From pjotr.public14 at thebird.nl  Thu May  9 06:02:08 2013
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Thu, 9 May 2013 12:02:08 +0200
Subject: [BioRuby] GSoC 2013 is ON
In-Reply-To: <20130303144729.GE6566@thebird.nl>
References: <20130303144729.GE6566@thebird.nl>
Message-ID: <20130509100208.GA14250@thebird.nl>

Hi everyone,

As you know BioRuby Google Summer of Code is now part of the SciRuby mentoring
organization. As it stands SciRuby has slots for 3 students. Students have put
in promising proposals for machine learning, D3 graphics, and data persistance
using Semweb technology. I invite anyone interested in these topics to
subscribe to the sciruby-dev mailing list. You can find it on
http://sciruby.com/.

Pj.

From cjfields at illinois.edu  Thu May 16 00:43:22 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 16 May 2013 04:43:22 +0000
Subject: [BioRuby] [Bioperl-l] Workshop on Sustainable Software for
 Science: Practice	and Experiences
In-Reply-To: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>
References: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E1F8C8@CHIMBX5.ad.uillinois.edu>

Jason and I have discussed looking into opportunity's like this, I think it makes sense to try a joint submission.  

chris

On May 15, 2013, at 3:44 PM, Hilmar Lapp <hlapp at drycafe.net> wrote:

> FYI, if you haven't seen this yet:
> 
> http://wssspe.researchcomputing.org.uk/
> 
> It seems to me that the Bio* projects, perhaps led by BioPerl as the oldest and thus longest running (nowadays more fancily called "sustained") of them would have a lot to say about the subject. Anyone interested in a joint submission?
> 
> Also, I notice that Biojava's Andreas is on the organizing committee, so maybe he's been conspiring on something already :-)
> 
> 	-hilmar
> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From p.j.a.cock at googlemail.com  Thu May 16 05:10:25 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 16 May 2013 10:10:25 +0100
Subject: [BioRuby] [Bioperl-l] Workshop on Sustainable Software for
 Science: Practice and Experiences
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74E1F8C8@CHIMBX5.ad.uillinois.edu>
References: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>
	<118F034CF4C3EF48A96F86CE585B94BF74E1F8C8@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAKVJ-_4=xseYz+2pZzVaEC7uiWnN7H0umUAJvZX8Ouaoa3FbRw@mail.gmail.com>

On Thu, May 16, 2013 at 5:43 AM, Fields, Christopher J
<cjfields at illinois.edu> wrote:
> Jason and I have discussed looking into opportunity's like this, I think it makes
> sense to try a joint submission.
>
> chris

This sounds like a good idea, although given the time and place I am
unlikely to be able to attend in person:

First Workshop on Sustainable Software for Science: Practice and
Experiences (WSSSPE)
(to held in conjunction with SC13, Sunday, 17 November 2013, Denver, CO, USA)
http://wssspe.researchcomputing.org.uk/

Rather than trying to discuss this over four mailing lists should we switch
to the cross project list open-bio-l, or continue off-list?
http://lists.open-bio.org/mailman/listinfo/open-bio-l

Thanks,

Peter

From cjfields at illinois.edu  Thu May 16 09:09:45 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 16 May 2013 13:09:45 +0000
Subject: [BioRuby] [Bioperl-l] Workshop on Sustainable Software for
 Science: Practice and Experiences
In-Reply-To: <CAKVJ-_4=xseYz+2pZzVaEC7uiWnN7H0umUAJvZX8Ouaoa3FbRw@mail.gmail.com>
References: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>
	<118F034CF4C3EF48A96F86CE585B94BF74E1F8C8@CHIMBX5.ad.uillinois.edu>
	<CAKVJ-_4=xseYz+2pZzVaEC7uiWnN7H0umUAJvZX8Ouaoa3FbRw@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E1FBCF@CHIMBX5.ad.uillinois.edu>

Yes, though we need to make sure others (e.g. those not subscribed to open-bio-l) are in the loop.

November is a possibility for me.

chris

On May 16, 2013, at 4:10 AM, Peter Cock <p.j.a.cock at googlemail.com>
 wrote:

> On Thu, May 16, 2013 at 5:43 AM, Fields, Christopher J
> <cjfields at illinois.edu> wrote:
>> Jason and I have discussed looking into opportunity's like this, I think it makes
>> sense to try a joint submission.
>> 
>> chris
> 
> This sounds like a good idea, although given the time and place I am
> unlikely to be able to attend in person:
> 
> First Workshop on Sustainable Software for Science: Practice and
> Experiences (WSSSPE)
> (to held in conjunction with SC13, Sunday, 17 November 2013, Denver, CO, USA)
> http://wssspe.researchcomputing.org.uk/
> 
> Rather than trying to discuss this over four mailing lists should we switch
> to the cross project list open-bio-l, or continue off-list?
> http://lists.open-bio.org/mailman/listinfo/open-bio-l
> 
> Thanks,
> 
> Peter



From tomoakin at kenroku.kanazawa-u.ac.jp  Fri May 17 03:40:49 2013
From: tomoakin at kenroku.kanazawa-u.ac.jp (Tomoaki NISHIYAMA)
Date: Fri, 17 May 2013 16:40:49 +0900
Subject: [BioRuby] ruby-2.0.0 and gem
Message-ID: <FF324627-1AEC-432A-AB5A-50FB10E1319C@kenroku.kanazawa-u.ac.jp>

Hi,

Installing bioruby from gem on ruby-2.0.0 produced the following error.
I assume these are effectively harmless for normal operation,
but we should address in 1.4.4 or any next version.

It looks like the system tries to convert ChangeLog to document using RDoc,
which should just useless. 
I still don't have found the right document of gem, RDoc systems...

Best regards,

/opt/appl/ruby2/bin/gem install bio
Fetching: bio-1.4.3.gem (100%)
Successfully installed bio-1.4.3
Parsing documentation for bio-1.4.3
Before reporting this, could you check that the file you're documenting
has proper syntax:

  /opt/appl/ruby2/bin/ruby -c ChangeLog

RDoc is not a full Ruby parser and will fail when fed invalid ruby programs.

The internal error was:

	(RangeError) integer 76984313719700134 too big to convert to `int'

ERROR:  While executing gem ... (RangeError)
    integer 76984313719700134 too big to convert to `int'
-- 
Tomoaki NISHIYAMA

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



From ngoto at gen-info.osaka-u.ac.jp  Fri May 24 15:19:04 2013
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Sat, 25 May 2013 04:19:04 +0900
Subject: [BioRuby] ruby-2.0.0 and gem
In-Reply-To: <FF324627-1AEC-432A-AB5A-50FB10E1319C@kenroku.kanazawa-u.ac.jp>
References: <FF324627-1AEC-432A-AB5A-50FB10E1319C@kenroku.kanazawa-u.ac.jp>
Message-ID: <201305241924.r4OJOODf003484@portal.open-bio.org>

Hi,

Thank you for reporting bug.
I've just released bio-1.4.3.0001.gem.
This release fixes the gem installation bug, and some other
bug fixes are included.

https://rubygems.org/gems/bio

Naohisa Goto
ng at bioruby.org

On Fri, 17 May 2013 16:40:49 +0900
Tomoaki NISHIYAMA <tomoakin at kenroku.kanazawa-u.ac.jp> wrote:

> Hi,
> 
> Installing bioruby from gem on ruby-2.0.0 produced the following error.
> I assume these are effectively harmless for normal operation,
> but we should address in 1.4.4 or any next version.
> 
> It looks like the system tries to convert ChangeLog to document using RDoc,
> which should just useless. 
> I still don't have found the right document of gem, RDoc systems...
> 
> Best regards,
> 
> /opt/appl/ruby2/bin/gem install bio
> Fetching: bio-1.4.3.gem (100%)
> Successfully installed bio-1.4.3
> Parsing documentation for bio-1.4.3
> Before reporting this, could you check that the file you're documenting
> has proper syntax:
> 
>   /opt/appl/ruby2/bin/ruby -c ChangeLog
> 
> RDoc is not a full Ruby parser and will fail when fed invalid ruby programs.
> 
> The internal error was:
> 
> 	(RangeError) integer 76984313719700134 too big to convert to `int'
> 
> ERROR:  While executing gem ... (RangeError)
>     integer 76984313719700134 too big to convert to `int'
> -- 
> Tomoaki NISHIYAMA
> 
> Advanced Science Research Center,
> Kanazawa University,
> 13-1 Takara-machi, 
> Kanazawa, 920-0934, Japan
> 
> 
> _______________________________________________
> 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 May  9 10:02:08 2013
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Thu, 9 May 2013 12:02:08 +0200
Subject: [BioRuby] GSoC 2013 is ON
In-Reply-To: <20130303144729.GE6566@thebird.nl>
References: <20130303144729.GE6566@thebird.nl>
Message-ID: <20130509100208.GA14250@thebird.nl>

Hi everyone,

As you know BioRuby Google Summer of Code is now part of the SciRuby mentoring
organization. As it stands SciRuby has slots for 3 students. Students have put
in promising proposals for machine learning, D3 graphics, and data persistance
using Semweb technology. I invite anyone interested in these topics to
subscribe to the sciruby-dev mailing list. You can find it on
http://sciruby.com/.

Pj.


From cjfields at illinois.edu  Thu May 16 04:43:22 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 16 May 2013 04:43:22 +0000
Subject: [BioRuby] [Bioperl-l] Workshop on Sustainable Software for
 Science: Practice	and Experiences
In-Reply-To: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>
References: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E1F8C8@CHIMBX5.ad.uillinois.edu>

Jason and I have discussed looking into opportunity's like this, I think it makes sense to try a joint submission.  

chris

On May 15, 2013, at 3:44 PM, Hilmar Lapp <hlapp at drycafe.net> wrote:

> FYI, if you haven't seen this yet:
> 
> http://wssspe.researchcomputing.org.uk/
> 
> It seems to me that the Bio* projects, perhaps led by BioPerl as the oldest and thus longest running (nowadays more fancily called "sustained") of them would have a lot to say about the subject. Anyone interested in a joint submission?
> 
> Also, I notice that Biojava's Andreas is on the organizing committee, so maybe he's been conspiring on something already :-)
> 
> 	-hilmar
> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From p.j.a.cock at googlemail.com  Thu May 16 09:10:25 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 16 May 2013 10:10:25 +0100
Subject: [BioRuby] [Bioperl-l] Workshop on Sustainable Software for
 Science: Practice and Experiences
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74E1F8C8@CHIMBX5.ad.uillinois.edu>
References: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>
	<118F034CF4C3EF48A96F86CE585B94BF74E1F8C8@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAKVJ-_4=xseYz+2pZzVaEC7uiWnN7H0umUAJvZX8Ouaoa3FbRw@mail.gmail.com>

On Thu, May 16, 2013 at 5:43 AM, Fields, Christopher J
<cjfields at illinois.edu> wrote:
> Jason and I have discussed looking into opportunity's like this, I think it makes
> sense to try a joint submission.
>
> chris

This sounds like a good idea, although given the time and place I am
unlikely to be able to attend in person:

First Workshop on Sustainable Software for Science: Practice and
Experiences (WSSSPE)
(to held in conjunction with SC13, Sunday, 17 November 2013, Denver, CO, USA)
http://wssspe.researchcomputing.org.uk/

Rather than trying to discuss this over four mailing lists should we switch
to the cross project list open-bio-l, or continue off-list?
http://lists.open-bio.org/mailman/listinfo/open-bio-l

Thanks,

Peter


From cjfields at illinois.edu  Thu May 16 13:09:45 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 16 May 2013 13:09:45 +0000
Subject: [BioRuby] [Bioperl-l] Workshop on Sustainable Software for
 Science: Practice and Experiences
In-Reply-To: <CAKVJ-_4=xseYz+2pZzVaEC7uiWnN7H0umUAJvZX8Ouaoa3FbRw@mail.gmail.com>
References: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>
	<118F034CF4C3EF48A96F86CE585B94BF74E1F8C8@CHIMBX5.ad.uillinois.edu>
	<CAKVJ-_4=xseYz+2pZzVaEC7uiWnN7H0umUAJvZX8Ouaoa3FbRw@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E1FBCF@CHIMBX5.ad.uillinois.edu>

Yes, though we need to make sure others (e.g. those not subscribed to open-bio-l) are in the loop.

November is a possibility for me.

chris

On May 16, 2013, at 4:10 AM, Peter Cock <p.j.a.cock at googlemail.com>
 wrote:

> On Thu, May 16, 2013 at 5:43 AM, Fields, Christopher J
> <cjfields at illinois.edu> wrote:
>> Jason and I have discussed looking into opportunity's like this, I think it makes
>> sense to try a joint submission.
>> 
>> chris
> 
> This sounds like a good idea, although given the time and place I am
> unlikely to be able to attend in person:
> 
> First Workshop on Sustainable Software for Science: Practice and
> Experiences (WSSSPE)
> (to held in conjunction with SC13, Sunday, 17 November 2013, Denver, CO, USA)
> http://wssspe.researchcomputing.org.uk/
> 
> Rather than trying to discuss this over four mailing lists should we switch
> to the cross project list open-bio-l, or continue off-list?
> http://lists.open-bio.org/mailman/listinfo/open-bio-l
> 
> Thanks,
> 
> Peter




From tomoakin at kenroku.kanazawa-u.ac.jp  Fri May 17 07:40:49 2013
From: tomoakin at kenroku.kanazawa-u.ac.jp (Tomoaki NISHIYAMA)
Date: Fri, 17 May 2013 16:40:49 +0900
Subject: [BioRuby] ruby-2.0.0 and gem
Message-ID: <FF324627-1AEC-432A-AB5A-50FB10E1319C@kenroku.kanazawa-u.ac.jp>

Hi,

Installing bioruby from gem on ruby-2.0.0 produced the following error.
I assume these are effectively harmless for normal operation,
but we should address in 1.4.4 or any next version.

It looks like the system tries to convert ChangeLog to document using RDoc,
which should just useless. 
I still don't have found the right document of gem, RDoc systems...

Best regards,

/opt/appl/ruby2/bin/gem install bio
Fetching: bio-1.4.3.gem (100%)
Successfully installed bio-1.4.3
Parsing documentation for bio-1.4.3
Before reporting this, could you check that the file you're documenting
has proper syntax:

  /opt/appl/ruby2/bin/ruby -c ChangeLog

RDoc is not a full Ruby parser and will fail when fed invalid ruby programs.

The internal error was:

	(RangeError) integer 76984313719700134 too big to convert to `int'

ERROR:  While executing gem ... (RangeError)
    integer 76984313719700134 too big to convert to `int'
-- 
Tomoaki NISHIYAMA

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




From ngoto at gen-info.osaka-u.ac.jp  Fri May 24 19:19:04 2013
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Sat, 25 May 2013 04:19:04 +0900
Subject: [BioRuby] ruby-2.0.0 and gem
In-Reply-To: <FF324627-1AEC-432A-AB5A-50FB10E1319C@kenroku.kanazawa-u.ac.jp>
References: <FF324627-1AEC-432A-AB5A-50FB10E1319C@kenroku.kanazawa-u.ac.jp>
Message-ID: <201305241924.r4OJOODf003484@portal.open-bio.org>

Hi,

Thank you for reporting bug.
I've just released bio-1.4.3.0001.gem.
This release fixes the gem installation bug, and some other
bug fixes are included.

https://rubygems.org/gems/bio

Naohisa Goto
ng at bioruby.org

On Fri, 17 May 2013 16:40:49 +0900
Tomoaki NISHIYAMA <tomoakin at kenroku.kanazawa-u.ac.jp> wrote:

> Hi,
> 
> Installing bioruby from gem on ruby-2.0.0 produced the following error.
> I assume these are effectively harmless for normal operation,
> but we should address in 1.4.4 or any next version.
> 
> It looks like the system tries to convert ChangeLog to document using RDoc,
> which should just useless. 
> I still don't have found the right document of gem, RDoc systems...
> 
> Best regards,
> 
> /opt/appl/ruby2/bin/gem install bio
> Fetching: bio-1.4.3.gem (100%)
> Successfully installed bio-1.4.3
> Parsing documentation for bio-1.4.3
> Before reporting this, could you check that the file you're documenting
> has proper syntax:
> 
>   /opt/appl/ruby2/bin/ruby -c ChangeLog
> 
> RDoc is not a full Ruby parser and will fail when fed invalid ruby programs.
> 
> The internal error was:
> 
> 	(RangeError) integer 76984313719700134 too big to convert to `int'
> 
> ERROR:  While executing gem ... (RangeError)
>     integer 76984313719700134 too big to convert to `int'
> -- 
> Tomoaki NISHIYAMA
> 
> Advanced Science Research Center,
> Kanazawa University,
> 13-1 Takara-machi, 
> Kanazawa, 920-0934, Japan
> 
> 
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby