides them a
> > facility to store it online in the form of an archive so that they an
> acess
> > it later.
> >
> > 2. Include sharing facility on "Scratchpad" so  that one user can share
> his
> > code online with other users/community and get feedback/comments. On the
> > lines of "Sage <http://www.sagenb.org/>" notebooks.
> >
> > 3. Develop an Online Board on the lines of "Quora <https://www.quora.com
> >"
> > Boards  so that users can pin certain codes/algorithms on to their own
> > boards for their reference this would reduce the overhead of searching
> for
> > a particular algorithm again and again .
> >
> > Let me know you views on these ideas. I would send a mockup of the same
> > incase these ideas seem feasible to you.
> >
> > Thanks
> >
> >  Saket Choudhary
> > IIT Bombay
> > _______________________________________________
> > GSoC mailing list
> > GSoC at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/gsoc
>

From pjotr.public14 at thebird.nl  Mon Mar 26 22:49:14 2012
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Tue, 27 Mar 2012 04:49:14 +0200
Subject: [BioRuby] [GSoC] [GSoC2012] BioRuby
In-Reply-To: <CAEDHeisH+7cUPp2EsFNJ9yOevb4kDG78kL-3d-We8of0+7G+Rg@mail.gmail.com>
References: <CAEDHeive9DOXSMMPXfjNEu1i6X0iqC0czqBtnAvrar1MUjb+yQ@mail.gmail.com>
	<20120326133700.GA22488@thebird.nl>
	<CAEDHeisH+7cUPp2EsFNJ9yOevb4kDG78kL-3d-We8of0+7G+Rg@mail.gmail.com>
Message-ID: <20120327024914.GA25873@thebird.nl>

To all GSoC applicants: be sure to start on your proposal and share it
with your project mentors. It is a surprisingly thorough and
competitive selection process, and if you want to succeed, the plan
and presentation has to be good. Every year we see students who start
too late. We can give feedback now, do use that to your advantage. We
want you to succeed.

Pj.

On Mon, Mar 26, 2012 at 09:02:40PM +0530, Saket Choudhary wrote:
> Hi Pjotr,
> 
> Thanks !
> 
> I have been using BioRuby and BioPython for 6 months now to solve the
> "Protein Loop Closure" problem. I use it mainly to manipulate the atom
> positions in a given PDB file, thus perturbing their positions.
> 
> I went through the discussion that happened on the mailing list last month:
> Here are my notes about the same
> 
> 1.http://lists.open-bio.org/pipermail/bioruby/2012-February/002087.html
> 
> Even I am a big fan of Jruby homepage. Here are my suggestiosn :
> 1. Ruby is simple, clear , intutitve and this makes Biouby intutive to
> everyone. This needs to be emphasised the very first time a user comes to
> the webpage : Instead of giving them examples on Wiki[
> http://bioruby.open-bio.org/wiki/SampleCodes] to "read" through a tutorial
> in the form of a short writeup/description about Ruby/BioRuby foolwed by a
> challenge would be more appealing and intuitive to the user even though he
> is being exposed to Ruby/BioRuby for the first time. Say some tutorial on
> the lines of http://www.codecademy.com/ , a short tutorial followed by your
> Scratchpad. !
> 
> 
> 2. Calendar/Tweet/Conference widget:
> 
> Something again on the lines of Jruby website.
> 
> 
> 3. Favicon missing ?
> 
> Though a very trivial issue , but just wanted to know why isn't there a
> favicon for bioruby.org ?
> 
> These are the stuff I gathered , I am still digging the old threads, will
> post here if something relevant comes up !
> 
> 
> Saket Choudhary
> IIT Bombay
> github.com/saketkc
> 
> 
> 
> On 26 March 2012 19:07, Pjotr Prins <pjotr2012 at thebird.nl> wrote:
> 
> > Hi Saket,
> >
> > Welcome!
> >
> > It would be good if you also introduce yourself to the BioRuby ML, and
> > post your ideas. We are working on the website (should I say
> > web 'experience'), and I like what you propose. Also check out the ML
> > archive of the last months, you'll find a lot of information.
> >
> > Pj.
> >
> > On Mon, Mar 26, 2012 at 02:10:51PM +0530, Saket Choudhary wrote:
> > > Hi !
> > >
> > > I am Saket Choudhary, a third year undergraduate student at IIT Bombay,
> > > India.
> > >
> > > Ruby has been my first love for programming. My last project[internship]
> > > was at SlideShare <http://www.slideshare.net>, one of the biggest Ruby
> > on
> > > Rails website in the world. I had developed the Admin interface for
> > > SlideShare which could enable suspending users, reconversion/deletion of
> > > SlideShows , and user deletion/suspension.
> > >
> > > My hack at Yahoo! Open Hack India -2011 qualified among the Top 50 hacks
> > ,
> > > I built a Sinatra app for fetching a defined file from a Dropbox account
> > > and sending it to a specified email address , just on a SMS.[
> > > https://github.com/saketkc/dropbox_on_sms]
> > >
> > > I went through the GSoC idea page and "Adding social networking
> > > functionality to BioRuby.org", is of my special interest. I have an
> > > experience working on the Rails platform. My plans for making the website
> > > more "Social" is as follows:
> > >
> > > 1. Provide an online 'Scratchpad' for Ruby/BioRuby enthusiasts that not
> > > only allows them to run their codes online but also provides them a
> > > facility to store it online in the form of an archive so that they an
> > acess
> > > it later.
> > >
> > > 2. Include sharing facility on "Scratchpad" so  that one user can share
> > his
> > > code online with other users/community and get feedback/comments. On the
> > > lines of "Sage <http://www.sagenb.org/>" notebooks.
> > >
> > > 3. Develop an Online Board on the lines of "Quora <https://www.quora.com
> > >"
> > > Boards  so that users can pin certain codes/algorithms on to their own
> > > boards for their reference this would reduce the overhead of searching
> > for
> > > a particular algorithm again and again .
> > >
> > > Let me know you views on these ideas. I would send a mockup of the same
> > > incase these ideas seem feasible to you.
> > >
> > > Thanks
> > >
> > >  Saket Choudhary
> > > IIT Bombay
> > > _______________________________________________
> > > GSoC mailing list
> > > GSoC at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/gsoc
> >
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
> 

From bonnal at ingm.org  Tue Mar 27 04:25:58 2012
From: bonnal at ingm.org (Raoul Bonnal)
Date: Tue, 27 Mar 2012 10:25:58 +0200
Subject: [BioRuby] GSoC: MAF parser questions
In-Reply-To: <DEB9EA3D-4E72-4348-A02A-D701571D6ECF@umich.edu>
Message-ID: <CB974636.89B4%bonnal@ingm.org>

Hi Clayton,
Welcome.

On 26/03/12 09.26, "Clayton Wheeler" <cswh at umich.edu> wrote:

> Hello,
> 
> I'm Clayton Wheeler, an undergraduate microbiology student at the University
> of Michigan. I'm particularly interested in molecular biology and microbial
> ecology, but in a previous life I was a programmer and system administrator
> for 11 years, so I'm very interested in applying that background to
> bioinformatics, also. The lab I've been working in uses bioinformatics tools
> and next-generation sequencing quite a bit, especially for studying
> hydrothermal plume communities; I've been working on the wet-lab side, but
> this is an area I'd like to learn more about. Moreover, I've been using Ruby
> for the last six years or so, and so I'd like to help develop it as a
> bioinformatics platform. The GSoC projects for BioRuby caught my eye, and I'd
> like to see if there's a good way I could contribute there.
> 
> The parser projects for MAF and GFF3 seem interesting and doable; I've been
> looking into the MAF parser project in particular, and I have a few questions
> about it. 
> 
> First, does the set of operations on MAF data described in Blankenberg et al
> (http://1.usa.gov/GQRYvX) cover the use cases that such a parser and indexing
> system should support?
Yes, I think that having all those features implemented will be great. Maybe
it would be better if you define a priority list of all the features.
> 
> Is https://github.com/polyatail/biopython the correct location of the
> BioPython MAF code described in
> http://biopython.org/wiki/Multiple_Alignment_Format? (It looks like it's been
> 11 months since the last commit.)

>From Peter:" Yes, specifically this
branch:https://github.com/polyatail/biopython/tree/alignio-maf

This is something we're going to be looking at merging for Biopython 1.60,
http://lists.open-bio.org/pipermail/biopython-dev/2012-February/009384.html

Peter"


Specs: http://genome.ucsc.edu/FAQ/FAQformat.html#format5

Some MAF app http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
 
> Also, I've found a few existing tools for working with MAF files such as the
> scripts shipped with bx-python and PHAST, but not too many worked examples of
> how they'd be used in practice. Are there any more or less real-world examples
> available of MAF operations demonstrating the kinds of indexed access, large
> data sizes, etc. that should be supported in bio-alignment?
This is an application which uses MAF as input
https://github.com/mlin/PhyloCSF/wiki


--
Ra



From pjotr.public14 at thebird.nl  Tue Mar 27 07:54:25 2012
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Tue, 27 Mar 2012 13:54:25 +0200
Subject: [BioRuby] biogems.info updated
In-Reply-To: <20111014080815.GA25807@thebird.nl>
References: <20110920165601.GA8933@thebird.nl>
	<20111014080815.GA25807@thebird.nl>
Message-ID: <20120327115425.GA29301@thebird.nl>

Marjan updated the site

    http://biogems.info/

Now we track the number of commits in the last week, and 90 days, to
show development activity.

Pj.

From bonnal at ingm.org  Tue Mar 27 08:12:42 2012
From: bonnal at ingm.org (Raoul Bonnal)
Date: Tue, 27 Mar 2012 14:12:42 +0200
Subject: [BioRuby] biogems.info updated
In-Reply-To: <20120327115425.GA29301@thebird.nl>
Message-ID: <CB977B5A.89C0%bonnal@ingm.org>

Wow, well done.



On 27/03/12 13.54, "Pjotr Prins" <pjotr.public14 at thebird.nl> wrote:

> Marjan updated the site
> 
>     http://biogems.info/
> 
> Now we track the number of commits in the last week, and 90 days, to
> show development activity.
> 
> Pj.
> _______________________________________________
> 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  Thu Mar  1 07:14:36 2012
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Thu, 1 Mar 2012 08:14:36 +0100
Subject: [BioRuby] IRC
Message-ID: <20120301071436.GA860@thebird.nl>

We will be on IRC, most of the day.

Pj.


From mictadlo at gmail.com  Fri Mar  2 09:11:35 2012
From: mictadlo at gmail.com (Mic)
Date: Fri, 2 Mar 2012 19:11:35 +1000
Subject: [BioRuby] Bio::Faster plugin
In-Reply-To: <CALf85+V1-a+i2dc0YKf95vgrEX1pipXSZ_gHayii2ayGs8m+4Q@mail.gmail.com>
References: <CACtet2TWTXMRkpgbai0=Fue7Cmn3v6EBbuXWd32cOa_xiD90AA@mail.gmail.com>
	<CB2A292C.747B%bonnal@ingm.org>
	<CALf85+V1-a+i2dc0YKf95vgrEX1pipXSZ_gHayii2ayGs8m+4Q@mail.gmail.com>
Message-ID: <CAOP6n=h3JcZ7=_bp51LRdX1nQDKnHY-o3eQo9_g9EZ4t4OZcuA@mail.gmail.com>

Did also compare the speed between biofaster and reading 4 lines (fastq)/2
lines (fasta) at the time?

Cheers,

On Thu, Jan 5, 2012 at 1:20 AM, George Githinji <georgkam at gmail.com> wrote:

> ++1 Sounds cool!
>
>
> On Wed, Jan 4, 2012 at 6:05 PM, Raoul Bonnal <bonnal at ingm.org> wrote:
> > Hi Francesco,
> > It's very cool!
> >
> > And you can access to the seq object/array also in this way:
> > Bio::Faster.parse(File.join(TEST_DATA,"sample.fastq")) do |id, comments,
> > sequence, quality|
> >  puts "#{id} #{comments} #{sequence} #{quality}"
> > end
> >
> > Obviously I like it more than using the raw array :-)
> > I suppose in case of no quality value you get a nil object
> >
> >
> > +1
> >
> >
> > On 04/01/12 10.50, "Francesco Strozzi" <francesco.strozzi at gmail.com>
> wrote:
> >
> >> Hi guys,
> >>
> >> I have created a BioRuby plugin called bio-faster, that implements a
> fast
> >> and simple parser for FastA and FastQ files. It's based on the C library
> >> Kseq written by Heng Li (author of Samtools and BWA). Compared to
> >> Bio::FastQ it is actually 4-5 times faster in parsing large FastQ files.
> >> The code will not create a Bio object for each sequence but it will
> return
> >> a simple array with sequence data and quality values for FastQ (it
> supports
> >> Sanger/Phred format only).
> >> Bio::Faster could be a good choice when you just need to parse huge
> files,
> >> for example to extract information or to store sequence data in a
> database,
> >> and you don't need to create an object for each sequence but you only
> want
> >> to parse the dataset easily and quickly.
> >>
> >> Here is the code: https://github.com/fstrozzi/bioruby-faster
> >> Here is the wiki for more details:
> >> https://github.com/fstrozzi/bioruby-faster/wiki
> >> To get the gem: gem install bio-faster
> >>
> >> Tested with Ruby 1.9 only.
> >>
> >> Any comment or feedback is much appreciated!
> >>
> >> Cheers
> >
> >
> > _______________________________________________
> > BioRuby Project - http://www.bioruby.org/
> > 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/
> Twitter: http://twitter.com/#!/george_l
>
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>


From p.j.a.cock at googlemail.com  Fri Mar  2 14:04:21 2012
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 2 Mar 2012 14:04:21 +0000
Subject: [BioRuby] Google Summer of Code project ideas
In-Reply-To: <CF39235E-DD8E-4B28-B2CE-5C1E9F80A54B@illinois.edu>
References: <4F355910.4060203@gmail.com>
	<CF39235E-DD8E-4B28-B2CE-5C1E9F80A54B@illinois.edu>
Message-ID: <CAKVJ-_5uKFqH_krSzEemCikVN-pDK1C9E0s4yfk=JGNbkqk=3g@mail.gmail.com>

On 10 Feb, Robert Buels wrote (posted by Chris Field):
> Hi all,
>
> I'm going to be OBF project admin again this year for Google Summer of
> code. ?OBF's application is due in a couple of weeks, and we need to update
> our project ideas on the OBF wiki page and on each project's individual wiki
> pages.
>
> So, for each of the OBF projects that wants to do GSoC again this year,
> please:
>
> a.) Update the list of project ideas on your project's GSoC page
> (BioPython, BioPerl, BioRuby, etc). ?Add new ones, remove ones that have
> already been done or no longer relevant, etc.
>
> b.) Update the list of project ideas on the main OBF GSoC page
> (http://www.open-bio.org/wiki/Google_Summer_of_Code) to match.
>
> c.) Let me know via email that you have done so and it's ready for Google
> to peruse.
>
> Please have the updates done, if possible, by this Friday (March 11). The
> number and quality of the project ideas are part of the evaluation process
> for whether OBF is accepted as a Summer of Code organization again this
> year, so let's come up with some good ones. ?:-)
>
> Rob
>
> ----
> Robert Buels

Hi BioRuby folk,

You seem to have been the most organized Bio* project for GSoC so far, and have
put together good set of GSoC project ideas by Rob's target date. Well done :)

Is the list here complete now?
http://bioruby.open-bio.org/wiki/Google_Summer_of_Code

    3.1.1 Write the world's fastest parallelized GFF3/GTF parser in D,
for Ruby FFI
    3.1.2 Extend bio-alignment plug-in with Multiple Alignment Format
-MAF- parser (FFI?)
    3.1.3 Testing framework for biogem plugins
    3.1.4 Adding social networking functionality to BioRuby.org
    3.1.5 Update bio-images a plugin to represent bio-object with cool images
    3.1.6 Update to the Ruby Ensembl API

I noticed "Testing framework for biogem plugins" was missing on the OBF
summary page, so I added it:
http://www.open-bio.org/wiki/Google_Summer_of_Code

Regards,

Peter



From mictadlo at gmail.com  Sat Mar  3 01:14:40 2012
From: mictadlo at gmail.com (Mic)
Date: Sat, 3 Mar 2012 11:14:40 +1000
Subject: [BioRuby] Google Summer of Code project ideas
In-Reply-To: <CAKVJ-_5uKFqH_krSzEemCikVN-pDK1C9E0s4yfk=JGNbkqk=3g@mail.gmail.com>
References: <4F355910.4060203@gmail.com>
	<CF39235E-DD8E-4B28-B2CE-5C1E9F80A54B@illinois.edu>
	<CAKVJ-_5uKFqH_krSzEemCikVN-pDK1C9E0s4yfk=JGNbkqk=3g@mail.gmail.com>
Message-ID: <CAOP6n=h8bWUaBra-N35AxqnZm2H6p8WH+akx5tB9q9fdhwgkfw@mail.gmail.com>

Howabout to include:
* Bedtools
* tabix


On Sat, Mar 3, 2012 at 12:04 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On 10 Feb, Robert Buels wrote (posted by Chris Field):
> > Hi all,
> >
> > I'm going to be OBF project admin again this year for Google Summer of
> > code.  OBF's application is due in a couple of weeks, and we need to
> update
> > our project ideas on the OBF wiki page and on each project's individual
> wiki
> > pages.
> >
> > So, for each of the OBF projects that wants to do GSoC again this year,
> > please:
> >
> > a.) Update the list of project ideas on your project's GSoC page
> > (BioPython, BioPerl, BioRuby, etc).  Add new ones, remove ones that have
> > already been done or no longer relevant, etc.
> >
> > b.) Update the list of project ideas on the main OBF GSoC page
> > (http://www.open-bio.org/wiki/Google_Summer_of_Code) to match.
> >
> > c.) Let me know via email that you have done so and it's ready for Google
> > to peruse.
> >
> > Please have the updates done, if possible, by this Friday (March 11). The
> > number and quality of the project ideas are part of the evaluation
> process
> > for whether OBF is accepted as a Summer of Code organization again this
> > year, so let's come up with some good ones.  :-)
> >
> > Rob
> >
> > ----
> > Robert Buels
>
> Hi BioRuby folk,
>
> You seem to have been the most organized Bio* project for GSoC so far, and
> have
> put together good set of GSoC project ideas by Rob's target date. Well
> done :)
>
> Is the list here complete now?
> http://bioruby.open-bio.org/wiki/Google_Summer_of_Code
>
>    3.1.1 Write the world's fastest parallelized GFF3/GTF parser in D,
> for Ruby FFI
>    3.1.2 Extend bio-alignment plug-in with Multiple Alignment Format
> -MAF- parser (FFI?)
>    3.1.3 Testing framework for biogem plugins
>    3.1.4 Adding social networking functionality to BioRuby.org
>    3.1.5 Update bio-images a plugin to represent bio-object with cool
> images
>    3.1.6 Update to the Ruby Ensembl API
>
> I noticed "Testing framework for biogem plugins" was missing on the OBF
> summary page, so I added it:
> http://www.open-bio.org/wiki/Google_Summer_of_Code
>
> Regards,
>
> Peter
>
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>


From francesco.strozzi at gmail.com  Sat Mar  3 07:38:54 2012
From: francesco.strozzi at gmail.com (Francesco Strozzi)
Date: Sat, 3 Mar 2012 08:38:54 +0100
Subject: [BioRuby] Bio::Faster plugin
In-Reply-To: <CAOP6n=h3JcZ7=_bp51LRdX1nQDKnHY-o3eQo9_g9EZ4t4OZcuA@mail.gmail.com>
References: <CACtet2TWTXMRkpgbai0=Fue7Cmn3v6EBbuXWd32cOa_xiD90AA@mail.gmail.com>
	<CB2A292C.747B%bonnal@ingm.org>
	<CALf85+V1-a+i2dc0YKf95vgrEX1pipXSZ_gHayii2ayGs8m+4Q@mail.gmail.com>
	<CAOP6n=h3JcZ7=_bp51LRdX1nQDKnHY-o3eQo9_g9EZ4t4OZcuA@mail.gmail.com>
Message-ID: <CACtet2T__UCO8Eq6WXkCHEQr+FFaO93_vm7p1dqt=iOZRFVB=Q@mail.gmail.com>

Hi,
I haven't done this comparison, but if you want to run it I will be happy
to put the outputs on the wiki.

Cheers

On Friday, March 2, 2012, Mic <mictadlo at gmail.com> wrote:
> Did also compare the speed between biofaster and reading 4 lines (fastq)/2
> lines (fasta) at the time?
>
> Cheers,
>
> On Thu, Jan 5, 2012 at 1:20 AM, George Githinji <georgkam at gmail.com>
wrote:
>
>> ++1 Sounds cool!
>>
>>
>> On Wed, Jan 4, 2012 at 6:05 PM, Raoul Bonnal <bonnal at ingm.org> wrote:
>> > Hi Francesco,
>> > It's very cool!
>> >
>> > And you can access to the seq object/array also in this way:
>> > Bio::Faster.parse(File.join(TEST_DATA,"sample.fastq")) do |id,
comments,
>> > sequence, quality|
>> >  puts "#{id} #{comments} #{sequence} #{quality}"
>> > end
>> >
>> > Obviously I like it more than using the raw array :-)
>> > I suppose in case of no quality value you get a nil object
>> >
>> >
>> > +1
>> >
>> >
>> > On 04/01/12 10.50, "Francesco Strozzi" <francesco.strozzi at gmail.com>
>> wrote:
>> >
>> >> Hi guys,
>> >>
>> >> I have created a BioRuby plugin called bio-faster, that implements a
>> fast
>> >> and simple parser for FastA and FastQ files. It's based on the C
library
>> >> Kseq written by Heng Li (author of Samtools and BWA). Compared to
>> >> Bio::FastQ it is actually 4-5 times faster in parsing large FastQ
files.
>> >> The code will not create a Bio object for each sequence but it will
>> return
>> >> a simple array with sequence data and quality values for FastQ (it
>> supports
>> >> Sanger/Phred format only).
>> >> Bio::Faster could be a good choice when you just need to parse huge
>> files,
>> >> for example to extract information or to store sequence data in a
>> database,
>> >> and you don't need to create an object for each sequence but you only
>> want
>> >> to parse the dataset easily and quickly.
>> >>
>> >> Here is the code: https://github.com/fstrozzi/bioruby-faster
>> >> Here is the wiki for more details:
>> >> https://github.com/fstrozzi/bioruby-faster/wiki
>> >> To get the gem: gem install bio-faster
>> >>
>> >> Tested with Ruby 1.9 only.
>> >>
>> >> Any comment or feedback is much appreciated!
>> >>
>> >> Cheers
>> >
>> >
>> > _______________________________________________
>> > BioRuby Project - http://www.bioruby.org/
>> > 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/
>> Twitter: http://twitter.com/#!/george_l
>>
>> _______________________________________________
>> 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
>

-- 

Francesco


From bonnal at ingm.org  Sat Mar  3 11:15:56 2012
From: bonnal at ingm.org (Raoul Bonnal)
Date: Sat, 03 Mar 2012 12:15:56 +0100
Subject: [BioRuby] Google Summer of Code project ideas
In-Reply-To: <CAOP6n=h8bWUaBra-N35AxqnZm2H6p8WH+akx5tB9q9fdhwgkfw@mail.gmail.com>
Message-ID: <CB77BBFC.84F8%bonnal@ingm.org>

What you mean ?

I would add "Extract BioSQL form BioRuby and create a biogem plug-in,
updating the library where needed."

Is there more time to add this project?


On 03/03/12 02.14, "Mic" <mictadlo at gmail.com> wrote:

> Howabout to include:
> * Bedtools
> * tabix
> 
> 
> On Sat, Mar 3, 2012 at 12:04 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:
> 
>> On 10 Feb, Robert Buels wrote (posted by Chris Field):
>>> Hi all,
>>> 
>>> I'm going to be OBF project admin again this year for Google Summer of
>>> code.  OBF's application is due in a couple of weeks, and we need to
>> update
>>> our project ideas on the OBF wiki page and on each project's individual
>> wiki
>>> pages.
>>> 
>>> So, for each of the OBF projects that wants to do GSoC again this year,
>>> please:
>>> 
>>> a.) Update the list of project ideas on your project's GSoC page
>>> (BioPython, BioPerl, BioRuby, etc).  Add new ones, remove ones that have
>>> already been done or no longer relevant, etc.
>>> 
>>> b.) Update the list of project ideas on the main OBF GSoC page
>>> (http://www.open-bio.org/wiki/Google_Summer_of_Code) to match.
>>> 
>>> c.) Let me know via email that you have done so and it's ready for Google
>>> to peruse.
>>> 
>>> Please have the updates done, if possible, by this Friday (March 11). The
>>> number and quality of the project ideas are part of the evaluation
>> process
>>> for whether OBF is accepted as a Summer of Code organization again this
>>> year, so let's come up with some good ones.  :-)
>>> 
>>> Rob
>>> 
>>> ----
>>> Robert Buels
>> 
>> Hi BioRuby folk,
>> 
>> You seem to have been the most organized Bio* project for GSoC so far, and
>> have
>> put together good set of GSoC project ideas by Rob's target date. Well
>> done :)
>> 
>> Is the list here complete now?
>> http://bioruby.open-bio.org/wiki/Google_Summer_of_Code
>> 
>>    3.1.1 Write the world's fastest parallelized GFF3/GTF parser in D,
>> for Ruby FFI
>>    3.1.2 Extend bio-alignment plug-in with Multiple Alignment Format
>> -MAF- parser (FFI?)
>>    3.1.3 Testing framework for biogem plugins
>>    3.1.4 Adding social networking functionality to BioRuby.org
>>    3.1.5 Update bio-images a plugin to represent bio-object with cool
>> images
>>    3.1.6 Update to the Ruby Ensembl API
>> 
>> I noticed "Testing framework for biogem plugins" was missing on the OBF
>> summary page, so I added it:
>> http://www.open-bio.org/wiki/Google_Summer_of_Code
>> 
>> Regards,
>> 
>> Peter
>> 
>> _______________________________________________
>> 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 bonnal at ingm.org  Sat Mar  3 11:15:57 2012
From: bonnal at ingm.org (Raoul Bonnal)
Date: Sat, 03 Mar 2012 12:15:57 +0100
Subject: [BioRuby] Google Summer of Code project ideas
In-Reply-To: <CAKVJ-_5uKFqH_krSzEemCikVN-pDK1C9E0s4yfk=JGNbkqk=3g@mail.gmail.com>
Message-ID: <CB77BBFD.84F8%bonnal@ingm.org>

Thanks !

Rob is aware that our page is ready to go.

Good job BioRubyGuys


On 02/03/12 15.04, "Peter Cock" <p.j.a.cock at googlemail.com> wrote:

> On 10 Feb, Robert Buels wrote (posted by Chris Field):
>> Hi all,
>> 
>> I'm going to be OBF project admin again this year for Google Summer of
>> code. ?OBF's application is due in a couple of weeks, and we need to update
>> our project ideas on the OBF wiki page and on each project's individual wiki
>> pages.
>> 
>> So, for each of the OBF projects that wants to do GSoC again this year,
>> please:
>> 
>> a.) Update the list of project ideas on your project's GSoC page
>> (BioPython, BioPerl, BioRuby, etc). ?Add new ones, remove ones that have
>> already been done or no longer relevant, etc.
>> 
>> b.) Update the list of project ideas on the main OBF GSoC page
>> (http://www.open-bio.org/wiki/Google_Summer_of_Code) to match.
>> 
>> c.) Let me know via email that you have done so and it's ready for Google
>> to peruse.
>> 
>> Please have the updates done, if possible, by this Friday (March 11). The
>> number and quality of the project ideas are part of the evaluation process
>> for whether OBF is accepted as a Summer of Code organization again this
>> year, so let's come up with some good ones. ?:-)
>> 
>> Rob
>> 
>> ----
>> Robert Buels
> 
> Hi BioRuby folk,
> 
> You seem to have been the most organized Bio* project for GSoC so far, and
> have
> put together good set of GSoC project ideas by Rob's target date. Well done :)
> 
> Is the list here complete now?
> http://bioruby.open-bio.org/wiki/Google_Summer_of_Code
> 
>     3.1.1 Write the world's fastest parallelized GFF3/GTF parser in D,
> for Ruby FFI
>     3.1.2 Extend bio-alignment plug-in with Multiple Alignment Format
> -MAF- parser (FFI?)
>     3.1.3 Testing framework for biogem plugins
>     3.1.4 Adding social networking functionality to BioRuby.org
>     3.1.5 Update bio-images a plugin to represent bio-object with cool images
>     3.1.6 Update to the Ruby Ensembl API
> 
> I noticed "Testing framework for biogem plugins" was missing on the OBF
> summary page, so I added it:
> http://www.open-bio.org/wiki/Google_Summer_of_Code
> 
> Regards,
> 
> Peter
> 
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby





From cjfields at illinois.edu  Sat Mar  3 13:44:40 2012
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Sat, 3 Mar 2012 13:44:40 +0000
Subject: [BioRuby] Bio::Faster plugin
In-Reply-To: <CACtet2T__UCO8Eq6WXkCHEQr+FFaO93_vm7p1dqt=iOZRFVB=Q@mail.gmail.com>
References: <CACtet2TWTXMRkpgbai0=Fue7Cmn3v6EBbuXWd32cOa_xiD90AA@mail.gmail.com>
	<CB2A292C.747B%bonnal@ingm.org>
	<CALf85+V1-a+i2dc0YKf95vgrEX1pipXSZ_gHayii2ayGs8m+4Q@mail.gmail.com>
	<CAOP6n=h3JcZ7=_bp51LRdX1nQDKnHY-o3eQo9_g9EZ4t4OZcuA@mail.gmail.com>
	<CACtet2T__UCO8Eq6WXkCHEQr+FFaO93_vm7p1dqt=iOZRFVB=Q@mail.gmail.com>
Message-ID: <F1BDB21F-8CEC-4880-B2F1-56AF003CCA44@illinois.edu>

I have a perl binding to the same C lib implementation (Heng Li's readfq), haven't benchmarked it against our low-level pure perl version but it does seem to be significantly faster.  Not to mention it covers both FASTQ and FASTA.

Not sure how it handles the FASTQ test suite we came up with, might be worth checking out.

chris

On Mar 3, 2012, at 1:38 AM, Francesco Strozzi wrote:

> Hi,
> I haven't done this comparison, but if you want to run it I will be happy
> to put the outputs on the wiki.
> 
> Cheers
> 
> On Friday, March 2, 2012, Mic <mictadlo at gmail.com> wrote:
>> Did also compare the speed between biofaster and reading 4 lines (fastq)/2
>> lines (fasta) at the time?
>> 
>> Cheers,
>> 
>> On Thu, Jan 5, 2012 at 1:20 AM, George Githinji <georgkam at gmail.com>
> wrote:
>> 
>>> ++1 Sounds cool!
>>> 
>>> 
>>> On Wed, Jan 4, 2012 at 6:05 PM, Raoul Bonnal <bonnal at ingm.org> wrote:
>>>> Hi Francesco,
>>>> It's very cool!
>>>> 
>>>> And you can access to the seq object/array also in this way:
>>>> Bio::Faster.parse(File.join(TEST_DATA,"sample.fastq")) do |id,
> comments,
>>>> sequence, quality|
>>>> puts "#{id} #{comments} #{sequence} #{quality}"
>>>> end
>>>> 
>>>> Obviously I like it more than using the raw array :-)
>>>> I suppose in case of no quality value you get a nil object
>>>> 
>>>> 
>>>> +1
>>>> 
>>>> 
>>>> On 04/01/12 10.50, "Francesco Strozzi" <francesco.strozzi at gmail.com>
>>> wrote:
>>>> 
>>>>> Hi guys,
>>>>> 
>>>>> I have created a BioRuby plugin called bio-faster, that implements a
>>> fast
>>>>> and simple parser for FastA and FastQ files. It's based on the C
> library
>>>>> Kseq written by Heng Li (author of Samtools and BWA). Compared to
>>>>> Bio::FastQ it is actually 4-5 times faster in parsing large FastQ
> files.
>>>>> The code will not create a Bio object for each sequence but it will
>>> return
>>>>> a simple array with sequence data and quality values for FastQ (it
>>> supports
>>>>> Sanger/Phred format only).
>>>>> Bio::Faster could be a good choice when you just need to parse huge
>>> files,
>>>>> for example to extract information or to store sequence data in a
>>> database,
>>>>> and you don't need to create an object for each sequence but you only
>>> want
>>>>> to parse the dataset easily and quickly.
>>>>> 
>>>>> Here is the code: https://github.com/fstrozzi/bioruby-faster
>>>>> Here is the wiki for more details:
>>>>> https://github.com/fstrozzi/bioruby-faster/wiki
>>>>> To get the gem: gem install bio-faster
>>>>> 
>>>>> Tested with Ruby 1.9 only.
>>>>> 
>>>>> Any comment or feedback is much appreciated!
>>>>> 
>>>>> Cheers
>>>> 
>>>> 
>>>> _______________________________________________
>>>> BioRuby Project - http://www.bioruby.org/
>>>> 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/
>>> Twitter: http://twitter.com/#!/george_l
>>> 
>>> _______________________________________________
>>> 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
>> 
> 
> -- 
> 
> Francesco
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby




From bonnal at ingm.org  Mon Mar  5 14:19:10 2012
From: bonnal at ingm.org (Raoul Bonnal)
Date: Mon, 05 Mar 2012 15:19:10 +0100
Subject: [BioRuby] RubyMine
Message-ID: <CB7A89EE.854F%bonnal@ingm.org>

Some time ago I asked JetBrains to support our project with their Open
Source License program.

So if you are interested in using RubyMine http://www.jetbrains.com/ruby/
drop me an e-mail and I?ll share the license code with you; the license is
one year from now.

I can not publish it and I invite you to not publish it on
webpages/site/forums/any social network.

--
Ra



From mictadlo at gmail.com  Wed Mar  7 06:58:00 2012
From: mictadlo at gmail.com (Mic)
Date: Wed, 7 Mar 2012 16:58:00 +1000
Subject: [BioRuby] Google Summer of Code project ideas
In-Reply-To: <CB7B84C5.8586%bonnal@ingm.org>
References: <CAOP6n=j=7cMp0B=G1MuYj0XvMbCW6sY++XV7OjALCKdinWhcHQ@mail.gmail.com>
	<CB7B84C5.8586%bonnal@ingm.org>
Message-ID: <CAOP6n=hcuH4cxQnkpxdumHYaXuQu-6dVWx54mRGY4+9YyiUUsw@mail.gmail.com>

HI Raoul,
Analogous to Samfile, a Tabixfile allows fast random access to compressed
and tabix indexed tab-separated file formats with genomic data:

*import pysam*
*tabixfile = pysam.Tabixfile( "example.gtf.gz" )*
*
*
*for gtf in tabixfile.fetch('chr1', 1000, 2000):*
*    print gtf.contig, gtf.start, gtf.end, gtf.gene_id*
*
*
*
*
I am not suitable for a mentor, because I have not used Ruby for years. I
just observe BioRuby and try give some ideas.

Cheers,

On Tue, Mar 6, 2012 at 6:09 PM, Raoul Bonnal <bonnal at ingm.org> wrote:

>  Hi Mic,
>
> >* a ruby version of
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232365/?tool=pubmed
> If you want to help us with GSoC please add it to the list and put
> yourself as a mentor ( later you?ll need to register yourself as a mentor),
> for us (the panel) any bioruby developer/user can be a mentor, it?s not
> much work and you?ll not be alone :)
>
>
> >a ruby interface for tabix ( http://samtools.sourceforge.net/tabix.shtml) see pysam
> http://code.google.com/p/pysam/source/browse/tests/tabix_test.py?r=2fff972c6b60390e4962d3f46f7c269acd9aa33e
>  Is it an interface to sam/bam ? Have you see this
> https://github.com/helios/bioruby-samtools project ? Can you evaluate the
> main differences between the two projects ?
>
> Please add them to GSoC (on our wik) in any case, we?ll keep there the
> list of desired things. If you do not have time to be a mentor just write
> the projects and maybe someone will lead it.
>
> Thanks a lot!
>
>
> On 06/03/12 02.18, "Mic" <mictadlo at gmail.com> wrote:
>
>
>    - a ruby version of
>    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232365/?tool=pubmed
>
>
>
>
> * a ruby interface for tabix ( http://samtools.sourceforge.net/tabix.shtml) see pysam
> http://code.google.com/p/pysam/source/browse/tests/tabix_test.py?r=2fff972c6b60390e4962d3f46f7c269acd9aa33e
>
>
> On Sat, Mar 3, 2012 at 9:15 PM, Raoul Bonnal <bonnal at ingm.org> wrote:
>
> Thanks !
>
> Rob is aware that our page is ready to go.
>
> Good job BioRubyGuys
>
>
> On 02/03/12 15.04, "Peter Cock" <p.j.a.cock at googlemail.com> wrote:
>
> > On 10 Feb, Robert Buels wrote (posted by Chris Field):
> >> Hi all,
> >>
> >> I'm going to be OBF project admin again this year for Google Summer of
> >> code.  OBF's application is due in a couple of weeks, and we need to
> update
> >> our project ideas on the OBF wiki page and on each project's individual
> wiki
> >> pages.
> >>
> >> So, for each of the OBF projects that wants to do GSoC again this year,
> >> please:
> >>
> >> a.) Update the list of project ideas on your project's GSoC page
> >> (BioPython, BioPerl, BioRuby, etc).  Add new ones, remove ones that have
> >> already been done or no longer relevant, etc.
> >>
> >> b.) Update the list of project ideas on the main OBF GSoC page
> >> (http://www.open-bio.org/wiki/Google_Summer_of_Code) to match.
> >>
> >> c.) Let me know via email that you have done so and it's ready for
> Google
> >> to peruse.
> >>
> >> Please have the updates done, if possible, by this Friday (March 11).
> The
> >> number and quality of the project ideas are part of the evaluation
> process
> >> for whether OBF is accepted as a Summer of Code organization again this
> >> year, so let's come up with some good ones.  :-)
> >>
> >> Rob
> >>
> >> ----
> >> Robert Buels
> >
> > Hi BioRuby folk,
> >
> > You seem to have been the most organized Bio* project for GSoC so far,
> and
> > have
> > put together good set of GSoC project ideas by Rob's target date. Well
> done :)
> >
> > Is the list here complete now?
> > http://bioruby.open-bio.org/wiki/Google_Summer_of_Code
> >
> >     3.1.1 Write the world's fastest parallelized GFF3/GTF parser in D,
> > for Ruby FFI
> >     3.1.2 Extend bio-alignment plug-in with Multiple Alignment Format
> > -MAF- parser (FFI?)
> >     3.1.3 Testing framework for biogem plugins
> >     3.1.4 Adding social networking functionality to BioRuby.org
> >     3.1.5 Update bio-images a plugin to represent bio-object with cool
> images
> >     3.1.6 Update to the Ruby Ensembl API
> >
> > I noticed "Testing framework for biogem plugins" was missing on the OBF
> > summary page, so I added it:
> > http://www.open-bio.org/wiki/Google_Summer_of_Code
> >
> > Regards,
> >
> > Peter
> >
> > _______________________________________________
> > 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 missy at be.to  Thu Mar  8 02:55:43 2012
From: missy at be.to (MISHIMA, Hiroyuki)
Date: Thu, 08 Mar 2012 11:55:43 +0900
Subject: [BioRuby] Ruby UCSC API v0.4.0 is released
Message-ID: <4F581FAF.8050005@be.to>

Hi all,

Ruby UCSC API, a BioGem to access the UCSC genome database using Ruby, 
is updated. The API is refined (simplified) with keeping backward 
compatibility. Rails/ActiveRecord v3.1 and later are supported.

GitHub:
https://github.com/misshie/bioruby-ucsc-api

RubyGems:
https://rubygems.org/gems/bio-ucsc-api

User feedback forum:
http://rubyucscapi.userecho.com/

Your comments and suggestions are *very* welcome!

Sincerely yours,
Hiro.
-- 
MISHIMA, Hiroyuki, DDS, Ph.D.
COE Research Fellow
Department of Human Genetics
Nagasaki University Graduate School of Biomedical Sciences


From pjotr.public14 at thebird.nl  Sun Mar 11 12:53:08 2012
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Sun, 11 Mar 2012 13:53:08 +0100
Subject: [BioRuby] BioRuby: newick parser
Message-ID: <20120311125308.GB4204@thebird.nl>

Hi Naohisa and others,

I am looking at the Newick/Nexux/PhyloXML parsers at the moment. The
BioRuby ones look rather complete, if not a tad overcomplicated. 

Are you happy with the state of affairs, or do you thing it could be
improved/simplified?  Also, for walking the tree, is the interface now
the one you would choose to implement?

I am asking, because I am looking for the most intuitive way of
parsing and traversing tree information. I see Christian has done a
lot of work in this area (mostly in Java), even to the point of
taking standards forward. Maybe I should ask him? It appears to me we
have solid parsers and data structures. Walking the trees, however,
is less straightforward, and documentation somewhat lacking.

Anyone happy to correct me?

Pj.


From ngoto at gen-info.osaka-u.ac.jp  Mon Mar 12 06:18:48 2012
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Mon, 12 Mar 2012 15:18:48 +0900
Subject: [BioRuby] BioRuby: newick parser
In-Reply-To: <20120311125308.GB4204@thebird.nl>
References: <20120311125308.GB4204@thebird.nl>
Message-ID: <201203120625.q2C6POXo013432@portal.open-bio.org>

Hi Pjotr,

They can be divided into several parts.

1. Newick/NHX parser and writer: 

1-1. Implementation: I think it is enough quiality. The implementation
complexity is due to the Newick specification (e.g. escaping of special
characters) and some undocumented conventions (e.g. bootstrap values).
For refactoring, using Racc (parser generator for Ruby) seems good,
but low priority.

1-2. Parser API: Parsing a string is simple. Reading from files is
depended on Bio::FlatFile system, which is enough for most cases.

1-3. Writer API: depending on Bio::Tree API.

2. Nexus parser and writer:

2-1: Implementation: I don't know details of current status,
but for trees, it only passes the data to Bio::Newick class.
Please ask Christian for details.

2-2: API: Nexus Parser API is complicated because the Nexus
specification is very complex.
It seems that Nexus writer is missing.

3: PhyloXML parser and writer:

3-1: Parser implementation and API: Enough quality. Its
complexity is mainly due to the on-demand partial reading of
XML files, which saves memory for a large tree file.

3-2: Writer implementation and API: Not enough. It can only
write PhyloXML data, and it is very hard to output Bio::Tree
as PhyloXML format.

3-3: Other topics: It uses libxml-ruby, but it seems that
Ruby XML parser de-facto standard is now Nokogiri, and
I think it may be rewritten by using Nokogiri in some days.

4. Bio::Tree data structure:

4-1. Implementation: It is based on BioRuby internal graph
library. It can be changed to use other graph library.

4-2. API: The API design is based on tree API of other
open-bio projects and generic graph library API.

When writing HOWTO based on BioPerl HOWTO:Trees,
(http://bioruby.open-bio.org/wiki/HOWTO:Trees but still incomplete)
I'm thinking to add/modify some API about speficying nodes/edges.


> I see Christian has done a lot of work in this area (mostly in Java),
> even to the point of taking standards forward. Maybe I should ask him?

I'd like to hear his advice, too.

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


On Sun, 11 Mar 2012 13:53:08 +0100
Pjotr Prins <pjotr.public14 at thebird.nl> wrote:

> Hi Naohisa and others,
> 
> I am looking at the Newick/Nexux/PhyloXML parsers at the moment. The
> BioRuby ones look rather complete, if not a tad overcomplicated. 
> 
> Are you happy with the state of affairs, or do you thing it could be
> improved/simplified?  Also, for walking the tree, is the interface now
> the one you would choose to implement?
> 
> I am asking, because I am looking for the most intuitive way of
> parsing and traversing tree information. I see Christian has done a
> lot of work in this area (mostly in Java), even to the point of
> taking standards forward. Maybe I should ask him? It appears to me we
> have solid parsers and data structures. Walking the trees, however,
> is less straightforward, and documentation somewhat lacking.
> 
> Anyone happy to correct me?
> 
> Pj.



From pjotr.public14 at thebird.nl  Mon Mar 12 10:08:41 2012
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Mon, 12 Mar 2012 11:08:41 +0100
Subject: [BioRuby] BioRuby: newick parser
References: <20120311125308.GB4204@thebird.nl>
Message-ID: <20120312100841.GA8543@thebird.nl>

Hi Naohisa,

Thanks for the quick reply. I think the Newick parser and Phyloxml
parser are the way to go. I guess it is partly due to me that the
latter is somewhat complex for not reading the DOM in RAM ;).

I'll start using the string based Newick parser for MSA, as it is so
common, and see if I can make it flow naturally :)

Pj.

On Mon, Mar 12, 2012 at 03:18:48PM +0900, Naohisa GOTO wrote:
> Hi Pjotr,
> 
> They can be divided into several parts.
> 
> 1. Newick/NHX parser and writer: 
> 
> 1-1. Implementation: I think it is enough quiality. The implementation
> complexity is due to the Newick specification (e.g. escaping of special
> characters) and some undocumented conventions (e.g. bootstrap values).
> For refactoring, using Racc (parser generator for Ruby) seems good,
> but low priority.
> 
> 1-2. Parser API: Parsing a string is simple. Reading from files is
> depended on Bio::FlatFile system, which is enough for most cases.
> 
> 1-3. Writer API: depending on Bio::Tree API.
> 
> 2. Nexus parser and writer:
> 
> 2-1: Implementation: I don't know details of current status,
> but for trees, it only passes the data to Bio::Newick class.
> Please ask Christian for details.
> 
> 2-2: API: Nexus Parser API is complicated because the Nexus
> specification is very complex.
> It seems that Nexus writer is missing.
> 
> 3: PhyloXML parser and writer:
> 
> 3-1: Parser implementation and API: Enough quality. Its
> complexity is mainly due to the on-demand partial reading of
> XML files, which saves memory for a large tree file.
> 
> 3-2: Writer implementation and API: Not enough. It can only
> write PhyloXML data, and it is very hard to output Bio::Tree
> as PhyloXML format.
> 
> 3-3: Other topics: It uses libxml-ruby, but it seems that
> Ruby XML parser de-facto standard is now Nokogiri, and
> I think it may be rewritten by using Nokogiri in some days.
> 
> 4. Bio::Tree data structure:
> 
> 4-1. Implementation: It is based on BioRuby internal graph
> library. It can be changed to use other graph library.
> 
> 4-2. API: The API design is based on tree API of other
> open-bio projects and generic graph library API.
> 
> When writing HOWTO based on BioPerl HOWTO:Trees,
> (http://bioruby.open-bio.org/wiki/HOWTO:Trees but still incomplete)
> I'm thinking to add/modify some API about speficying nodes/edges.
> 
> 
> > I see Christian has done a lot of work in this area (mostly in Java),
> > even to the point of taking standards forward. Maybe I should ask him?
> 
> I'd like to hear his advice, too.
> 
> Naohisa Goto
> ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
> 
> 
> On Sun, 11 Mar 2012 13:53:08 +0100
> Pjotr Prins <pjotr.public14 at thebird.nl> wrote:
> 
> > Hi Naohisa and others,
> > 
> > I am looking at the Newick/Nexux/PhyloXML parsers at the moment. The
> > BioRuby ones look rather complete, if not a tad overcomplicated. 
> > 
> > Are you happy with the state of affairs, or do you thing it could be
> > improved/simplified?  Also, for walking the tree, is the interface now
> > the one you would choose to implement?
> > 
> > I am asking, because I am looking for the most intuitive way of
> > parsing and traversing tree information. I see Christian has done a
> > lot of work in this area (mostly in Java), even to the point of
> > taking standards forward. Maybe I should ask him? It appears to me we
> > have solid parsers and data structures. Walking the trees, however,
> > is less straightforward, and documentation somewhat lacking.
> > 
> > Anyone happy to correct me?
> > 
> > Pj.
> 


From pjotr.public14 at thebird.nl  Mon Mar 12 16:24:38 2012
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Mon, 12 Mar 2012 17:24:38 +0100
Subject: [BioRuby] BioRuby: newick parser
References: <20120311125308.GB4204@thebird.nl>
Message-ID: <20120312162438.GA11131@thebird.nl>

On Mon, Mar 12, 2012 at 03:18:48PM +0900, Naohisa GOTO wrote:
> When writing HOWTO based on BioPerl HOWTO:Trees,
> (http://bioruby.open-bio.org/wiki/HOWTO:Trees but still incomplete)
> I'm thinking to add/modify some API about speficying nodes/edges.

After some trying I agree. The Bio::Tree::Node object should know
'more' about its state. I would like to do something like:

  root.leaf?.should == false
  node = root.childeren.first
  node.leaf?.should == false
  node2 == node.childeren.first
  node.leaf?.should == true
  node2.edge(node).distance.should == 1.34

now I need to do something like 

  tree = @tree
  node = tree.get_node_by_name('node')
  tree.get_edge(node, tree.parent(node)).distance.should == 1.34

which uses the tree state to get a node edge, and does not feel that
intuitive.

I'll try to extend Bio::Tree for bio-alignment, see what works.

Pj.


From pjotr.public14 at thebird.nl  Mon Mar 12 16:36:29 2012
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Mon, 12 Mar 2012 17:36:29 +0100
Subject: [BioRuby] RFC: the BioRuby panel
Message-ID: <20120312163629.GA11785@thebird.nl>

Please comment. We have come up with the following:

What is the BioRuby panel?

    The BioRuby panel is an elected body of volunteers out of the
    BioRuby community consisting of active code contributors to the
    BioRuby project.  BioRuby is defined in the widest sense here,
    i.e. the library, website, and biogems.

What is the goal of the BioRuby panel?

    The goal of the BioRuby panel is to represent the BioRuby project
    in terms of directing software and tool development and
    popularizing BioRuby. 

for more, see

    http://bioruby.open-bio.org/wiki/BioRuby_Panel




From pjotr.public14 at thebird.nl  Mon Mar 12 17:05:26 2012
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Mon, 12 Mar 2012 18:05:26 +0100
Subject: [BioRuby] BioRuby: newick parser
In-Reply-To: <20120312162438.GA11131@thebird.nl>
References: <20120311125308.GB4204@thebird.nl>
	<20120312162438.GA11131@thebird.nl>
Message-ID: <20120312170526.GA11997@thebird.nl>

OK, this works:

  @aln.link_tree(@tree)  # @tree contains a parsed Newick tree
  root = @aln.root # get the root of the tree
  root.leaf?.should == false
  children = root.children
  children.map { |n| n.name }.sort.should == ["","seq7"]
  seq7 = children.last
  seq7.name.should == 'seq7'
  seq7.leaf?.should == true
  seq7.parent.should == root

the added functionality for BioRuby's Bio::Tree::Node can be seen here

  https://github.com/pjotrp/bioruby-alignment/blob/development/lib/bio-alignment/tree.rb

basically I inject the @tree info into every existing Node object.
>From then on, I can use it to make the interface nicer. A monkey
patch, indeed.

Good enough for now.

Pj.

On Mon, Mar 12, 2012 at 05:24:38PM +0100, Pjotr Prins wrote:
> On Mon, Mar 12, 2012 at 03:18:48PM +0900, Naohisa GOTO wrote:
> > When writing HOWTO based on BioPerl HOWTO:Trees,
> > (http://bioruby.open-bio.org/wiki/HOWTO:Trees but still incomplete)
> > I'm thinking to add/modify some API about speficying nodes/edges.
> 
> After some trying I agree. The Bio::Tree::Node object should know
> 'more' about its state. I would like to do something like:
> 
>   root.leaf?.should == false
>   node = root.childeren.first
>   node.leaf?.should == false
>   node2 == node.childeren.first
>   node.leaf?.should == true
>   node2.edge(node).distance.should == 1.34
> 
> now I need to do something like 
> 
>   tree = @tree
>   node = tree.get_node_by_name('node')
>   tree.get_edge(node, tree.parent(node)).distance.should == 1.34
> 
> which uses the tree state to get a node edge, and does not feel that
> intuitive.
> 
> I'll try to extend Bio::Tree for bio-alignment, see what works.
> 
> Pj.
> 


From pjotr.public14 at thebird.nl  Mon Mar 12 20:11:59 2012
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Mon, 12 Mar 2012 21:11:59 +0100
Subject: [BioRuby] BioRuby: newick parser
In-Reply-To: <20120312170526.GA11997@thebird.nl>
References: <20120311125308.GB4204@thebird.nl>
	<20120312162438.GA11131@thebird.nl>
	<20120312170526.GA11997@thebird.nl>
Message-ID: <20120312201159.GA12553@thebird.nl>

Bio::Tree::distance(node1,node2)'s calculating the path distance is
pretty cool :)

http://bioruby.open-bio.org/rdoc/Bio/Pathway.html#method-i-breadth_first_search

  seq7.parent.should == root
  seq4 = tree.find("seq4")
  seq4.distance(seq7).should == 19.387756600000003 

Pj.

On Mon, Mar 12, 2012 at 06:05:26PM +0100, Pjotr Prins wrote:
> OK, this works:
> 
>   @aln.link_tree(@tree)  # @tree contains a parsed Newick tree
>   root = @aln.root # get the root of the tree
>   root.leaf?.should == false
>   children = root.children
>   children.map { |n| n.name }.sort.should == ["","seq7"]
>   seq7 = children.last
>   seq7.name.should == 'seq7'
>   seq7.leaf?.should == true
>   seq7.parent.should == root
> 
> the added functionality for BioRuby's Bio::Tree::Node can be seen here
> 
>   https://github.com/pjotrp/bioruby-alignment/blob/development/lib/bio-alignment/tree.rb
> 
> basically I inject the @tree info into every existing Node object.
> From then on, I can use it to make the interface nicer. A monkey
> patch, indeed.
> 
> Good enough for now.
> 
> Pj.
> 
> On Mon, Mar 12, 2012 at 05:24:38PM +0100, Pjotr Prins wrote:
> > On Mon, Mar 12, 2012 at 03:18:48PM +0900, Naohisa GOTO wrote:
> > > When writing HOWTO based on BioPerl HOWTO:Trees,
> > > (http://bioruby.open-bio.org/wiki/HOWTO:Trees but still incomplete)
> > > I'm thinking to add/modify some API about speficying nodes/edges.
> > 
> > After some trying I agree. The Bio::Tree::Node object should know
> > 'more' about its state. I would like to do something like:
> > 
> >   root.leaf?.should == false
> >   node = root.childeren.first
> >   node.leaf?.should == false
> >   node2 == node.childeren.first
> >   node.leaf?.should == true
> >   node2.edge(node).distance.should == 1.34
> > 
> > now I need to do something like 
> > 
> >   tree = @tree
> >   node = tree.get_node_by_name('node')
> >   tree.get_edge(node, tree.parent(node)).distance.should == 1.34
> > 
> > which uses the tree state to get a node edge, and does not feel that
> > intuitive.
> > 
> > I'll try to extend Bio::Tree for bio-alignment, see what works.
> > 
> > Pj.
> > 
> 


From rutgeraldo at gmail.com  Mon Mar 12 23:56:16 2012
From: rutgeraldo at gmail.com (Rutger Vos)
Date: Tue, 13 Mar 2012 00:56:16 +0100
Subject: [BioRuby] BioRuby: newick parser
In-Reply-To: <20120312201159.GA12553@thebird.nl>
References: <20120311125308.GB4204@thebird.nl>
	<20120312162438.GA11131@thebird.nl>
	<20120312170526.GA11997@thebird.nl>
	<20120312201159.GA12553@thebird.nl>
Message-ID: <CAC9cYqH60L=eE5scS9Fh26wUMFngeOZ476sA0u5PXULknUB46Q@mail.gmail.com>

I would be flattered if you would find something of interest or
inspiration about the API of  Bio::Phylo::Forest::Tree
(http://search.cpan.org/~rvosa/Bio-Phylo-0.46/lib/Bio/Phylo/Forest/Tree.pm)
and the node objects
(http://search.cpan.org/~rvosa/Bio-Phylo-0.46/lib/Bio/Phylo/Forest/Node.pm)

On Mon, Mar 12, 2012 at 9:11 PM, Pjotr Prins <pjotr.public14 at thebird.nl> wrote:
> Bio::Tree::distance(node1,node2)'s calculating the path distance is
> pretty cool :)
>
> http://bioruby.open-bio.org/rdoc/Bio/Pathway.html#method-i-breadth_first_search
>
> ?seq7.parent.should == root
> ?seq4 = tree.find("seq4")
> ?seq4.distance(seq7).should == 19.387756600000003
>
> Pj.
>
> On Mon, Mar 12, 2012 at 06:05:26PM +0100, Pjotr Prins wrote:
>> OK, this works:
>>
>> ? @aln.link_tree(@tree) ?# @tree contains a parsed Newick tree
>> ? root = @aln.root # get the root of the tree
>> ? root.leaf?.should == false
>> ? children = root.children
>> ? children.map { |n| n.name }.sort.should == ["","seq7"]
>> ? seq7 = children.last
>> ? seq7.name.should == 'seq7'
>> ? seq7.leaf?.should == true
>> ? seq7.parent.should == root
>>
>> the added functionality for BioRuby's Bio::Tree::Node can be seen here
>>
>> ? https://github.com/pjotrp/bioruby-alignment/blob/development/lib/bio-alignment/tree.rb
>>
>> basically I inject the @tree info into every existing Node object.
>> From then on, I can use it to make the interface nicer. A monkey
>> patch, indeed.
>>
>> Good enough for now.
>>
>> Pj.
>>
>> On Mon, Mar 12, 2012 at 05:24:38PM +0100, Pjotr Prins wrote:
>> > On Mon, Mar 12, 2012 at 03:18:48PM +0900, Naohisa GOTO wrote:
>> > > When writing HOWTO based on BioPerl HOWTO:Trees,
>> > > (http://bioruby.open-bio.org/wiki/HOWTO:Trees but still incomplete)
>> > > I'm thinking to add/modify some API about speficying nodes/edges.
>> >
>> > After some trying I agree. The Bio::Tree::Node object should know
>> > 'more' about its state. I would like to do something like:
>> >
>> > ? root.leaf?.should == false
>> > ? node = root.childeren.first
>> > ? node.leaf?.should == false
>> > ? node2 == node.childeren.first
>> > ? node.leaf?.should == true
>> > ? node2.edge(node).distance.should == 1.34
>> >
>> > now I need to do something like
>> >
>> > ? tree = @tree
>> > ? node = tree.get_node_by_name('node')
>> > ? tree.get_edge(node, tree.parent(node)).distance.should == 1.34
>> >
>> > which uses the tree state to get a node edge, and does not feel that
>> > intuitive.
>> >
>> > I'll try to extend Bio::Tree for bio-alignment, see what works.
>> >
>> > Pj.
>> >
>>
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby



-- 
Dr. Rutger A. Vos
Bioinformaticist
NCB Naturalis
Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the Netherlands
Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands
http://rutgervos.blogspot.com



From ngoto at gen-info.osaka-u.ac.jp  Tue Mar 13 14:23:26 2012
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Tue, 13 Mar 2012 23:23:26 +0900
Subject: [BioRuby] BioRuby: newick parser
In-Reply-To: <20120312162438.GA11131@thebird.nl>
References: <20120311125308.GB4204@thebird.nl>
	<20120312162438.GA11131@thebird.nl>
Message-ID: <201203131423.q2DENTd0021313@portal.open-bio.org>

Hi Pjotr,

The design of Bio::Tree that a nod has no tree information and
only tree object have node information was what I intended.
This makes easy to split a tree into subtrees, to build a tree
from scratch, to concatenate trees, to replace nodes and edges, etc.
However, as you described, for traversing a static tree,
indirect operations are needed which are sometimes annoying.

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


On Mon, 12 Mar 2012 17:24:38 +0100
Pjotr Prins <pjotr.public14 at thebird.nl> wrote:

> On Mon, Mar 12, 2012 at 03:18:48PM +0900, Naohisa GOTO wrote:
> > When writing HOWTO based on BioPerl HOWTO:Trees,
> > (http://bioruby.open-bio.org/wiki/HOWTO:Trees but still incomplete)
> > I'm thinking to add/modify some API about speficying nodes/edges.
> 
> After some trying I agree. The Bio::Tree::Node object should know
> 'more' about its state. I would like to do something like:
> 
>   root.leaf?.should == false
>   node = root.childeren.first
>   node.leaf?.should == false
>   node2 == node.childeren.first
>   node.leaf?.should == true
>   node2.edge(node).distance.should == 1.34
> 
> now I need to do something like 
> 
>   tree = @tree
>   node = tree.get_node_by_name('node')
>   tree.get_edge(node, tree.parent(node)).distance.should == 1.34
> 
> which uses the tree state to get a node edge, and does not feel that
> intuitive.
> 
> I'll try to extend Bio::Tree for bio-alignment, see what works.
> 
> Pj.



From ngoto at gen-info.osaka-u.ac.jp  Tue Mar 13 14:37:27 2012
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Tue, 13 Mar 2012 23:37:27 +0900
Subject: [BioRuby] BioRuby: newick parser
In-Reply-To: <20120312201159.GA12553@thebird.nl>
References: <20120311125308.GB4204@thebird.nl>
	<20120312162438.GA11131@thebird.nl>
	<20120312170526.GA11997@thebird.nl>
	<20120312201159.GA12553@thebird.nl>
Message-ID: <201203131437.q2DEbS6S021797@portal.open-bio.org>

Hi Pjotr,

On Mon, 12 Mar 2012 21:11:59 +0100
Pjotr Prins <pjotr.public14 at thebird.nl> wrote:

> Bio::Tree::distance(node1,node2)'s calculating the path distance is
> pretty cool :)
> 
> http://bioruby.open-bio.org/rdoc/Bio/Pathway.html#method-i-breadth_first_search
> 
>   seq7.parent.should == root
>   seq4 = tree.find("seq4")
>   seq4.distance(seq7).should == 19.387756600000003 

This is a problem of floating point numbers.
Calculating sum of floating point numbers frequently causes
accumulation of errors and/or loss of significant digits.

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


From pjotr.public14 at thebird.nl  Fri Mar 16 13:51:53 2012
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Fri, 16 Mar 2012 14:51:53 +0100
Subject: [BioRuby] Drawing a phylogeny ASCII tree
References: <20120311125308.GB4204@thebird.nl>
	<20120312162438.GA11131@thebird.nl>
Message-ID: <20120316135153.GA11119@thebird.nl>

Anyone interesting in a little coding challenge? I wrote a feature
for drawing a phylogeny ASCII tree:

When you have an alignment, with a Newick tree attached, as supported
by the bio-alignment gem, I would like to get the following ASCII 
drawings:

And draw the MSA with the tree
  """
  +--9.69----------------------------------------- seq7  ----------PTIIFSGCSKACSGK-----VCGIFHAVRSFM
  |                                   ,--1.19----- seq1  ----SNSFSRPTIIFSGCSTACSGK--SELVCGFRSFMLSDV
  |                          ,--1.79--|        ,-- seq2  SSIISNSFSRPTIIFSGCSTACSGK--SEQVCGFR---LSDV
  |                 ,--1.07--+        `--1.19--+-- seq3  SSIISNSFSRPTIIFSGCSTACSGKLTSEQVCGFR---LSDV
  |                 |        |--1.79--+--1.19----- seq5  ----------PTIIFSGCSKACSGKGLSELVCGFRSFMLSDV
  |        ,--1.31--|                 `--1.19----- seq8  --------PTIIFSGCSKACSGK--SELVCGFRSFMLSAV
  |--4.34--|        `--4.05----------------------- seq4  ----PKLFSRPTIIFSGCSTACSGK--SEPVCGFRSFMLSDV
           `--5.36-------------------------------- seq6  ----------PTIIFSGCSKACSGK-----FRSFRSFMLSAV
  """
Then draw MSA with the short tree
  """
  +----------------- seq7  ----------PTIIFSGCSKACSGK-----VCGIFHAVRSFM
  |           ,----- seq1  ----SNSFSRPTIIFSGCSTACSGK--SELVCGFRSFMLSDV
  |        ,--|  ,-- seq2  SSIISNSFSRPTIIFSGCSTACSGK--SEQVCGFR---LSDV
  |     ,--+  `--+-- seq3  SSIISNSFSRPTIIFSGCSTACSGKLTSEQVCGFR---LSDV
  |     |  |--+----- seq5  ----------PTIIFSGCSKACSGKGLSELVCGFRSFMLSDV
  |  ,--|     `----- seq8  --------PTIIFSGCSKACSGK--SELVCGFRSFMLSAV
  |--|  `----------- seq4  ----PKLFSRPTIIFSGCSTACSGK--SEPVCGFRSFMLSDV
     `-------------- seq6  ----------PTIIFSGCSKACSGK-----FRSFRSFMLSAV
  """

BioPerl has someting similar here, but less useful:

  http://doc.bioperl.org/releases/bioperl-1.4/Bio/TreeIO/tabtree.html

And there are some good Ruby examples trees at

  http://www.rubyquiz.com/quiz40.html

The full feature description is here, and the bio-alignment module
allows for loading and traversing trees. It is only a matter of
getting the algorithm right :) See

  https://github.com/pjotrp/bioruby-alignment/blob/master/features/tree.feature

and 

  https://github.com/pjotrp/bioruby-alignment/blob/master/features/tree-feature.rb

The same algorithm will be used for a HTML drawing.

Pj.

On Tue, Mar 13, 2012 at 11:23:26PM +0900, Naohisa GOTO wrote:
> Hi Pjotr,
> 
> The design of Bio::Tree that a nod has no tree information and
> only tree object have node information was what I intended.
> This makes easy to split a tree into subtrees, to build a tree
> from scratch, to concatenate trees, to replace nodes and edges, etc.
> However, as you described, for traversing a static tree,
> indirect operations are needed which are sometimes annoying.
> 
> Naohisa Goto
> ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
> 
> 
> On Mon, 12 Mar 2012 17:24:38 +0100
> Pjotr Prins <pjotr.public14 at thebird.nl> wrote:
> 
> > On Mon, Mar 12, 2012 at 03:18:48PM +0900, Naohisa GOTO wrote:
> > > When writing HOWTO based on BioPerl HOWTO:Trees,
> > > (http://bioruby.open-bio.org/wiki/HOWTO:Trees but still incomplete)
> > > I'm thinking to add/modify some API about speficying nodes/edges.
> > 
> > After some trying I agree. The Bio::Tree::Node object should know
> > 'more' about its state. I would like to do something like:
> > 
> >   root.leaf?.should == false
> >   node = root.childeren.first
> >   node.leaf?.should == false
> >   node2 == node.childeren.first
> >   node.leaf?.should == true
> >   node2.edge(node).distance.should == 1.34
> > 
> > now I need to do something like 
> > 
> >   tree = @tree
> >   node = tree.get_node_by_name('node')
> >   tree.get_edge(node, tree.parent(node)).distance.should == 1.34
> > 
> > which uses the tree state to get a node edge, and does not feel that
> > intuitive.
> > 
> > I'll try to extend Bio::Tree for bio-alignment, see what works.
> > 
> > Pj.
> 


From dafian90 at gmail.com  Fri Mar 16 18:30:55 2012
From: dafian90 at gmail.com (Filippo Andrea D'Angelo)
Date: Fri, 16 Mar 2012 19:30:55 +0100
Subject: [BioRuby] New Trainee. BioRuby: Bio-Images Project
Message-ID: <CAK8_7p2bs4=sP4NqvJ_NMCtCF16PKRthv2TSWQpHXtbAYbvo4w@mail.gmail.com>

Hi everybody, my name is Filippo Andrea D'Angelo and I'm a student in
University of Milano-Bicocca. I chose to do my university stage with Bonnal
Raoul helping him in the project "BioRuby: Bio-Images Project". I hope that
I will learn a lot from this experience and be able to contribute as much
as possibile during this time.

D'Angelo F. Andrea


From freeparis2 at gmail.com  Fri Mar 16 19:36:38 2012
From: freeparis2 at gmail.com (Kazuo Ishii)
Date: Sat, 17 Mar 2012 04:36:38 +0900
Subject: [BioRuby] New Trainee. BioRuby: Bio-Images Project
In-Reply-To: <CAK8_7p2bs4=sP4NqvJ_NMCtCF16PKRthv2TSWQpHXtbAYbvo4w@mail.gmail.com>
References: <CAK8_7p2bs4=sP4NqvJ_NMCtCF16PKRthv2TSWQpHXtbAYbvo4w@mail.gmail.com>
Message-ID: <CAJDOTrJRWL_ifhwGLdYuM4qqs6a354ECsmhGjV6_GZdK9-bSCw@mail.gmail.com>

You are very welcome and good luck.

2012/3/17, Filippo Andrea D'Angelo <dafian90 at gmail.com>:
> Hi everybody, my name is Filippo Andrea D'Angelo and I'm a student in
> University of Milano-Bicocca. I chose to do my university stage with Bonnal
> Raoul helping him in the project "BioRuby: Bio-Images Project". I hope that
> I will learn a lot from this experience and be able to contribute as much
> as possibile during this time.
>
> D'Angelo F. Andrea
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>


-- 
Kazuo Ishii, Ph.D., Professor of Genome Science,
Tokyo University of Agriculture and Technology
3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, JAPAN
Email: kishii at cc.tuat.ac.jp


From bonnal at ingm.org  Sat Mar 17 18:22:48 2012
From: bonnal at ingm.org (Raoul Bonnal)
Date: Sat, 17 Mar 2012 19:22:48 +0100
Subject: [BioRuby] New Trainee. BioRuby: Bio-Images Project
In-Reply-To: <CAJDOTrJRWL_ifhwGLdYuM4qqs6a354ECsmhGjV6_GZdK9-bSCw@mail.gmail.com>
Message-ID: <CB8A9508.8805%bonnal@ingm.org>

Welcome ;-)


On 16/03/12 20.36, "Kazuo Ishii" <freeparis2 at gmail.com> wrote:

> You are very welcome and good luck.
> 
> 2012/3/17, Filippo Andrea D'Angelo <dafian90 at gmail.com>:
>> Hi everybody, my name is Filippo Andrea D'Angelo and I'm a student in
>> University of Milano-Bicocca. I chose to do my university stage with Bonnal
>> Raoul helping him in the project "BioRuby: Bio-Images Project". I hope that
>> I will learn a lot from this experience and be able to contribute as much
>> as possibile during this time.
>> 
>> D'Angelo F. Andrea
>> _______________________________________________
>> BioRuby Project - http://www.bioruby.org/
>> BioRuby mailing list
>> BioRuby at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioruby
>> 
> 




From andrea.nodari91 at gmail.com  Sat Mar 17 19:29:52 2012
From: andrea.nodari91 at gmail.com (Andrea Nodari)
Date: Sat, 17 Mar 2012 20:29:52 +0100
Subject: [BioRuby] restyle of bioruby.org
Message-ID: <CA+FV2YYX2Sy98ed4vHzaK+hA4-DPng0nbM7-cV+VGyw_qqiwgw@mail.gmail.com>

Hi all,
I'm Andrea Nodari and I'm a student of CS @ University of Trento , Italy,
I'm working as web developer and I am stronlgy interested in the
project of GSoC about restyling bioruby.org.
I hope to learn and contribute as much as possible to this comunity :)

-- 
Andrea


From francesco.strozzi at gmail.com  Sat Mar 17 20:03:35 2012
From: francesco.strozzi at gmail.com (Francesco Strozzi)
Date: Sat, 17 Mar 2012 21:03:35 +0100
Subject: [BioRuby] restyle of bioruby.org
In-Reply-To: <CA+FV2YYX2Sy98ed4vHzaK+hA4-DPng0nbM7-cV+VGyw_qqiwgw@mail.gmail.com>
References: <CA+FV2YYX2Sy98ed4vHzaK+hA4-DPng0nbM7-cV+VGyw_qqiwgw@mail.gmail.com>
Message-ID: <CACtet2QmczOSdG07eUXV13k9qPi+k0LKZcHt0nAprLbLaR+nGQ@mail.gmail.com>

Hi Andrea and welcome!
The deadline for student proposals is April 6th. You can find below the
details of the GSoC and how to apply for OBF projects.

We are here to help you develop your work proposal on GSoC, so feel free to
write on the ML and/or directly to the mentors to receive advise and
feedbacks. As BioRuby we have an IRC channel #bioruby on irc.freenode.net.
You can reach us there, we also have a weekly IRC meeting on Thursday
afternoon at 16.00 CET but you can find us there almost every working day.

Cheers
Francesco


----------

GSoC is a Google-sponsored student internship program for open-source
projects, open to students from around the world (not just US
residents).   Students are paid a $5000 USD stipend to work as a
developer on an open-source project for the summer. For more on GSoC,
see GSoC 2012 FAQ at http://goo.gl/kNv48

Student applications are due April 6, 2012 at 19:00 UTC.  Students who
are interested in participating should look at the OBF's GSoC page at
http://open-bio.org/wiki/**Google_Summer_of_Code<http://open-bio.org/wiki/Google_Summer_of_Code>,
which lists project
ideas, and whom to contact about applying.

-----------

On Sat, Mar 17, 2012 at 20:29, Andrea Nodari <andrea.nodari91 at gmail.com>wrote:

> Hi all,
> I'm Andrea Nodari and I'm a student of CS @ University of Trento , Italy,
> I'm working as web developer and I am stronlgy interested in the
> project of GSoC about restyling bioruby.org.
> I hope to learn and contribute as much as possible to this comunity :)
>
> --
> Andrea
> _______________________________________________
> 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 bonnal at ingm.org  Sat Mar 17 20:20:06 2012
From: bonnal at ingm.org (Raoul Bonnal)
Date: Sat, 17 Mar 2012 21:20:06 +0100
Subject: [BioRuby] restyle of bioruby.org
In-Reply-To: <CACtet2QmczOSdG07eUXV13k9qPi+k0LKZcHt0nAprLbLaR+nGQ@mail.gmail.com>
Message-ID: <CB8AB086.880E%bonnal@ingm.org>

Hello Andrea,
I read your chat with Marjan on irc, I think now you have all the references
github and wiki links so ... Welcome.
As Francesco said, please feel free to contact us on the ml (which is the
preferred way for official GSoC communications -so that other mentors from
other project can follow the progresses).

Ciao! 


On 17/03/12 21.03, "Francesco Strozzi" <francesco.strozzi at gmail.com> wrote:

> Hi Andrea and welcome!
> The deadline for student proposals is April 6th. You can find below the
> details of the GSoC and how to apply for OBF projects.
> 
> We are here to help you develop your work proposal on GSoC, so feel free to
> write on the ML and/or directly to the mentors to receive advise and
> feedbacks. As BioRuby we have an IRC channel #bioruby on irc.freenode.net.
> You can reach us there, we also have a weekly IRC meeting on Thursday
> afternoon at 16.00 CET but you can find us there almost every working day.
> 
> Cheers
> Francesco
> 
> 
> ----------
> 
> GSoC is a Google-sponsored student internship program for open-source
> projects, open to students from around the world (not just US
> residents).   Students are paid a $5000 USD stipend to work as a
> developer on an open-source project for the summer. For more on GSoC,
> see GSoC 2012 FAQ at http://goo.gl/kNv48
> 
> Student applications are due April 6, 2012 at 19:00 UTC.  Students who
> are interested in participating should look at the OBF's GSoC page at
> http://open-bio.org/wiki/**Google_Summer_of_Code<http://open-bio.org/wiki/Goog
> le_Summer_of_Code>,
> which lists project
> ideas, and whom to contact about applying.
> 
> -----------
> 
> On Sat, Mar 17, 2012 at 20:29, Andrea Nodari <andrea.nodari91 at gmail.com>wrote:
> 
>> Hi all,
>> I'm Andrea Nodari and I'm a student of CS @ University of Trento , Italy,
>> I'm working as web developer and I am stronlgy interested in the
>> project of GSoC about restyling bioruby.org.
>> I hope to learn and contribute as much as possible to this comunity :)
>> 
>> --
>> Andrea
>> _______________________________________________
>> BioRuby Project - http://www.bioruby.org/
>> BioRuby mailing list
>> BioRuby at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioruby
>> 
> 
> 




From moduvyas at gmail.com  Sun Mar 18 02:54:06 2012
From: moduvyas at gmail.com (varun vyas)
Date: Sun, 18 Mar 2012 08:24:06 +0530
Subject: [BioRuby] Gsoc:Asking for suggestion and view for Bioruby project
Message-ID: <CAFjAtqLU0J94Sx45R=tSuLkHAzP-QN4Gii0abe6MNjPmvdL=Dw@mail.gmail.com>

Hi,
   This is Varun Vyas from DA-IICT,Gandhinagar,India, in last year of his
B.tech. I want to ask about project titled "Adding social networking
functionality to BioRuby.org".
I would like to know who will be the mentor for this project, so as to
contact him to discuss more about the same. If anyone can suggest me
correct approach to this project i.e. point that must be included in
proposal, any must prerequisites, What are the expectations for this
project,who will take design decision,will design be provided  or  any
design constraint for site.Any help or suggestion would be great.
I am doing my intership in a start-up, where i created its website with
Ruby-on-rails 3.2. Have intermediate knowledge of Ruby and
Javascript(Jquery), learned as much was needed for completing my project
will working on it.  Though i know only basics of Coffescript  and Haml,
but can quickly learn and apply them if needed.

Thanks for any advice.



Thanking you
varun vyas


From pjotr.public14 at thebird.nl  Sun Mar 18 09:18:46 2012
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Sun, 18 Mar 2012 10:18:46 +0100
Subject: [BioRuby] Gsoc:Asking for suggestion and view for Bioruby
 project
In-Reply-To: <CAFjAtqLU0J94Sx45R=tSuLkHAzP-QN4Gii0abe6MNjPmvdL=Dw@mail.gmail.com>
References: <CAFjAtqLU0J94Sx45R=tSuLkHAzP-QN4Gii0abe6MNjPmvdL=Dw@mail.gmail.com>
Message-ID: <20120318091846.GA23224@thebird.nl>

Hi Varun,

On Sun, Mar 18, 2012 at 08:24:06AM +0530, varun vyas wrote:
> Hi,
>    This is Varun Vyas from DA-IICT,Gandhinagar,India, in last year of his
> B.tech. I want to ask about project titled "Adding social networking
> functionality to BioRuby.org".

You are welcome :)

> I would like to know who will be the mentor for this project, so as to
> contact him to discuss more about the same. If anyone can suggest me
> correct approach to this project i.e. point that must be included in
> proposal, any must prerequisites, What are the expectations for this
> project,who will take design decision,will design be provided  or  any
> design constraint for site.Any help or suggestion would be great.
> I am doing my intership in a start-up, where i created its website with
> Ruby-on-rails 3.2. Have intermediate knowledge of Ruby and
> Javascript(Jquery), learned as much was needed for completing my project
> will working on it.  Though i know only basics of Coffescript  and Haml,
> but can quickly learn and apply them if needed.

Programming experience is actually not really a requirement for GSoC.
The idea is to get people into OSS projects and make them long-term
contributors to OSS. If this project proposal appeals to you, please
do apply. One of BioRuby's little successes is Kharagpur based Anurag
Priyam, who came in with GSoC and is a very active OSS contributor,
see https://github.com/yeban (kudos to Anurag, sukria/donobad, I
wanted an excuse to mention that!).

Most of your questions will be answered by reading the GSoC
instructions

  http://code.google.com/p/google-summer-of-code/wiki/AdviceforStudents

and the OBF pages. Our projects have *multiple* mentors, and the
BioRuby panel also monitors actively. If you frame your questions
right, you will get answers on the mailing list (ML) or IRC.

Another important point is that the application process of GSoC is
rather competitive. More students apply than get selected! The only
way to get in is to produce a good proposal. A good proposal shows
the motivation of the student. A mentor will help, once there is
something on the table. Don't expect mentors to put in time for
'free'.

Enjoy :)

Pj.


From pjotr.public14 at thebird.nl  Sun Mar 18 10:09:05 2012
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Sun, 18 Mar 2012 11:09:05 +0100
Subject: [BioRuby] Drawing a phylogeny ASCII tree
In-Reply-To: <20120316135153.GA11119@thebird.nl>
References: <20120311125308.GB4204@thebird.nl>
	<20120312162438.GA11131@thebird.nl>
	<20120316135153.GA11119@thebird.nl>
Message-ID: <20120318100905.GA24171@thebird.nl>

On Fri, Mar 16, 2012 at 02:51:53PM +0100, Pjotr Prins wrote:
> Anyone interesting in a little coding challenge? I wrote a feature
> for drawing a phylogeny ASCII tree:
> 
> (snip)
>
> Then draw MSA with the short tree
>   """
>   +----------------- seq7  ----------PTIIFSGCSKACSGK-----VCGIFHAVRSFM
>   |           ,----- seq1  ----SNSFSRPTIIFSGCSTACSGK--SELVCGFRSFMLSDV
>   |        ,--|  ,-- seq2  SSIISNSFSRPTIIFSGCSTACSGK--SEQVCGFR---LSDV
>   |     ,--+  `--+-- seq3  SSIISNSFSRPTIIFSGCSTACSGKLTSEQVCGFR---LSDV
>   |     |  |--+----- seq5  ----------PTIIFSGCSKACSGKGLSELVCGFRSFMLSDV
>   |  ,--|     `----- seq8  --------PTIIFSGCSKACSGK--SELVCGFRSFMLSAV
>   |--|  `----------- seq4  ----PKLFSRPTIIFSGCSTACSGK--SEPVCGFRSFMLSDV
>      `-------------- seq6  ----------PTIIFSGCSKACSGK-----FRSFRSFMLSAV
>      1  2  3  4  5
>   """

I have been thinking about this 'ASCII cladogram' algorithm, as it
would be very useful for testing code. Unfortunately I have found no
example that really appeals to me in the other Bio* projects (we are
talking text here, not graphics; the graphics ones are actually
nicer). 

The examples I have are

* BioPerl tabtree
* Ruby challenge http://blade.nagaokaut.ac.jp/cgi-bin/scat.rb/ruby/ruby-talk/149701
* BioPythons http://biopython.org/DIST/docs/api/Bio.Phylo._utils-pysrc.html#draw_ascii

I have mailed T. Mike Keesey, of
http://www.palaeos.org/Ascii_phylogenetic_tree, as he has some interesting
generator, but he has not responded, yet.

So, assuming I am on my own, I was thinking that the tree needs to be
drawn in a matrix of characters. The pseudo code I come up with is
based on 'matrix expansion' - every time a sequence gets added, we
add a line. If a tree goes left (up), e.g. the last node before seq2, 
we expand the matrix by injecting a new line and extending the
verticals. We extend the horizontals in the final step.

Assuming we know the tree with leafs and nodes:

step 1, start with the first leaf seq7 (R=root, L=Leaf, o=node, N=new node)

  R--L seq7

step 2, add seq1 (4 nodes)

  R--L seq7
  `--o--o--o--o--L seq1

step 3, add seq2 (5 nodes)

  R--L seq7
  |           ,--L seq1
  `--o--o--o--N--o--L seq2

Now what you see is that seq1 is on the branch of new seq2. So after
adding seq2, we wipe seq1 to the left of N and copy the verticals on
the left side of the new node (N). 

step 4, add seq 3


  R--L seq7
  |           ,--L seq1
  |           |  ,--L seq2
  `--o--o--o--|--N--L seq3

Same principle. After adding seq3, we find seq2 is connected and we
split seq2 - left side extend verticals, right side connect

step 5, add seq5 (4 nodes)

  R--L seq7
  |           ,--L seq1
  |           |  ,--L seq2
  |        ,--|--N--L seq3
  `--o--o--N--o--L seq5

Again, seq5 connects at the 3rd node. So we split the above

step 6, seq 8 (4 nodes)

  R--L seq7
  |           ,--L seq1
  |           |  ,--L seq2
  |        ,--|--N--L seq3
  |        |  ,--L seq5
  `--o--o--|--N--L seq8

Split on node 4. Expand verticals to the left of N.
Here the algorithm changed the original drawing a little.

step 7, seq 4 (2 nodes)

  R--L seq7
  |           ,--L seq1
  |           |  ,--L seq2
  |        ,--|--N--L seq3
  |        |  ,--L seq5
  |     ,--|--N--L seq8
  `--o--N--L seq4

step 8, seq6 (1 node)


  R--L seq7
  |           ,--L seq1
  |           |  ,--L seq2
  |        ,--|--N--L seq3
  |        |  ,--L seq5
  |     ,--|--N--L seq8
  |  ,--N--L seq4
  `--N--L seq6

step 9, we can expand horizontally


  R----------------- seq7
  |           ,----- seq1
  |           |  ,-- seq2
  |        ,--+--+-- seq3
  |        |  ,----- seq5
  |     ,--+--+----- seq8
  |  ,--+----------- seq4
  `--+-------------- seq6
     1  2  3  4  5

I think this is pretty much what Mike Keesey does on

  http://namesonnodes.org/texttree/

Anyone see a flaw in my reasoning?

Pj.


From yannick.wurm at unil.ch  Mon Mar 19 03:19:56 2012
From: yannick.wurm at unil.ch (Yannick Wurm)
Date: Mon, 19 Mar 2012 03:19:56 +0000
Subject: [BioRuby] Drawing a phylogeny ASCII tree
In-Reply-To: <mailman.5.1332086407.20174.bioruby@lists.open-bio.org>
References: <mailman.5.1332086407.20174.bioruby@lists.open-bio.org>
Message-ID: <50203D1A-A35A-40FF-96C9-34045977210E@unil.ch>

On 18 Mar 2012, at 16:00, bioruby-request at lists.open-bio.org wrote:

> I have found no
> example that really appeals to me in the other Bio* projects (we are
> talking text here, not graphics; the graphics ones are actually
> nicer). 


Here's another example 
http://cegg.unige.ch/newick_utils

The tool nw_display outputs your tree in the console in text format...

cheers,

yannick



Yannick Wurm
Ants, Genomes & Evolution ? y.wurm at qmul.ac.uk ? skype:yannickwurm ? +44 207 882 3049
5.03A Fogg ? School of Biological & Chemical Sciences ? Queen Mary, University of London ? Mile End Road ? E1 4NX London ? UK



From pjotr.public14 at thebird.nl  Mon Mar 19 07:03:04 2012
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Mon, 19 Mar 2012 08:03:04 +0100
Subject: [BioRuby] Drawing a phylogeny ASCII tree
In-Reply-To: <50203D1A-A35A-40FF-96C9-34045977210E@unil.ch>
References: <mailman.5.1332086407.20174.bioruby@lists.open-bio.org>
	<50203D1A-A35A-40FF-96C9-34045977210E@unil.ch>
Message-ID: <20120319070304.GC29236@thebird.nl>

On Mon, Mar 19, 2012 at 03:19:56AM +0000, Yannick Wurm wrote:
> On 18 Mar 2012, at 16:00, bioruby-request at lists.open-bio.org wrote:
> 
> > I have found no
> > example that really appeals to me in the other Bio* projects (we are
> > talking text here, not graphics; the graphics ones are actually
> > nicer). 
> 
> 
> Here's another example 
> http://cegg.unige.ch/newick_utils
> 
> The tool nw_display outputs your tree in the console in text format...

Excellent!

Also, Mike Keesey sent me his code:

  http://code.google.com/p/a3lbmonkeybrain-as3/source/browse/trunk/src/a3lbmonkeybrain/calculia/collections/graphs/exporters/TextCladogramExporter.as?spec=svn26&r=26

No need to fully reinvent the wheel then.

Pj.


From naliwajek at gmail.com  Mon Mar 19 16:29:24 2012
From: naliwajek at gmail.com (Jakub Naliwajek)
Date: Mon, 19 Mar 2012 17:29:24 +0100
Subject: [BioRuby] GSoC: Testing framework for biogem plugins
Message-ID: <CAO--zKeD34pqYry3UUoxhO-NShz++MEKkt4i1Rmrrabd_AFiJw@mail.gmail.com>

Hi,

My name's Jakub. I'm a CS student and a back-end RoR developer from Poland.

I just wanted to check if my reasoning of whole process of adding a new bio
gem is right:

1. New bio gem is created by someone on GitHub;
2. Then gem is added by him to RubyGems;
3. Then gem is added (by him and *accepted* by OBF?) to BioGems;
4. Then all three services are automatically linked together by a framework;
5. Tests (all tests across gem and its dependencies) run for a first time
(initial release);
6. After that tests run only:
   *** when manually triggered (BioGems link action somewhere) OR;
   *** labeled on GitHub OR;
   *** new release (check if pushed to BioGems [or RubyGems if they have
such event handler]) is out;

7. (Eventually) with person responsible about restyle of bioruby.org we
decide how (if any) those results are going to look at main
bioruby.orgsite (not dev-only BioGems.info)

(For already existing gems let's say we begin from point 5 treating current
release as an initial one)

Of course, besides testing each gem with its dependencies individually, we
include option to test different BioGems together (different setups) and
display results at BioGems.info too.

Test results are displayed not only with "failed/passed" statement but also
with error log so developer can see straight from BioGems site what is
wrong, right?

Is it okay or did I forget something?

Also, I lack CoffeeScript knowledge but I guess it's not that hard to learn.


Cheers,
-- 
Jakub Naliwajek


From pjotr.public14 at thebird.nl  Tue Mar 20 09:34:06 2012
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Tue, 20 Mar 2012 10:34:06 +0100
Subject: [BioRuby] GSoC: Testing framework for biogem plugins
In-Reply-To: <CAO--zKeD34pqYry3UUoxhO-NShz++MEKkt4i1Rmrrabd_AFiJw@mail.gmail.com>
References: <CAO--zKeD34pqYry3UUoxhO-NShz++MEKkt4i1Rmrrabd_AFiJw@mail.gmail.com>
Message-ID: <20120320093406.GA4581@thebird.nl>

Hi Jakub,

On Mon, Mar 19, 2012 at 05:29:24PM +0100, Jakub Naliwajek wrote:
> Hi,
> 
> My name's Jakub. I'm a CS student and a back-end RoR developer from Poland.
> 
> I just wanted to check if my reasoning of whole process of adding a new bio
> gem is right:
> 
> 1. New bio gem is created by someone on GitHub;
> 2. Then gem is added by him to RubyGems;
> 3. Then gem is added (by him and *accepted* by OBF?) to BioGems;

No, it is automatic. If you gem starts with bio- it will
automatically show up on http://biogems.info/

> 4. Then all three services are automatically linked together by a framework;
> 5. Tests (all tests across gem and its dependencies) run for a first time
> (initial release);

At the moment the tests are handled by travis-ci. You need to
register your project with them (two small steps!), and create a
.travis.yml file in your tree.

I like travis-ci, even when the service would disappear, it would be
reasonably easy to recreate ourselves (the source code is online).

> 6. After that tests run only:
>    *** when manually triggered (BioGems link action somewhere) OR;
>    *** labeled on GitHub OR;
>    *** new release (check if pushed to BioGems [or RubyGems if they have
> such event handler]) is out;

The default for travis is to run a test, every time you push to
github. There is also a manual override.

> 7. (Eventually) with person responsible about restyle of bioruby.org we
> decide how (if any) those results are going to look at main
> bioruby.orgsite (not dev-only BioGems.info)

Yes, both sites could be one site, but I agree biogems.info mostly
targets experienced developers. Design decisions are part of the
discussion on the ML. We created the BioRuby panel to ascertain we
find the best solution for the community.

> (For already existing gems let's say we begin from point 5 treating current
> release as an initial one)

That would be great.

> Of course, besides testing each gem with its dependencies individually, we
> include option to test different BioGems together (different setups) and
> display results at BioGems.info too.

Agree. 

Gems posted on rubygems.org have tagged releases on github. We can
test each release, with its dependencies. Travis-ci, btw, would also
allow us to run the test in dependent gems in one go(!)

> Test results are displayed not only with "failed/passed" statement but also
> with error log so developer can see straight from BioGems site what is
> wrong, right?
> 
> Is it okay or did I forget something?

Sounds right to me. I am glad you appreciate the importance of a
proper testing framework.

> Also, I lack CoffeeScript knowledge but I guess it's not that hard to learn.

Yes.

Pj.


From pjotr.public14 at thebird.nl  Tue Mar 20 09:41:55 2012
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Tue, 20 Mar 2012 10:41:55 +0100
Subject: [BioRuby] IRC
Message-ID: <20120320094155.GA6229@thebird.nl>

We'll be on IRC today.


From naliwajek at gmail.com  Thu Mar 22 15:27:15 2012
From: naliwajek at gmail.com (Jakub Naliwajek)
Date: Thu, 22 Mar 2012 16:27:15 +0100
Subject: [BioRuby] GSoC: Testing framework for biogem plugins
In-Reply-To: <20120320093406.GA4581@thebird.nl>
References: <CAO--zKeD34pqYry3UUoxhO-NShz++MEKkt4i1Rmrrabd_AFiJw@mail.gmail.com>
	<20120320093406.GA4581@thebird.nl>
Message-ID: <CAO--zKdJ5qiK_=HTeg_u1dLjsehwU=7v9d9X1_W44xTs33RJSg@mail.gmail.com>

Thanks for your response, Pjotr.

I was trying to plan project's timeline and here are 2 additional questions
I thought about:

1. Biogems.info is written in Ruby on Rails, right?

2. Travis-CI handles users via their GitHub accounts. Would we also like to
handle users that way, so they can hit "run my test" straight from
biogems.info? (and upload travis.yml file by/through our framwork, register
new gem in travis-ci straight from biogems.info etc.)

Cheers,
-- 
Jakub Naliwajek


From pjotr.public14 at thebird.nl  Thu Mar 22 15:37:30 2012
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Thu, 22 Mar 2012 16:37:30 +0100
Subject: [BioRuby] GSoC: Testing framework for biogem plugins
In-Reply-To: <CAO--zKdJ5qiK_=HTeg_u1dLjsehwU=7v9d9X1_W44xTs33RJSg@mail.gmail.com>
References: <CAO--zKeD34pqYry3UUoxhO-NShz++MEKkt4i1Rmrrabd_AFiJw@mail.gmail.com>
	<20120320093406.GA4581@thebird.nl>
	<CAO--zKdJ5qiK_=HTeg_u1dLjsehwU=7v9d9X1_W44xTs33RJSg@mail.gmail.com>
Message-ID: <20120322153730.GA24105@thebird.nl>

On Thu, Mar 22, 2012 at 04:27:15PM +0100, Jakub Naliwajek wrote:
> Thanks for your response, Pjotr.
> 
> I was trying to plan project's timeline and here are 2 additional questions
> I thought about:
> 
> 1. Biogems.info is written in Ruby on Rails, right?

Nope. staticmatic - see https://github.com/pjotrp/biogems.info

> 2. Travis-CI handles users via their GitHub accounts. Would we also like to
> handle users that way, so they can hit "run my test" straight from
> biogems.info? (and upload travis.yml file by/through our framwork, register
> new gem in travis-ci straight from biogems.info etc.)

I think Marjan has put github authentication in.

Pj.


From marian.povolny at gmail.com  Thu Mar 22 17:39:36 2012
From: marian.povolny at gmail.com (Marjan Povolni)
Date: Thu, 22 Mar 2012 18:39:36 +0100
Subject: [BioRuby] GSoC: Testing framework for biogem plugins
In-Reply-To: <20120322153730.GA24105@thebird.nl>
References: <CAO--zKeD34pqYry3UUoxhO-NShz++MEKkt4i1Rmrrabd_AFiJw@mail.gmail.com>
	<20120320093406.GA4581@thebird.nl>
	<CAO--zKdJ5qiK_=HTeg_u1dLjsehwU=7v9d9X1_W44xTs33RJSg@mail.gmail.com>
	<20120322153730.GA24105@thebird.nl>
Message-ID: <CADKP5C=NKabtbtoyo5M-XBtZR41zeEKcTrNuYtkoSbFWsn-hXQ@mail.gmail.com>

Hi,


> > 2. Travis-CI handles users via their GitHub accounts. Would we also like
> to
> > handle users that way, so they can hit "run my test" straight from
> > biogems.info? (and upload travis.yml file by/through our framwork,
> register
> > new gem in travis-ci straight from biogems.info etc.)
>
> I think Marjan has put github authentication in.
>
>
Yes, that's correct, users can sign into the new website using their GitHub
account. We're using OmniAuth gem to make this possible, the wiki page on
restyling bioruby.org has some additional details on this.

However, from reading GitHub API docs, I would say that it' not possible to
create a new commit to add travis.yml file to the repository in question
from the site. The site has only read access of all repositories which
belong to a user:

http://developer.github.com/v3/oauth/#scopes


--
Marjan


From pjotr.public14 at thebird.nl  Thu Mar 22 19:29:01 2012
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Thu, 22 Mar 2012 20:29:01 +0100
Subject: [BioRuby] GSoC: Testing framework for biogem plugins
In-Reply-To: <CADKP5C=NKabtbtoyo5M-XBtZR41zeEKcTrNuYtkoSbFWsn-hXQ@mail.gmail.com>
References: <CAO--zKeD34pqYry3UUoxhO-NShz++MEKkt4i1Rmrrabd_AFiJw@mail.gmail.com>
	<20120320093406.GA4581@thebird.nl>
	<CAO--zKdJ5qiK_=HTeg_u1dLjsehwU=7v9d9X1_W44xTs33RJSg@mail.gmail.com>
	<20120322153730.GA24105@thebird.nl>
	<CADKP5C=NKabtbtoyo5M-XBtZR41zeEKcTrNuYtkoSbFWsn-hXQ@mail.gmail.com>
Message-ID: <20120322192901.GA24808@thebird.nl>

On Thu, Mar 22, 2012 at 06:39:36PM +0100, Marjan Povolni wrote:
>    Hi,
> 
>      > 2. Travis-CI handles users via their GitHub accounts. Would we also
>      like to
>      > handle users that way, so they can hit "run my test" straight from
>      > [1]biogems.info? (and upload travis.yml file by/through our framwork,
>      register
>      > new gem in travis-ci straight from [2]biogems.info etc.)
> 
>      I think Marjan has put github authentication in.
> 
>    Yes, that's correct, users can sign into the new website using their
>    GitHub account. We're using OmniAuth gem to make this possible, the wiki
>    page on restyling [3]bioruby.org has some additional details on this.
>    However, from reading GitHub API docs, I would say that it' not possible
>    to create a new commit to add travis.yml file to the repository in
>    question from the site. The site has only read access of all repositories
>    which belong to a user:
>    [4]http://developer.github.com/v3/oauth/#scopes

Rightly so :).

biogem does generate the travis.yml file now, by default, on
generation of a new gem.

Pj.


From pjotr.public14 at thebird.nl  Thu Mar 22 19:51:39 2012
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Thu, 22 Mar 2012 20:51:39 +0100
Subject: [BioRuby] BioRuby.org website
In-Reply-To: <20120229172026.GA29664@thebird.nl>
References: <20120229090233.GB27695@thebird.nl>
	<CAKVJ-_4pgFXg9fMaKTV96MkmeBvuzmHHNbnfYQwVwW_vr00+tg@mail.gmail.com>
	<20120229145443.GA28775@thebird.nl>
	<CAKVJ-_5n3w5nVF4jCz9_Oh=eJwYWqwPHf=tyQWruKVwV-k0HzQ@mail.gmail.com>
	<098C48D9-F855-4E5A-B978-FE9B690B785D@illinois.edu>
	<20120229172026.GA29664@thebird.nl>
Message-ID: <20120322195139.GA25227@thebird.nl>

Feature: Create challenges for newbies using github issues

  We want to create a page that lists challenges for newbies. These
  challenges are harvested from github issues tagged with the 'newbie' 
  tag.

  Scenario: The coding challenges page
    Given a user visits the BioRuby challenges page
    When the page gets shown
    Then I want to show all known issues in all biogems that have been tagged 'newbie'
 
see also https://github.com/pjotrp/NA-BioRuby.org/tree/master/features


From gianluca at dellavedova.org  Fri Mar 23 05:27:51 2012
From: gianluca at dellavedova.org (Gianluca Della Vedova)
Date: Fri, 23 Mar 2012 06:27:51 +0100
Subject: [BioRuby] BioRuby.org website
In-Reply-To: <20120322195139.GA25227@thebird.nl>
References: <20120229090233.GB27695@thebird.nl>
	<CAKVJ-_4pgFXg9fMaKTV96MkmeBvuzmHHNbnfYQwVwW_vr00+tg@mail.gmail.com>
	<20120229145443.GA28775@thebird.nl>
	<CAKVJ-_5n3w5nVF4jCz9_Oh=eJwYWqwPHf=tyQWruKVwV-k0HzQ@mail.gmail.com>
	<098C48D9-F855-4E5A-B978-FE9B690B785D@illinois.edu>
	<20120229172026.GA29664@thebird.nl>
	<20120322195139.GA25227@thebird.nl>
Message-ID: <20120323052751.GA4749@dellavedova-E4310.dellavedova.org>

That's a great idea.
--
Gianluca Della Vedova
* Pjotr Prins <pjotr.public14 at thebird.nl> [2012-03-22 20:51:39 +0100]:

>Feature: Create challenges for newbies using github issues
>
>  We want to create a page that lists challenges for newbies. These
>  challenges are harvested from github issues tagged with the 'newbie'
>  tag.
>
>  Scenario: The coding challenges page
>    Given a user visits the BioRuby challenges page
>    When the page gets shown
>    Then I want to show all known issues in all biogems that have been tagged 'newbie'
>
>see also https://github.com/pjotrp/NA-BioRuby.org/tree/master/features
>_______________________________________________
>BioRuby Project - http://www.bioruby.org/
>BioRuby mailing list
>BioRuby at lists.open-bio.org
>http://lists.open-bio.org/mailman/listinfo/bioruby


From info at orbicule.com  Fri Mar 23 10:52:54 2012
From: info at orbicule.com (Peter Schols)
Date: Fri, 23 Mar 2012 11:52:54 +0100
Subject: [BioRuby] [STUDENT JOB] BioRuby summer job in human genomics
Message-ID: <07B2DC43-18F3-4C86-B03E-7C4023BF3A12@orbicule.com>

Dear list,

We are looking for a student who is passionate about bioinformatics and (Bio)Ruby to join our team this summer.
Candidates should have:

- some background in biology / genetics / bioinformatics
- good knowledge of Ruby 
- preferably some experience with BioRuby and bio gems
- experience with Rails is a plus

You will be working with our developers and designers on an exciting new project in the field of human genomics.
We can offer you:

- super flexible schedule
- highly motivated team
- the possibility to work from home
- the possibility to have your work seen by thousands of people worldwide, a great addition to your cv
- 1500 euro (about $1950) net monthly wage

Interested? Please send your resume to jobs at orbicule.com

Peter Schols
Orbicule


From cswh at umich.edu  Mon Mar 26 07:26:14 2012
From: cswh at umich.edu (Clayton Wheeler)
Date: Mon, 26 Mar 2012 03:26:14 -0400
Subject: [BioRuby] GSoC: MAF parser questions
Message-ID: <DEB9EA3D-4E72-4348-A02A-D701571D6ECF@umich.edu>

Hello,

I'm Clayton Wheeler, an undergraduate microbiology student at the University of Michigan. I'm particularly interested in molecular biology and microbial ecology, but in a previous life I was a programmer and system administrator for 11 years, so I'm very interested in applying that background to bioinformatics, also. The lab I've been working in uses bioinformatics tools and next-generation sequencing quite a bit, especially for studying hydrothermal plume communities; I've been working on the wet-lab side, but this is an area I'd like to learn more about. Moreover, I've been using Ruby for the last six years or so, and so I'd like to help develop it as a bioinformatics platform. The GSoC projects for BioRuby caught my eye, and I'd like to see if there's a good way I could contribute there.

The parser projects for MAF and GFF3 seem interesting and doable; I've been looking into the MAF parser project in particular, and I have a few questions about it. 

First, does the set of operations on MAF data described in Blankenberg et al (http://1.usa.gov/GQRYvX) cover the use cases that such a parser and indexing system should support?

Is https://github.com/polyatail/biopython the correct location of the BioPython MAF code described in http://biopython.org/wiki/Multiple_Alignment_Format? (It looks like it's been 11 months since the last commit.) 

Also, I've found a few existing tools for working with MAF files such as the scripts shipped with bx-python and PHAST, but not too many worked examples of how they'd be used in practice. Are there any more or less real-world examples available of MAF operations demonstrating the kinds of indexed access, large data sizes, etc. that should be supported in bio-alignment? 

Thanks,

Clayton Wheeler
cswh at umich.edu





From p.j.a.cock at googlemail.com  Mon Mar 26 09:09:50 2012
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 26 Mar 2012 10:09:50 +0100
Subject: [BioRuby] GSoC: MAF parser questions
In-Reply-To: <DEB9EA3D-4E72-4348-A02A-D701571D6ECF@umich.edu>
References: <DEB9EA3D-4E72-4348-A02A-D701571D6ECF@umich.edu>
Message-ID: <CAKVJ-_6=1ThQ4c27CBtS_fU2at_1CQHpwL7oBHFh2oz5eFPHYw@mail.gmail.com>

On Mon, Mar 26, 2012 at 8:26 AM, Clayton Wheeler <cswh at umich.edu> wrote:
> Is https://github.com/polyatail/biopython the correct location of the BioPython
> MAF code described in http://biopython.org/wiki/Multiple_Alignment_Format?
> (It looks like it's been 11 months since the last commit.)

Yes, specifically this
branch:https://github.com/polyatail/biopython/tree/alignio-maf

This is something we're going to be looking at merging for Biopython 1.60,
http://lists.open-bio.org/pipermail/biopython-dev/2012-February/009384.html

Peter


From saketkc at gmail.com  Mon Mar 26 15:32:40 2012
From: saketkc at gmail.com (Saket Choudhary)
Date: Mon, 26 Mar 2012 21:02:40 +0530
Subject: [BioRuby] [GSoC] [GSoC2012] BioRuby
In-Reply-To: <20120326133700.GA22488@thebird.nl>
References: <CAEDHeive9DOXSMMPXfjNEu1i6X0iqC0czqBtnAvrar1MUjb+yQ@mail.gmail.com>
	<20120326133700.GA22488@thebird.nl>
Message-ID: <CAEDHeisH+7cUPp2EsFNJ9yOevb4kDG78kL-3d-We8of0+7G+Rg@mail.gmail.com>

Hi Pjotr,

Thanks !

I have been using BioRuby and BioPython for 6 months now to solve the
"Protein Loop Closure" problem. I use it mainly to manipulate the atom
positions in a given PDB file, thus perturbing their positions.

I went through the discussion that happened on the mailing list last month:
Here are my notes about the same

1.http://lists.open-bio.org/pipermail/bioruby/2012-February/002087.html

Even I am a big fan of Jruby homepage. Here are my suggestiosn :
1. Ruby is simple, clear , intutitve and this makes Biouby intutive to
everyone. This needs to be emphasised the very first time a user comes to
the webpage : Instead of giving them examples on Wiki[
http://bioruby.open-bio.org/wiki/SampleCodes] to "read" through a tutorial
in the form of a short writeup/description about Ruby/BioRuby foolwed by a
challenge would be more appealing and intuitive to the user even though he
is being exposed to Ruby/BioRuby for the first time. Say some tutorial on
the lines of http://www.codecademy.com/ , a short tutorial followed by your
Scratchpad. !


2. Calendar/Tweet/Conference widget:

Something again on the lines of Jruby website.


3. Favicon missing ?

Though a very trivial issue , but just wanted to know why isn't there a
favicon for bioruby.org ?

These are the stuff I gathered , I am still digging the old threads, will
post here if something relevant comes up !


Saket Choudhary
IIT Bombay
github.com/saketkc



On 26 March 2012 19:07, Pjotr Prins <pjotr2012 at thebird.nl> wrote:

> Hi Saket,
>
> Welcome!
>
> It would be good if you also introduce yourself to the BioRuby ML, and
> post your ideas. We are working on the website (should I say
> web 'experience'), and I like what you propose. Also check out the ML
> archive of the last months, you'll find a lot of information.
>
> Pj.
>
> On Mon, Mar 26, 2012 at 02:10:51PM +0530, Saket Choudhary wrote:
> > Hi !
> >
> > I am Saket Choudhary, a third year undergraduate student at IIT Bombay,
> > India.
> >
> > Ruby has been my first love for programming. My last project[internship]
> > was at SlideShare <http://www.slideshare.net>, one of the biggest Ruby
> on
> > Rails website in the world. I had developed the Admin interface for
> > SlideShare which could enable suspending users, reconversion/deletion of
> > SlideShows , and user deletion/suspension.
> >
> > My hack at Yahoo! Open Hack India -2011 qualified among the Top 50 hacks
> ,
> > I built a Sinatra app for fetching a defined file from a Dropbox account
> > and sending it to a specified email address , just on a SMS.[
> > https://github.com/saketkc/dropbox_on_sms]
> >
> > I went through the GSoC idea page and "Adding social networking
> > functionality to BioRuby.org", is of my special interest. I have an
> > experience working on the Rails platform. My plans for making the website
> > more "Social" is as follows:
> >
> > 1. Provide an online 'Scratchpad' for Ruby/BioRuby enthusiasts that not
> > only allows them to run their codes online but also provides them a
> > facility to store it online in the form of an archive so that they an
> acess
> > it later.
> >
> > 2. Include sharing facility on "Scratchpad" so  that one user can share
> his
> > code online with other users/community and get feedback/comments. On the
> > lines of "Sage <http://www.sagenb.org/>" notebooks.
> >
> > 3. Develop an Online Board on the lines of "Quora <https://www.quora.com
> >"
> > Boards  so that users can pin certain codes/algorithms on to their own
> > boards for their reference this would reduce the overhead of searching
> for
> > a particular algorithm again and again .
> >
> > Let me know you views on these ideas. I would send a mockup of the same
> > incase these ideas seem feasible to you.
> >
> > Thanks
> >
> >  Saket Choudhary
> > IIT Bombay
> > _______________________________________________
> > GSoC mailing list
> > GSoC at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/gsoc
>


From pjotr.public14 at thebird.nl  Tue Mar 27 02:49:14 2012
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Tue, 27 Mar 2012 04:49:14 +0200
Subject: [BioRuby] [GSoC] [GSoC2012] BioRuby
In-Reply-To: <CAEDHeisH+7cUPp2EsFNJ9yOevb4kDG78kL-3d-We8of0+7G+Rg@mail.gmail.com>
References: <CAEDHeive9DOXSMMPXfjNEu1i6X0iqC0czqBtnAvrar1MUjb+yQ@mail.gmail.com>
	<20120326133700.GA22488@thebird.nl>
	<CAEDHeisH+7cUPp2EsFNJ9yOevb4kDG78kL-3d-We8of0+7G+Rg@mail.gmail.com>
Message-ID: <20120327024914.GA25873@thebird.nl>

To all GSoC applicants: be sure to start on your proposal and share it
with your project mentors. It is a surprisingly thorough and
competitive selection process, and if you want to succeed, the plan
and presentation has to be good. Every year we see students who start
too late. We can give feedback now, do use that to your advantage. We
want you to succeed.

Pj.

On Mon, Mar 26, 2012 at 09:02:40PM +0530, Saket Choudhary wrote:
> Hi Pjotr,
> 
> Thanks !
> 
> I have been using BioRuby and BioPython for 6 months now to solve the
> "Protein Loop Closure" problem. I use it mainly to manipulate the atom
> positions in a given PDB file, thus perturbing their positions.
> 
> I went through the discussion that happened on the mailing list last month:
> Here are my notes about the same
> 
> 1.http://lists.open-bio.org/pipermail/bioruby/2012-February/002087.html
> 
> Even I am a big fan of Jruby homepage. Here are my suggestiosn :
> 1. Ruby is simple, clear , intutitve and this makes Biouby intutive to
> everyone. This needs to be emphasised the very first time a user comes to
> the webpage : Instead of giving them examples on Wiki[
> http://bioruby.open-bio.org/wiki/SampleCodes] to "read" through a tutorial
> in the form of a short writeup/description about Ruby/BioRuby foolwed by a
> challenge would be more appealing and intuitive to the user even though he
> is being exposed to Ruby/BioRuby for the first time. Say some tutorial on
> the lines of http://www.codecademy.com/ , a short tutorial followed by your
> Scratchpad. !
> 
> 
> 2. Calendar/Tweet/Conference widget:
> 
> Something again on the lines of Jruby website.
> 
> 
> 3. Favicon missing ?
> 
> Though a very trivial issue , but just wanted to know why isn't there a
> favicon for bioruby.org ?
> 
> These are the stuff I gathered , I am still digging the old threads, will
> post here if something relevant comes up !
> 
> 
> Saket Choudhary
> IIT Bombay
> github.com/saketkc
> 
> 
> 
> On 26 March 2012 19:07, Pjotr Prins <pjotr2012 at thebird.nl> wrote:
> 
> > Hi Saket,
> >
> > Welcome!
> >
> > It would be good if you also introduce yourself to the BioRuby ML, and
> > post your ideas. We are working on the website (should I say
> > web 'experience'), and I like what you propose. Also check out the ML
> > archive of the last months, you'll find a lot of information.
> >
> > Pj.
> >
> > On Mon, Mar 26, 2012 at 02:10:51PM +0530, Saket Choudhary wrote:
> > > Hi !
> > >
> > > I am Saket Choudhary, a third year undergraduate student at IIT Bombay,
> > > India.
> > >
> > > Ruby has been my first love for programming. My last project[internship]
> > > was at SlideShare <http://www.slideshare.net>, one of the biggest Ruby
> > on
> > > Rails website in the world. I had developed the Admin interface for
> > > SlideShare which could enable suspending users, reconversion/deletion of
> > > SlideShows , and user deletion/suspension.
> > >
> > > My hack at Yahoo! Open Hack India -2011 qualified among the Top 50 hacks
> > ,
> > > I built a Sinatra app for fetching a defined file from a Dropbox account
> > > and sending it to a specified email address , just on a SMS.[
> > > https://github.com/saketkc/dropbox_on_sms]
> > >
> > > I went through the GSoC idea page and "Adding social networking
> > > functionality to BioRuby.org", is of my special interest. I have an
> > > experience working on the Rails platform. My plans for making the website
> > > more "Social" is as follows:
> > >
> > > 1. Provide an online 'Scratchpad' for Ruby/BioRuby enthusiasts that not
> > > only allows them to run their codes online but also provides them a
> > > facility to store it online in the form of an archive so that they an
> > acess
> > > it later.
> > >
> > > 2. Include sharing facility on "Scratchpad" so  that one user can share
> > his
> > > code online with other users/community and get feedback/comments. On the
> > > lines of "Sage <http://www.sagenb.org/>" notebooks.
> > >
> > > 3. Develop an Online Board on the lines of "Quora <https://www.quora.com
> > >"
> > > Boards  so that users can pin certain codes/algorithms on to their own
> > > boards for their reference this would reduce the overhead of searching
> > for
> > > a particular algorithm again and again .
> > >
> > > Let me know you views on these ideas. I would send a mockup of the same
> > > incase these ideas seem feasible to you.
> > >
> > > Thanks
> > >
> > >  Saket Choudhary
> > > IIT Bombay
> > > _______________________________________________
> > > GSoC mailing list
> > > GSoC at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/gsoc
> >
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
> 


From bonnal at ingm.org  Tue Mar 27 08:25:58 2012
From: bonnal at ingm.org (Raoul Bonnal)
Date: Tue, 27 Mar 2012 10:25:58 +0200
Subject: [BioRuby] GSoC: MAF parser questions
In-Reply-To: <DEB9EA3D-4E72-4348-A02A-D701571D6ECF@umich.edu>
Message-ID: <CB974636.89B4%bonnal@ingm.org>

Hi Clayton,
Welcome.

On 26/03/12 09.26, "Clayton Wheeler" <cswh at umich.edu> wrote:

> Hello,
> 
> I'm Clayton Wheeler, an undergraduate microbiology student at the University
> of Michigan. I'm particularly interested in molecular biology and microbial
> ecology, but in a previous life I was a programmer and system administrator
> for 11 years, so I'm very interested in applying that background to
> bioinformatics, also. The lab I've been working in uses bioinformatics tools
> and next-generation sequencing quite a bit, especially for studying
> hydrothermal plume communities; I've been working on the wet-lab side, but
> this is an area I'd like to learn more about. Moreover, I've been using Ruby
> for the last six years or so, and so I'd like to help develop it as a
> bioinformatics platform. The GSoC projects for BioRuby caught my eye, and I'd
> like to see if there's a good way I could contribute there.
> 
> The parser projects for MAF and GFF3 seem interesting and doable; I've been
> looking into the MAF parser project in particular, and I have a few questions
> about it. 
> 
> First, does the set of operations on MAF data described in Blankenberg et al
> (http://1.usa.gov/GQRYvX) cover the use cases that such a parser and indexing
> system should support?
Yes, I think that having all those features implemented will be great. Maybe
it would be better if you define a priority list of all the features.
> 
> Is https://github.com/polyatail/biopython the correct location of the
> BioPython MAF code described in
> http://biopython.org/wiki/Multiple_Alignment_Format? (It looks like it's been
> 11 months since the last commit.)

>From Peter:" Yes, specifically this
branch:https://github.com/polyatail/biopython/tree/alignio-maf

This is something we're going to be looking at merging for Biopython 1.60,
http://lists.open-bio.org/pipermail/biopython-dev/2012-February/009384.html

Peter"


Specs: http://genome.ucsc.edu/FAQ/FAQformat.html#format5

Some MAF app http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
 
> Also, I've found a few existing tools for working with MAF files such as the
> scripts shipped with bx-python and PHAST, but not too many worked examples of
> how they'd be used in practice. Are there any more or less real-world examples
> available of MAF operations demonstrating the kinds of indexed access, large
> data sizes, etc. that should be supported in bio-alignment?
This is an application which uses MAF as input
https://github.com/mlin/PhyloCSF/wiki


--
Ra




From pjotr.public14 at thebird.nl  Tue Mar 27 11:54:25 2012
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Tue, 27 Mar 2012 13:54:25 +0200
Subject: [BioRuby] biogems.info updated
In-Reply-To: <20111014080815.GA25807@thebird.nl>
References: <20110920165601.GA8933@thebird.nl>
	<20111014080815.GA25807@thebird.nl>
Message-ID: <20120327115425.GA29301@thebird.nl>

Marjan updated the site

    http://biogems.info/

Now we track the number of commits in the last week, and 90 days, to
show development activity.

Pj.


From bonnal at ingm.org  Tue Mar 27 12:12:42 2012
From: bonnal at ingm.org (Raoul Bonnal)
Date: Tue, 27 Mar 2012 14:12:42 +0200
Subject: [BioRuby] biogems.info updated
In-Reply-To: <20120327115425.GA29301@thebird.nl>
Message-ID: <CB977B5A.89C0%bonnal@ingm.org>

Wow, well done.



On 27/03/12 13.54, "Pjotr Prins" <pjotr.public14 at thebird.nl> wrote:

> Marjan updated the site
> 
>     http://biogems.info/
> 
> Now we track the number of commits in the last week, and 90 days, to
> show development activity.
> 
> Pj.
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby