From p.j.a.cock at googlemail.com  Tue Apr  9 06:20:43 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Tue, 9 Apr 2013 11:20:43 +0100
Subject: [BioRuby] OBF not accepted for GSoC 2013
Message-ID: <CAKVJ-_6-+nyJk+7tp5YOyy7i7N7GtkRswZ_2Vs0uTuqGEV4wWQ@mail.gmail.com>

Dear all,

Unfortunately this year we have not been accepted on the Google
Summer of Code scheme:

I'm sure the rest of the OBF board and the other Bio* developers
will join me in thanking Pjotr Prins for his efforts as the OBF
GSoC administrator co-ordinating our application this year, as
well as last year's administrator Rob Bruels and the other mentors
for their efforts.

For those of you not subscribed to the OBF's GSoC mailing list,
I am forwarding Pjotr's email from last night (also below):
http://lists.open-bio.org/pipermail/gsoc/2013/000211.html

In all 177 organisations were accepted (about the same as the
last few years), and they will be listed here (once they have filled
out their profile information):
https://google-melange.appspot.com/gsoc/accepted_orgs/google/gsoc2013

To potential students this summer, the good news is that some
related organisations have been accepted, such as NESCent,
the National Resource for Network Biology (NRNB - known for
Cytoscape), SciRuby (Ruby Science Foundation), so there is
still some scope for doing a bioinformatics related project in
GSoC 2013, perhaps even with a Bio* developer as a co-mentor.

Thank you all,

Peter
(Biopython developer, OBF board member)

---------- Forwarded message ----------
From: Pjotr Prins <pjotr2010 at thebird.nl>
Date: Mon, Apr 8, 2013 at 9:13 PM
Subject: Re: GSoC 2013 is ON
To: Pjotr Prins <pjotr2010 at thebird.nl>
Cc: ..., OBF GSoC <gsoc at lists.open-bio.org>


Sadly, our application got rejected by GSoC this year. I am not sure
what the reason was, but I am convinced our application was similar to
that of other years. Maybe the project ideas could have been better
presented. I am not sure at this stage. I'll make a list of successful
projects to see if we can digest some truths.

The upside is that FOSS is going strong! And that the field is getting
increasingly competitive. As an open source geezer I can only be
happy, even if it hurts our own application.

Sorry everyone, and many thanks for the trouble you took getting
projects written up. Let's not feel discouraged for next year.

Pj.

From k at bioruby.org  Wed Apr 10 06:16:54 2013
From: k at bioruby.org (Toshiaki Katayama)
Date: Wed, 10 Apr 2013 19:16:54 +0900
Subject: [BioRuby] BOSC 2013 plan
Message-ID: <2949FBC3-25B5-4823-806D-F55DDF8629A2@bioruby.org>

Dear all,

It was unfortunate that OBF could not get approval of GSoC for this year.

By the way, the BOSC abstracts due is quickly approaching (Apr 12).

  http://www.open-bio.org/wiki/BOSC_2013

Does anybody plan to give a short talk on the BioRuby project update?

Cheers,
Toshiaki

From y.wurm at qmul.ac.uk  Wed Apr 10 05:34:38 2013
From: y.wurm at qmul.ac.uk (Yannick Wurm)
Date: Wed, 10 Apr 2013 10:34:38 +0100
Subject: [BioRuby] BioRuby Digest, Vol 90, Issue 1
In-Reply-To: <mailman.25.1365523207.6688.bioruby@lists.open-bio.org>
References: <mailman.25.1365523207.6688.bioruby@lists.open-bio.org>
Message-ID: <C888EA07-C8C8-4638-A731-F46D0D746595@qmul.ac.uk>

Dang that sucks I'm sorry :(

THnaks guys for putting in all the effort to put this together. 

A while ago I saw that LyX had "feature-specific donation buttons" (and ended up donating towards OSX support I think). This was before Crowdfounding stuff like kickstarter became popular. 

I wonder if a similar system  could create an alternative means of geting cash for getting manpower to get things done for bioruby. Just throwing the idea out there. 

Cheers
yannick

ps: it was http://www.lyx.org/Donate but they currently have no "requesting" projects. 



On 9 Apr 2013, at 17:00, bioruby-request at lists.open-bio.org wrote:

> Unfortunately this year we have not been accepted on the Google
> Summer of Code scheme



From ngoto at gen-info.osaka-u.ac.jp  Thu Apr 11 11:48:00 2013
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Fri, 12 Apr 2013 00:48:00 +0900
Subject: [BioRuby] Removal of Bio::DDBJ::XML,
 Bio::DDBJ::REST because of DDBJ web service reconstruction
Message-ID: <201304111554.r3BFs5ow002272@portal.open-bio.org>

Hi all,

Bio::DDBJ::XML and Bio::DDBJ::REST are the classes accessing
DDBJ Web API (WABI) web services. Since March 2012, the WABI
have been suspended because of the replacement of DDBJ computer
system. I've heard from some DDBJ people that it is now under
reconstruction and it will be completely renewed with new
improved API. So, I think the two classes are now useless and
are going to be removed.

After the new DDBJ Web API is released, new API client classes
will be written.

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

From pjotr.public14 at thebird.nl  Mon Apr 15 03:33:15 2013
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Mon, 15 Apr 2013 09:33:15 +0200
Subject: [BioRuby] GSoC 2013 is ON
In-Reply-To: <20130303144729.GE6566@thebird.nl>
References: <20130303144729.GE6566@thebird.nl>
Message-ID: <20130415073315.GA22590@thebird.nl>

Hi everyone,

You may have heard that OBF failed to get into GSoC this year. This is
disappointing for us: it was not for lack of commitment and effort
on our end.

The good news is that our main project ideas on machine learning, RDF
and D3 support have been incorporated into the SciRuby GSoC org. If
you consider participating in GSoC, either as a student or a mentor,
please take a look:

  https://github.com/SciRuby/sciruby/wiki/Google-Summer-of-Code-2013-Ideas

feedback is most welcome! Note: we may still change the project ideas.

Mentors: register as a mentor with SciRuby on

  http://www.google-melange.com/gsoc/dashboard/google/gsoc2013

Pj.

On Sun, Mar 03, 2013 at 03:47:29PM +0100, Pjotr Prins wrote:
> Game on! GSoC 2013 is ON. I am running with the OBF project
> administration this year for the Google Summer of code (GSoC). 
> First and foremost I want to thank Robert Buels and others for making
> OBF/GSoC a success in the previous three years! This year, Robert, Chris
> Fields and Hilmar Lapp will act as backup administrators.
> 
> The deadline for the OBF application for GSoC2013 as a mentoring
> organisation is Friday March 29! See
> 
>   http://www.google-melange.com/gsoc/events/google/gsoc2013
> 
> Similar to previous years, each Bio* project needs to update and add project
> ideas on the project's individual OBF wiki page and create links from the main
> OBF page at
> 
>   http://www.open-bio.org/wiki/Google_Summer_of_Code
> 
> (we will update the main information on that page soon).
> 
> So, for each of the OBF projects that wants to do GSoC again this
> year:
> 
> 1. 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. For an example see
> 
>      http://bioruby.open-bio.org/wiki/Google_Summer_of_Code
> 
> 2. Update the final list of project ideas on the main OBF GSoC page
>    to match.
> 
>      http://www.open-bio.org/wiki/Google_Summer_of_Code
> 
> 3. Register with gsoc at lists.open-bio.org
> 
> 4. Announce it on that list when you are ready :)
> 
> Anyone can submit a project idea! Former GSoC students are especially
> encouraged to contribute ideas to the mailing lists.
> 
> Please have the updates done by Friday March 22nd. The number and quality of
> the project ideas are part of the evaluation process for whether OBF is
> accepted as a Summer of Code organisation again this year, so let's come up
> with some good ones!
> 
> Pj. (Pjotr Prins)
> 
> Important dates: 
> 
>   * March 22nd: Finalise project ideas
>   * March 29th: Deadline OBF mentoring organisation submission to Google
> 
> http://www.open-bio.org/wiki/Google_Summer_of_Code
> 
> 
> _______________________________________________
> 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  Mon Apr 15 03:36:31 2013
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Mon, 15 Apr 2013 09:36:31 +0200
Subject: [BioRuby] GSoC 2013 is ON
In-Reply-To: <20130415073315.GA22590@thebird.nl>
References: <20130303144729.GE6566@thebird.nl>
	<20130415073315.GA22590@thebird.nl>
Message-ID: <20130415073631.GA22630@thebird.nl>

> Mentors: register as a mentor with SciRuby on
> 
>   http://www.google-melange.com/gsoc/dashboard/google/gsoc2013

should be 'click the apply button' on 

  https://google-melange.appspot.com/gsoc/homepage/google/gsoc2013

From pjotr.public14 at thebird.nl  Mon Apr 15 03:58:36 2013
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Mon, 15 Apr 2013 09:58:36 +0200
Subject: [BioRuby] Matz
Message-ID: <20130415075836.GA22684@thebird.nl>

http://fredwu.me/post/36493181321/an-interview-with-yukihiro-matz-matsumoto

From bonnal at ingm.org  Mon Apr 15 09:16:35 2013
From: bonnal at ingm.org (Raoul Bonnal)
Date: Mon, 15 Apr 2013 15:16:35 +0200
Subject: [BioRuby] GSoC 2013 is ON
In-Reply-To: <20130415073315.GA22590@thebird.nl>
References: <20130303144729.GE6566@thebird.nl>
	<20130415073315.GA22590@thebird.nl>
Message-ID: <03357A93-F516-4727-9A78-7A4481932E39@ingm.org>

i did it and I'm on.
On Apr 15, 2013, at 9:33 AM, Pjotr Prins <pjotr.public14 at thebird.nl> wrote:

> Hi everyone,
> 
> You may have heard that OBF failed to get into GSoC this year. This is
> disappointing for us: it was not for lack of commitment and effort
> on our end.
> 
> The good news is that our main project ideas on machine learning, RDF
> and D3 support have been incorporated into the SciRuby GSoC org. If
> you consider participating in GSoC, either as a student or a mentor,
> please take a look:
> 
>  https://github.com/SciRuby/sciruby/wiki/Google-Summer-of-Code-2013-Ideas
> 
> feedback is most welcome! Note: we may still change the project ideas.
> 
> Mentors: register as a mentor with SciRuby on
> 
>  http://www.google-melange.com/gsoc/dashboard/google/gsoc2013
> 
> Pj.
> 
> On Sun, Mar 03, 2013 at 03:47:29PM +0100, Pjotr Prins wrote:
>> Game on! GSoC 2013 is ON. I am running with the OBF project
>> administration this year for the Google Summer of code (GSoC). 
>> First and foremost I want to thank Robert Buels and others for making
>> OBF/GSoC a success in the previous three years! This year, Robert, Chris
>> Fields and Hilmar Lapp will act as backup administrators.
>> 
>> The deadline for the OBF application for GSoC2013 as a mentoring
>> organisation is Friday March 29! See
>> 
>>  http://www.google-melange.com/gsoc/events/google/gsoc2013
>> 
>> Similar to previous years, each Bio* project needs to update and add project
>> ideas on the project's individual OBF wiki page and create links from the main
>> OBF page at
>> 
>>  http://www.open-bio.org/wiki/Google_Summer_of_Code
>> 
>> (we will update the main information on that page soon).
>> 
>> So, for each of the OBF projects that wants to do GSoC again this
>> year:
>> 
>> 1. 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. For an example see
>> 
>>     http://bioruby.open-bio.org/wiki/Google_Summer_of_Code
>> 
>> 2. Update the final list of project ideas on the main OBF GSoC page
>>   to match.
>> 
>>     http://www.open-bio.org/wiki/Google_Summer_of_Code
>> 
>> 3. Register with gsoc at lists.open-bio.org
>> 
>> 4. Announce it on that list when you are ready :)
>> 
>> Anyone can submit a project idea! Former GSoC students are especially
>> encouraged to contribute ideas to the mailing lists.
>> 
>> Please have the updates done by Friday March 22nd. The number and quality of
>> the project ideas are part of the evaluation process for whether OBF is
>> accepted as a Summer of Code organisation again this year, so let's come up
>> with some good ones!
>> 
>> Pj. (Pjotr Prins)
>> 
>> Important dates: 
>> 
>>  * March 22nd: Finalise project ideas
>>  * March 29th: Deadline OBF mentoring organisation submission to Google
>> 
>> http://www.open-bio.org/wiki/Google_Summer_of_Code
>> 
>> 
>> _______________________________________________
>> 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 rob.syme at gmail.com  Mon Apr 15 09:33:58 2013
From: rob.syme at gmail.com (Rob Syme)
Date: Mon, 15 Apr 2013 21:33:58 +0800
Subject: [BioRuby] GSoC 2013 is ON
In-Reply-To: <03357A93-F516-4727-9A78-7A4481932E39@ingm.org>
References: <20130303144729.GE6566@thebird.nl>
	<20130415073315.GA22590@thebird.nl>
	<03357A93-F516-4727-9A78-7A4481932E39@ingm.org>
Message-ID: <CAEf4xgejPDVqcxWHVfygNhVKOe1OEin++w8gF6i2-kjjLhJOTA@mail.gmail.com>

Ditto
On 15 Apr 2013 21:33, "Raoul Bonnal" <bonnal at ingm.org> wrote:

> i did it and I'm on.
> On Apr 15, 2013, at 9:33 AM, Pjotr Prins <pjotr.public14 at thebird.nl>
> wrote:
>
> > Hi everyone,
> >
> > You may have heard that OBF failed to get into GSoC this year. This is
> > disappointing for us: it was not for lack of commitment and effort
> > on our end.
> >
> > The good news is that our main project ideas on machine learning, RDF
> > and D3 support have been incorporated into the SciRuby GSoC org. If
> > you consider participating in GSoC, either as a student or a mentor,
> > please take a look:
> >
> >
> https://github.com/SciRuby/sciruby/wiki/Google-Summer-of-Code-2013-Ideas
> >
> > feedback is most welcome! Note: we may still change the project ideas.
> >
> > Mentors: register as a mentor with SciRuby on
> >
> >  http://www.google-melange.com/gsoc/dashboard/google/gsoc2013
> >
> > Pj.
> >
> > On Sun, Mar 03, 2013 at 03:47:29PM +0100, Pjotr Prins wrote:
> >> Game on! GSoC 2013 is ON. I am running with the OBF project
> >> administration this year for the Google Summer of code (GSoC).
> >> First and foremost I want to thank Robert Buels and others for making
> >> OBF/GSoC a success in the previous three years! This year, Robert, Chris
> >> Fields and Hilmar Lapp will act as backup administrators.
> >>
> >> The deadline for the OBF application for GSoC2013 as a mentoring
> >> organisation is Friday March 29! See
> >>
> >>  http://www.google-melange.com/gsoc/events/google/gsoc2013
> >>
> >> Similar to previous years, each Bio* project needs to update and add
> project
> >> ideas on the project's individual OBF wiki page and create links from
> the main
> >> OBF page at
> >>
> >>  http://www.open-bio.org/wiki/Google_Summer_of_Code
> >>
> >> (we will update the main information on that page soon).
> >>
> >> So, for each of the OBF projects that wants to do GSoC again this
> >> year:
> >>
> >> 1. 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. For an example see
> >>
> >>     http://bioruby.open-bio.org/wiki/Google_Summer_of_Code
> >>
> >> 2. Update the final list of project ideas on the main OBF GSoC page
> >>   to match.
> >>
> >>     http://www.open-bio.org/wiki/Google_Summer_of_Code
> >>
> >> 3. Register with gsoc at lists.open-bio.org
> >>
> >> 4. Announce it on that list when you are ready :)
> >>
> >> Anyone can submit a project idea! Former GSoC students are especially
> >> encouraged to contribute ideas to the mailing lists.
> >>
> >> Please have the updates done by Friday March 22nd. The number and
> quality of
> >> the project ideas are part of the evaluation process for whether OBF is
> >> accepted as a Summer of Code organisation again this year, so let's
> come up
> >> with some good ones!
> >>
> >> Pj. (Pjotr Prins)
> >>
> >> Important dates:
> >>
> >>  * March 22nd: Finalise project ideas
> >>  * March 29th: Deadline OBF mentoring organisation submission to Google
> >>
> >> http://www.open-bio.org/wiki/Google_Summer_of_Code
> >>
> >>
> >> _______________________________________________
> >> 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
>
>
>
> _______________________________________________
> 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  Mon Apr 15 13:54:05 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 15 Apr 2013 17:54:05 +0000
Subject: [BioRuby] GSoC 2013 is ON
In-Reply-To: <CAEf4xgejPDVqcxWHVfygNhVKOe1OEin++w8gF6i2-kjjLhJOTA@mail.gmail.com>
References: <20130303144729.GE6566@thebird.nl>
	<20130415073315.GA22590@thebird.nl>
	<03357A93-F516-4727-9A78-7A4481932E39@ingm.org>
	<CAEf4xgejPDVqcxWHVfygNhVKOe1OEin++w8gF6i2-kjjLhJOTA@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DDFE64@CHIMBX5.ad.uillinois.edu>

Good to hear that Bioruby and Biopython have managed to get things going elsewhere!

chris

On Apr 15, 2013, at 8:33 AM, Rob Syme <rob.syme at gmail.com> wrote:

> Ditto
> On 15 Apr 2013 21:33, "Raoul Bonnal" <bonnal at ingm.org> wrote:
> 
>> i did it and I'm on.
>> On Apr 15, 2013, at 9:33 AM, Pjotr Prins <pjotr.public14 at thebird.nl>
>> wrote:
>> 
>>> Hi everyone,
>>> 
>>> You may have heard that OBF failed to get into GSoC this year. This is
>>> disappointing for us: it was not for lack of commitment and effort
>>> on our end.
>>> 
>>> The good news is that our main project ideas on machine learning, RDF
>>> and D3 support have been incorporated into the SciRuby GSoC org. If
>>> you consider participating in GSoC, either as a student or a mentor,
>>> please take a look:
>>> 
>>> 
>> https://github.com/SciRuby/sciruby/wiki/Google-Summer-of-Code-2013-Ideas
>>> 
>>> feedback is most welcome! Note: we may still change the project ideas.
>>> 
>>> Mentors: register as a mentor with SciRuby on
>>> 
>>> http://www.google-melange.com/gsoc/dashboard/google/gsoc2013
>>> 
>>> Pj.
>>> 
>>> On Sun, Mar 03, 2013 at 03:47:29PM +0100, Pjotr Prins wrote:
>>>> Game on! GSoC 2013 is ON. I am running with the OBF project
>>>> administration this year for the Google Summer of code (GSoC).
>>>> First and foremost I want to thank Robert Buels and others for making
>>>> OBF/GSoC a success in the previous three years! This year, Robert, Chris
>>>> Fields and Hilmar Lapp will act as backup administrators.
>>>> 
>>>> The deadline for the OBF application for GSoC2013 as a mentoring
>>>> organisation is Friday March 29! See
>>>> 
>>>> http://www.google-melange.com/gsoc/events/google/gsoc2013
>>>> 
>>>> Similar to previous years, each Bio* project needs to update and add
>> project
>>>> ideas on the project's individual OBF wiki page and create links from
>> the main
>>>> OBF page at
>>>> 
>>>> http://www.open-bio.org/wiki/Google_Summer_of_Code
>>>> 
>>>> (we will update the main information on that page soon).
>>>> 
>>>> So, for each of the OBF projects that wants to do GSoC again this
>>>> year:
>>>> 
>>>> 1. 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. For an example see
>>>> 
>>>>    http://bioruby.open-bio.org/wiki/Google_Summer_of_Code
>>>> 
>>>> 2. Update the final list of project ideas on the main OBF GSoC page
>>>>  to match.
>>>> 
>>>>    http://www.open-bio.org/wiki/Google_Summer_of_Code
>>>> 
>>>> 3. Register with gsoc at lists.open-bio.org
>>>> 
>>>> 4. Announce it on that list when you are ready :)
>>>> 
>>>> Anyone can submit a project idea! Former GSoC students are especially
>>>> encouraged to contribute ideas to the mailing lists.
>>>> 
>>>> Please have the updates done by Friday March 22nd. The number and
>> quality of
>>>> the project ideas are part of the evaluation process for whether OBF is
>>>> accepted as a Summer of Code organisation again this year, so let's
>> come up
>>>> with some good ones!
>>>> 
>>>> Pj. (Pjotr Prins)
>>>> 
>>>> Important dates:
>>>> 
>>>> * March 22nd: Finalise project ideas
>>>> * March 29th: Deadline OBF mentoring organisation submission to Google
>>>> 
>>>> http://www.open-bio.org/wiki/Google_Summer_of_Code
>>>> 
>>>> 
>>>> _______________________________________________
>>>> 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
>> 
>> 
>> 
>> _______________________________________________
>> BioRuby Project - http://www.bioruby.org/
>> BioRuby mailing list
>> BioRuby at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioruby
>> 
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby



From pjotr.public14 at thebird.nl  Wed Apr 17 12:34:31 2013
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Wed, 17 Apr 2013 18:34:31 +0200
Subject: [BioRuby] Coming Sunday BioRuby/biogems hacking!
Message-ID: <20130417163431.GA6826@thebird.nl>

Hi all,

Coming Sunday is BioRuby and biogems hacking day. Following the sun,
the Japanese and Australians will start, next the Dutch and Italians
and finally the Americans will work on fixing bugs and outstanding
issues. The bioruby IRC channel on freenode will be open for
discussions.

If you have any priorities right now, you can feed it to the mailing
list, or add github issues. On our end we want to update the biogem
tool and add some functionality to biogems.info.

Feel free to join the fun. Anyone want to add a country? ;)

Pj.

From pjotr.public14 at thebird.nl  Sat Apr 20 03:18:33 2013
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Sat, 20 Apr 2013 09:18:33 +0200
Subject: [BioRuby] Coming Sunday BioRuby/biogems hacking!
In-Reply-To: <20130417163431.GA6826@thebird.nl>
References: <20130417163431.GA6826@thebird.nl>
Message-ID: <20130420071833.GA19900@thebird.nl>

Reminder: tomorrow world wide Ruby hacking day!

On the agenda is fixing biogems: particularly fixing the biogem code
generator. Jeweler, apparently, is broken for Ruby2. A few patches may
fix it, or we move to creating our own templates on top of bundler. To
be decided.

Have a look at the issues list of biogems:

  https://github.com/helios/bioruby-gem/issues?state=open

and biogems.info:

  https://github.com/pjotrp/biogems.info/issues

see if anything strikes you are having priority for tomorrow. Or you
may offer to fix an issue yourself (how lucky can we be ;)

Everyone is encouraged to participate and work on owned gem(s).

We'll use the #bioruby IRC channel, and even move to Google hangout to
collaborate live.

Pj.

From pjotr.public14 at thebird.nl  Sun Apr 21 02:43:23 2013
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Sun, 21 Apr 2013 08:43:23 +0200
Subject: [BioRuby] Coming Sunday BioRuby/biogems hacking!
In-Reply-To: <20130417163431.GA6826@thebird.nl>
References: <20130417163431.GA6826@thebird.nl>
Message-ID: <20130421064323.GA23462@thebird.nl>

Game on!

http://irclog.perlgeek.de/bioruby/2013-04-21


From pjotr.public14 at thebird.nl  Sun Apr 21 12:07:01 2013
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Sun, 21 Apr 2013 18:07:01 +0200
Subject: [BioRuby] OBF Codefest Berlin July 17+18 2013
Message-ID: <20130421160701.GA27686@thebird.nl>

If you want to join the great annual OpenBio code fest:

  http://www.open-bio.org/wiki/Codefest_2013

please sign up - so you can get a seat!

Pj.

From p.j.a.cock at googlemail.com  Tue Apr  9 10:20:43 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Tue, 9 Apr 2013 11:20:43 +0100
Subject: [BioRuby] OBF not accepted for GSoC 2013
Message-ID: <CAKVJ-_6-+nyJk+7tp5YOyy7i7N7GtkRswZ_2Vs0uTuqGEV4wWQ@mail.gmail.com>

Dear all,

Unfortunately this year we have not been accepted on the Google
Summer of Code scheme:

I'm sure the rest of the OBF board and the other Bio* developers
will join me in thanking Pjotr Prins for his efforts as the OBF
GSoC administrator co-ordinating our application this year, as
well as last year's administrator Rob Bruels and the other mentors
for their efforts.

For those of you not subscribed to the OBF's GSoC mailing list,
I am forwarding Pjotr's email from last night (also below):
http://lists.open-bio.org/pipermail/gsoc/2013/000211.html

In all 177 organisations were accepted (about the same as the
last few years), and they will be listed here (once they have filled
out their profile information):
https://google-melange.appspot.com/gsoc/accepted_orgs/google/gsoc2013

To potential students this summer, the good news is that some
related organisations have been accepted, such as NESCent,
the National Resource for Network Biology (NRNB - known for
Cytoscape), SciRuby (Ruby Science Foundation), so there is
still some scope for doing a bioinformatics related project in
GSoC 2013, perhaps even with a Bio* developer as a co-mentor.

Thank you all,

Peter
(Biopython developer, OBF board member)

---------- Forwarded message ----------
From: Pjotr Prins <pjotr2010 at thebird.nl>
Date: Mon, Apr 8, 2013 at 9:13 PM
Subject: Re: GSoC 2013 is ON
To: Pjotr Prins <pjotr2010 at thebird.nl>
Cc: ..., OBF GSoC <gsoc at lists.open-bio.org>


Sadly, our application got rejected by GSoC this year. I am not sure
what the reason was, but I am convinced our application was similar to
that of other years. Maybe the project ideas could have been better
presented. I am not sure at this stage. I'll make a list of successful
projects to see if we can digest some truths.

The upside is that FOSS is going strong! And that the field is getting
increasingly competitive. As an open source geezer I can only be
happy, even if it hurts our own application.

Sorry everyone, and many thanks for the trouble you took getting
projects written up. Let's not feel discouraged for next year.

Pj.


From k at bioruby.org  Wed Apr 10 10:16:54 2013
From: k at bioruby.org (Toshiaki Katayama)
Date: Wed, 10 Apr 2013 19:16:54 +0900
Subject: [BioRuby] BOSC 2013 plan
Message-ID: <2949FBC3-25B5-4823-806D-F55DDF8629A2@bioruby.org>

Dear all,

It was unfortunate that OBF could not get approval of GSoC for this year.

By the way, the BOSC abstracts due is quickly approaching (Apr 12).

  http://www.open-bio.org/wiki/BOSC_2013

Does anybody plan to give a short talk on the BioRuby project update?

Cheers,
Toshiaki


From y.wurm at qmul.ac.uk  Wed Apr 10 09:34:38 2013
From: y.wurm at qmul.ac.uk (Yannick Wurm)
Date: Wed, 10 Apr 2013 10:34:38 +0100
Subject: [BioRuby] BioRuby Digest, Vol 90, Issue 1
In-Reply-To: <mailman.25.1365523207.6688.bioruby@lists.open-bio.org>
References: <mailman.25.1365523207.6688.bioruby@lists.open-bio.org>
Message-ID: <C888EA07-C8C8-4638-A731-F46D0D746595@qmul.ac.uk>

Dang that sucks I'm sorry :(

THnaks guys for putting in all the effort to put this together. 

A while ago I saw that LyX had "feature-specific donation buttons" (and ended up donating towards OSX support I think). This was before Crowdfounding stuff like kickstarter became popular. 

I wonder if a similar system  could create an alternative means of geting cash for getting manpower to get things done for bioruby. Just throwing the idea out there. 

Cheers
yannick

ps: it was http://www.lyx.org/Donate but they currently have no "requesting" projects. 



On 9 Apr 2013, at 17:00, bioruby-request at lists.open-bio.org wrote:

> Unfortunately this year we have not been accepted on the Google
> Summer of Code scheme




From ngoto at gen-info.osaka-u.ac.jp  Thu Apr 11 15:48:00 2013
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Fri, 12 Apr 2013 00:48:00 +0900
Subject: [BioRuby] Removal of Bio::DDBJ::XML,
 Bio::DDBJ::REST because of DDBJ web service reconstruction
Message-ID: <201304111554.r3BFs5ow002272@portal.open-bio.org>

Hi all,

Bio::DDBJ::XML and Bio::DDBJ::REST are the classes accessing
DDBJ Web API (WABI) web services. Since March 2012, the WABI
have been suspended because of the replacement of DDBJ computer
system. I've heard from some DDBJ people that it is now under
reconstruction and it will be completely renewed with new
improved API. So, I think the two classes are now useless and
are going to be removed.

After the new DDBJ Web API is released, new API client classes
will be written.

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


From pjotr.public14 at thebird.nl  Mon Apr 15 07:33:15 2013
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Mon, 15 Apr 2013 09:33:15 +0200
Subject: [BioRuby] GSoC 2013 is ON
In-Reply-To: <20130303144729.GE6566@thebird.nl>
References: <20130303144729.GE6566@thebird.nl>
Message-ID: <20130415073315.GA22590@thebird.nl>

Hi everyone,

You may have heard that OBF failed to get into GSoC this year. This is
disappointing for us: it was not for lack of commitment and effort
on our end.

The good news is that our main project ideas on machine learning, RDF
and D3 support have been incorporated into the SciRuby GSoC org. If
you consider participating in GSoC, either as a student or a mentor,
please take a look:

  https://github.com/SciRuby/sciruby/wiki/Google-Summer-of-Code-2013-Ideas

feedback is most welcome! Note: we may still change the project ideas.

Mentors: register as a mentor with SciRuby on

  http://www.google-melange.com/gsoc/dashboard/google/gsoc2013

Pj.

On Sun, Mar 03, 2013 at 03:47:29PM +0100, Pjotr Prins wrote:
> Game on! GSoC 2013 is ON. I am running with the OBF project
> administration this year for the Google Summer of code (GSoC). 
> First and foremost I want to thank Robert Buels and others for making
> OBF/GSoC a success in the previous three years! This year, Robert, Chris
> Fields and Hilmar Lapp will act as backup administrators.
> 
> The deadline for the OBF application for GSoC2013 as a mentoring
> organisation is Friday March 29! See
> 
>   http://www.google-melange.com/gsoc/events/google/gsoc2013
> 
> Similar to previous years, each Bio* project needs to update and add project
> ideas on the project's individual OBF wiki page and create links from the main
> OBF page at
> 
>   http://www.open-bio.org/wiki/Google_Summer_of_Code
> 
> (we will update the main information on that page soon).
> 
> So, for each of the OBF projects that wants to do GSoC again this
> year:
> 
> 1. 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. For an example see
> 
>      http://bioruby.open-bio.org/wiki/Google_Summer_of_Code
> 
> 2. Update the final list of project ideas on the main OBF GSoC page
>    to match.
> 
>      http://www.open-bio.org/wiki/Google_Summer_of_Code
> 
> 3. Register with gsoc at lists.open-bio.org
> 
> 4. Announce it on that list when you are ready :)
> 
> Anyone can submit a project idea! Former GSoC students are especially
> encouraged to contribute ideas to the mailing lists.
> 
> Please have the updates done by Friday March 22nd. The number and quality of
> the project ideas are part of the evaluation process for whether OBF is
> accepted as a Summer of Code organisation again this year, so let's come up
> with some good ones!
> 
> Pj. (Pjotr Prins)
> 
> Important dates: 
> 
>   * March 22nd: Finalise project ideas
>   * March 29th: Deadline OBF mentoring organisation submission to Google
> 
> http://www.open-bio.org/wiki/Google_Summer_of_Code
> 
> 
> _______________________________________________
> 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  Mon Apr 15 07:36:31 2013
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Mon, 15 Apr 2013 09:36:31 +0200
Subject: [BioRuby] GSoC 2013 is ON
In-Reply-To: <20130415073315.GA22590@thebird.nl>
References: <20130303144729.GE6566@thebird.nl>
	<20130415073315.GA22590@thebird.nl>
Message-ID: <20130415073631.GA22630@thebird.nl>

> Mentors: register as a mentor with SciRuby on
> 
>   http://www.google-melange.com/gsoc/dashboard/google/gsoc2013

should be 'click the apply button' on 

  https://google-melange.appspot.com/gsoc/homepage/google/gsoc2013


From pjotr.public14 at thebird.nl  Mon Apr 15 07:58:36 2013
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Mon, 15 Apr 2013 09:58:36 +0200
Subject: [BioRuby] Matz
Message-ID: <20130415075836.GA22684@thebird.nl>

http://fredwu.me/post/36493181321/an-interview-with-yukihiro-matz-matsumoto


From bonnal at ingm.org  Mon Apr 15 13:16:35 2013
From: bonnal at ingm.org (Raoul Bonnal)
Date: Mon, 15 Apr 2013 15:16:35 +0200
Subject: [BioRuby] GSoC 2013 is ON
In-Reply-To: <20130415073315.GA22590@thebird.nl>
References: <20130303144729.GE6566@thebird.nl>
	<20130415073315.GA22590@thebird.nl>
Message-ID: <03357A93-F516-4727-9A78-7A4481932E39@ingm.org>

i did it and I'm on.
On Apr 15, 2013, at 9:33 AM, Pjotr Prins <pjotr.public14 at thebird.nl> wrote:

> Hi everyone,
> 
> You may have heard that OBF failed to get into GSoC this year. This is
> disappointing for us: it was not for lack of commitment and effort
> on our end.
> 
> The good news is that our main project ideas on machine learning, RDF
> and D3 support have been incorporated into the SciRuby GSoC org. If
> you consider participating in GSoC, either as a student or a mentor,
> please take a look:
> 
>  https://github.com/SciRuby/sciruby/wiki/Google-Summer-of-Code-2013-Ideas
> 
> feedback is most welcome! Note: we may still change the project ideas.
> 
> Mentors: register as a mentor with SciRuby on
> 
>  http://www.google-melange.com/gsoc/dashboard/google/gsoc2013
> 
> Pj.
> 
> On Sun, Mar 03, 2013 at 03:47:29PM +0100, Pjotr Prins wrote:
>> Game on! GSoC 2013 is ON. I am running with the OBF project
>> administration this year for the Google Summer of code (GSoC). 
>> First and foremost I want to thank Robert Buels and others for making
>> OBF/GSoC a success in the previous three years! This year, Robert, Chris
>> Fields and Hilmar Lapp will act as backup administrators.
>> 
>> The deadline for the OBF application for GSoC2013 as a mentoring
>> organisation is Friday March 29! See
>> 
>>  http://www.google-melange.com/gsoc/events/google/gsoc2013
>> 
>> Similar to previous years, each Bio* project needs to update and add project
>> ideas on the project's individual OBF wiki page and create links from the main
>> OBF page at
>> 
>>  http://www.open-bio.org/wiki/Google_Summer_of_Code
>> 
>> (we will update the main information on that page soon).
>> 
>> So, for each of the OBF projects that wants to do GSoC again this
>> year:
>> 
>> 1. 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. For an example see
>> 
>>     http://bioruby.open-bio.org/wiki/Google_Summer_of_Code
>> 
>> 2. Update the final list of project ideas on the main OBF GSoC page
>>   to match.
>> 
>>     http://www.open-bio.org/wiki/Google_Summer_of_Code
>> 
>> 3. Register with gsoc at lists.open-bio.org
>> 
>> 4. Announce it on that list when you are ready :)
>> 
>> Anyone can submit a project idea! Former GSoC students are especially
>> encouraged to contribute ideas to the mailing lists.
>> 
>> Please have the updates done by Friday March 22nd. The number and quality of
>> the project ideas are part of the evaluation process for whether OBF is
>> accepted as a Summer of Code organisation again this year, so let's come up
>> with some good ones!
>> 
>> Pj. (Pjotr Prins)
>> 
>> Important dates: 
>> 
>>  * March 22nd: Finalise project ideas
>>  * March 29th: Deadline OBF mentoring organisation submission to Google
>> 
>> http://www.open-bio.org/wiki/Google_Summer_of_Code
>> 
>> 
>> _______________________________________________
>> 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 rob.syme at gmail.com  Mon Apr 15 13:33:58 2013
From: rob.syme at gmail.com (Rob Syme)
Date: Mon, 15 Apr 2013 21:33:58 +0800
Subject: [BioRuby] GSoC 2013 is ON
In-Reply-To: <03357A93-F516-4727-9A78-7A4481932E39@ingm.org>
References: <20130303144729.GE6566@thebird.nl>
	<20130415073315.GA22590@thebird.nl>
	<03357A93-F516-4727-9A78-7A4481932E39@ingm.org>
Message-ID: <CAEf4xgejPDVqcxWHVfygNhVKOe1OEin++w8gF6i2-kjjLhJOTA@mail.gmail.com>

Ditto
On 15 Apr 2013 21:33, "Raoul Bonnal" <bonnal at ingm.org> wrote:

> i did it and I'm on.
> On Apr 15, 2013, at 9:33 AM, Pjotr Prins <pjotr.public14 at thebird.nl>
> wrote:
>
> > Hi everyone,
> >
> > You may have heard that OBF failed to get into GSoC this year. This is
> > disappointing for us: it was not for lack of commitment and effort
> > on our end.
> >
> > The good news is that our main project ideas on machine learning, RDF
> > and D3 support have been incorporated into the SciRuby GSoC org. If
> > you consider participating in GSoC, either as a student or a mentor,
> > please take a look:
> >
> >
> https://github.com/SciRuby/sciruby/wiki/Google-Summer-of-Code-2013-Ideas
> >
> > feedback is most welcome! Note: we may still change the project ideas.
> >
> > Mentors: register as a mentor with SciRuby on
> >
> >  http://www.google-melange.com/gsoc/dashboard/google/gsoc2013
> >
> > Pj.
> >
> > On Sun, Mar 03, 2013 at 03:47:29PM +0100, Pjotr Prins wrote:
> >> Game on! GSoC 2013 is ON. I am running with the OBF project
> >> administration this year for the Google Summer of code (GSoC).
> >> First and foremost I want to thank Robert Buels and others for making
> >> OBF/GSoC a success in the previous three years! This year, Robert, Chris
> >> Fields and Hilmar Lapp will act as backup administrators.
> >>
> >> The deadline for the OBF application for GSoC2013 as a mentoring
> >> organisation is Friday March 29! See
> >>
> >>  http://www.google-melange.com/gsoc/events/google/gsoc2013
> >>
> >> Similar to previous years, each Bio* project needs to update and add
> project
> >> ideas on the project's individual OBF wiki page and create links from
> the main
> >> OBF page at
> >>
> >>  http://www.open-bio.org/wiki/Google_Summer_of_Code
> >>
> >> (we will update the main information on that page soon).
> >>
> >> So, for each of the OBF projects that wants to do GSoC again this
> >> year:
> >>
> >> 1. 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. For an example see
> >>
> >>     http://bioruby.open-bio.org/wiki/Google_Summer_of_Code
> >>
> >> 2. Update the final list of project ideas on the main OBF GSoC page
> >>   to match.
> >>
> >>     http://www.open-bio.org/wiki/Google_Summer_of_Code
> >>
> >> 3. Register with gsoc at lists.open-bio.org
> >>
> >> 4. Announce it on that list when you are ready :)
> >>
> >> Anyone can submit a project idea! Former GSoC students are especially
> >> encouraged to contribute ideas to the mailing lists.
> >>
> >> Please have the updates done by Friday March 22nd. The number and
> quality of
> >> the project ideas are part of the evaluation process for whether OBF is
> >> accepted as a Summer of Code organisation again this year, so let's
> come up
> >> with some good ones!
> >>
> >> Pj. (Pjotr Prins)
> >>
> >> Important dates:
> >>
> >>  * March 22nd: Finalise project ideas
> >>  * March 29th: Deadline OBF mentoring organisation submission to Google
> >>
> >> http://www.open-bio.org/wiki/Google_Summer_of_Code
> >>
> >>
> >> _______________________________________________
> >> 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
>
>
>
> _______________________________________________
> 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  Mon Apr 15 17:54:05 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 15 Apr 2013 17:54:05 +0000
Subject: [BioRuby] GSoC 2013 is ON
In-Reply-To: <CAEf4xgejPDVqcxWHVfygNhVKOe1OEin++w8gF6i2-kjjLhJOTA@mail.gmail.com>
References: <20130303144729.GE6566@thebird.nl>
	<20130415073315.GA22590@thebird.nl>
	<03357A93-F516-4727-9A78-7A4481932E39@ingm.org>
	<CAEf4xgejPDVqcxWHVfygNhVKOe1OEin++w8gF6i2-kjjLhJOTA@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DDFE64@CHIMBX5.ad.uillinois.edu>

Good to hear that Bioruby and Biopython have managed to get things going elsewhere!

chris

On Apr 15, 2013, at 8:33 AM, Rob Syme <rob.syme at gmail.com> wrote:

> Ditto
> On 15 Apr 2013 21:33, "Raoul Bonnal" <bonnal at ingm.org> wrote:
> 
>> i did it and I'm on.
>> On Apr 15, 2013, at 9:33 AM, Pjotr Prins <pjotr.public14 at thebird.nl>
>> wrote:
>> 
>>> Hi everyone,
>>> 
>>> You may have heard that OBF failed to get into GSoC this year. This is
>>> disappointing for us: it was not for lack of commitment and effort
>>> on our end.
>>> 
>>> The good news is that our main project ideas on machine learning, RDF
>>> and D3 support have been incorporated into the SciRuby GSoC org. If
>>> you consider participating in GSoC, either as a student or a mentor,
>>> please take a look:
>>> 
>>> 
>> https://github.com/SciRuby/sciruby/wiki/Google-Summer-of-Code-2013-Ideas
>>> 
>>> feedback is most welcome! Note: we may still change the project ideas.
>>> 
>>> Mentors: register as a mentor with SciRuby on
>>> 
>>> http://www.google-melange.com/gsoc/dashboard/google/gsoc2013
>>> 
>>> Pj.
>>> 
>>> On Sun, Mar 03, 2013 at 03:47:29PM +0100, Pjotr Prins wrote:
>>>> Game on! GSoC 2013 is ON. I am running with the OBF project
>>>> administration this year for the Google Summer of code (GSoC).
>>>> First and foremost I want to thank Robert Buels and others for making
>>>> OBF/GSoC a success in the previous three years! This year, Robert, Chris
>>>> Fields and Hilmar Lapp will act as backup administrators.
>>>> 
>>>> The deadline for the OBF application for GSoC2013 as a mentoring
>>>> organisation is Friday March 29! See
>>>> 
>>>> http://www.google-melange.com/gsoc/events/google/gsoc2013
>>>> 
>>>> Similar to previous years, each Bio* project needs to update and add
>> project
>>>> ideas on the project's individual OBF wiki page and create links from
>> the main
>>>> OBF page at
>>>> 
>>>> http://www.open-bio.org/wiki/Google_Summer_of_Code
>>>> 
>>>> (we will update the main information on that page soon).
>>>> 
>>>> So, for each of the OBF projects that wants to do GSoC again this
>>>> year:
>>>> 
>>>> 1. 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. For an example see
>>>> 
>>>>    http://bioruby.open-bio.org/wiki/Google_Summer_of_Code
>>>> 
>>>> 2. Update the final list of project ideas on the main OBF GSoC page
>>>>  to match.
>>>> 
>>>>    http://www.open-bio.org/wiki/Google_Summer_of_Code
>>>> 
>>>> 3. Register with gsoc at lists.open-bio.org
>>>> 
>>>> 4. Announce it on that list when you are ready :)
>>>> 
>>>> Anyone can submit a project idea! Former GSoC students are especially
>>>> encouraged to contribute ideas to the mailing lists.
>>>> 
>>>> Please have the updates done by Friday March 22nd. The number and
>> quality of
>>>> the project ideas are part of the evaluation process for whether OBF is
>>>> accepted as a Summer of Code organisation again this year, so let's
>> come up
>>>> with some good ones!
>>>> 
>>>> Pj. (Pjotr Prins)
>>>> 
>>>> Important dates:
>>>> 
>>>> * March 22nd: Finalise project ideas
>>>> * March 29th: Deadline OBF mentoring organisation submission to Google
>>>> 
>>>> http://www.open-bio.org/wiki/Google_Summer_of_Code
>>>> 
>>>> 
>>>> _______________________________________________
>>>> 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
>> 
>> 
>> 
>> _______________________________________________
>> BioRuby Project - http://www.bioruby.org/
>> BioRuby mailing list
>> BioRuby at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioruby
>> 
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby




From pjotr.public14 at thebird.nl  Wed Apr 17 16:34:31 2013
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Wed, 17 Apr 2013 18:34:31 +0200
Subject: [BioRuby] Coming Sunday BioRuby/biogems hacking!
Message-ID: <20130417163431.GA6826@thebird.nl>

Hi all,

Coming Sunday is BioRuby and biogems hacking day. Following the sun,
the Japanese and Australians will start, next the Dutch and Italians
and finally the Americans will work on fixing bugs and outstanding
issues. The bioruby IRC channel on freenode will be open for
discussions.

If you have any priorities right now, you can feed it to the mailing
list, or add github issues. On our end we want to update the biogem
tool and add some functionality to biogems.info.

Feel free to join the fun. Anyone want to add a country? ;)

Pj.


From pjotr.public14 at thebird.nl  Sat Apr 20 07:18:33 2013
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Sat, 20 Apr 2013 09:18:33 +0200
Subject: [BioRuby] Coming Sunday BioRuby/biogems hacking!
In-Reply-To: <20130417163431.GA6826@thebird.nl>
References: <20130417163431.GA6826@thebird.nl>
Message-ID: <20130420071833.GA19900@thebird.nl>

Reminder: tomorrow world wide Ruby hacking day!

On the agenda is fixing biogems: particularly fixing the biogem code
generator. Jeweler, apparently, is broken for Ruby2. A few patches may
fix it, or we move to creating our own templates on top of bundler. To
be decided.

Have a look at the issues list of biogems:

  https://github.com/helios/bioruby-gem/issues?state=open

and biogems.info:

  https://github.com/pjotrp/biogems.info/issues

see if anything strikes you are having priority for tomorrow. Or you
may offer to fix an issue yourself (how lucky can we be ;)

Everyone is encouraged to participate and work on owned gem(s).

We'll use the #bioruby IRC channel, and even move to Google hangout to
collaborate live.

Pj.


From pjotr.public14 at thebird.nl  Sun Apr 21 06:43:23 2013
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Sun, 21 Apr 2013 08:43:23 +0200
Subject: [BioRuby] Coming Sunday BioRuby/biogems hacking!
In-Reply-To: <20130417163431.GA6826@thebird.nl>
References: <20130417163431.GA6826@thebird.nl>
Message-ID: <20130421064323.GA23462@thebird.nl>

Game on!

http://irclog.perlgeek.de/bioruby/2013-04-21



From pjotr.public14 at thebird.nl  Sun Apr 21 16:07:01 2013
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Sun, 21 Apr 2013 18:07:01 +0200
Subject: [BioRuby] OBF Codefest Berlin July 17+18 2013
Message-ID: <20130421160701.GA27686@thebird.nl>

If you want to join the great annual OpenBio code fest:

  http://www.open-bio.org/wiki/Codefest_2013

please sign up - so you can get a seat!

Pj.