From p.j.a.cock at googlemail.com  Mon Feb 11 14:08:13 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 11 Feb 2013 19:08:13 +0000
Subject: [GSoC] [GSoC Mentors Announce] Google Summer of Code 2013
In-Reply-To: <CAEkQO61xzGb19SYi2wUVpA8Pe5XHzo+cR6S-9PeyoW_DOfc7JQ@mail.gmail.com>
References: <CAEkQO61xzGb19SYi2wUVpA8Pe5XHzo+cR6S-9PeyoW_DOfc7JQ@mail.gmail.com>
Message-ID: <CAKVJ-_56b+oxyAH-PYXTwSDT_KJ5y5tv0AjOEBntuNKsJA_qLw@mail.gmail.com>

Good news everyone, GSoC 2013 is happening :)

Hopefully the OBF will be accepted to take part once again.

Peter

On Mon, Feb 11, 2013 at 7:02 PM, Carol Smith <carols at google.com> wrote:
> Hi GSoC mentors and org admins,
>
> We've announced that we're doing Google Summer of Code 2013 [1]. Yay!
>
> If you would like to help spread the word about GSoC, we have presentations
> [2], logos [3], and flyers [4] for you to use. Please host meetups, tell
> your friends and colleagues about the program, go to conferences, talk to
> people about the program, and just generally do all the awesome
> word-of-mouth stuff you do every year to promote the program.
>
> The GSoC calendar, FAQ, and events timeline have all been updated with this
> year's important dates, so please refer to those for the milestones for this
> year's program. NB: the normal timeline for the program has been modified
> for this year. You'll probably want to examine the dates closely to make
> sure you know when important things are happening.
>
> Please consider translating the presentations and/or flyers into your native
> language and submitting them directly to me to post on the wiki.
> Localization for our material is integral to reaching the widest possible
> audience around the world. If you decide to translate a flyer, please fill
> out our form to request a thank you gift for your effort. [5]
>
> If you decide to host a meetup, please email me to let me know the date,
> time, and location so I can put it on the GSoC calendar. Also, remember to
> take pictures at your meetup and write up a blog post for our blog using our
> provided template for formatting [6]. If you need promotional items for your
> attendees, please fill out our form [7] to request some; we're happy to send
> some along. We can provide up to about 25 pens, notebooks, or stickers
> and/or a few t-shirts. Please keep in mind, though, that shipping
> restrictions and timeline vary country-to-country; request items early to
> make sure they get there on time! If you have questions about hosting
> meetups, please see the section in our FAQ [8].
>
> Please also consider applying to participate as an organization again this
> year or maybe joining as a mentor for your favorite organization if they are
> selected this year.
>
> We rely on you for your help for the success of this program, so thank you
> in advance for all the work you do!
>
> [1] -
> http://google-opensource.blogspot.com/2013/02/flip-bits-not-burgers-google-summer-of.html
> [2] -
> http://code.google.com/p/google-summer-of-code/wiki/ProgramPresentations
> [3] - http://code.google.com/p/google-summer-of-code/wiki/GsocLogos
> [4] - http://code.google.com/p/google-summer-of-code/wiki/GsocFlyers
> [5] - http://goo.gl/gEHDO
> [6] - http://goo.gl/wbZrt
> [7] - http://goo.gl/0BsR8
> [8] - http://goo.gl/2NGfp
>
> Cheers,
> Carol
>
> --
> You received this message because you are subscribed to the Google Groups
> "Google Summer of Code Mentors Announce List" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to gsoc-mentors-announce+unsubscribe at googlegroups.com.
> Visit this group at
> http://groups.google.com/group/gsoc-mentors-announce?hl=en-US.
> For more options, visit https://groups.google.com/groups/opt_out.
>
>

From rbuels at gmail.com  Mon Feb 11 14:14:39 2013
From: rbuels at gmail.com (Robert Buels)
Date: Mon, 11 Feb 2013 14:14:39 -0500
Subject: [GSoC] [GSoC Mentors Announce] Google Summer of Code 2013
In-Reply-To: <CAKVJ-_56b+oxyAH-PYXTwSDT_KJ5y5tv0AjOEBntuNKsJA_qLw@mail.gmail.com>
References: <CAEkQO61xzGb19SYi2wUVpA8Pe5XHzo+cR6S-9PeyoW_DOfc7JQ@mail.gmail.com>
	<CAKVJ-_56b+oxyAH-PYXTwSDT_KJ5y5tv0AjOEBntuNKsJA_qLw@mail.gmail.com>
Message-ID: <5119431F.90100@gmail.com>

Hurray!

Would someone else be interested in being the org admin for OBF this 
year?  Preferably someone who's been an OBF mentor in one of the 
previous years?  I've got a lot of things on my plate.

If someone else will be the primary, I can certainly volunteer as a backup.

Rob



On 02/11/2013 02:08 PM, Peter Cock wrote:
> Good news everyone, GSoC 2013 is happening :)
>
> Hopefully the OBF will be accepted to take part once again.
>
> Peter
>
> On Mon, Feb 11, 2013 at 7:02 PM, Carol Smith <carols at google.com> wrote:
>> Hi GSoC mentors and org admins,
>>
>> We've announced that we're doing Google Summer of Code 2013 [1]. Yay!
>>
>> If you would like to help spread the word about GSoC, we have presentations
>> [2], logos [3], and flyers [4] for you to use. Please host meetups, tell
>> your friends and colleagues about the program, go to conferences, talk to
>> people about the program, and just generally do all the awesome
>> word-of-mouth stuff you do every year to promote the program.
>>
>> The GSoC calendar, FAQ, and events timeline have all been updated with this
>> year's important dates, so please refer to those for the milestones for this
>> year's program. NB: the normal timeline for the program has been modified
>> for this year. You'll probably want to examine the dates closely to make
>> sure you know when important things are happening.
>>
>> Please consider translating the presentations and/or flyers into your native
>> language and submitting them directly to me to post on the wiki.
>> Localization for our material is integral to reaching the widest possible
>> audience around the world. If you decide to translate a flyer, please fill
>> out our form to request a thank you gift for your effort. [5]
>>
>> If you decide to host a meetup, please email me to let me know the date,
>> time, and location so I can put it on the GSoC calendar. Also, remember to
>> take pictures at your meetup and write up a blog post for our blog using our
>> provided template for formatting [6]. If you need promotional items for your
>> attendees, please fill out our form [7] to request some; we're happy to send
>> some along. We can provide up to about 25 pens, notebooks, or stickers
>> and/or a few t-shirts. Please keep in mind, though, that shipping
>> restrictions and timeline vary country-to-country; request items early to
>> make sure they get there on time! If you have questions about hosting
>> meetups, please see the section in our FAQ [8].
>>
>> Please also consider applying to participate as an organization again this
>> year or maybe joining as a mentor for your favorite organization if they are
>> selected this year.
>>
>> We rely on you for your help for the success of this program, so thank you
>> in advance for all the work you do!
>>
>> [1] -
>> http://google-opensource.blogspot.com/2013/02/flip-bits-not-burgers-google-summer-of.html
>> [2] -
>> http://code.google.com/p/google-summer-of-code/wiki/ProgramPresentations
>> [3] - http://code.google.com/p/google-summer-of-code/wiki/GsocLogos
>> [4] - http://code.google.com/p/google-summer-of-code/wiki/GsocFlyers
>> [5] - http://goo.gl/gEHDO
>> [6] - http://goo.gl/wbZrt
>> [7] - http://goo.gl/0BsR8
>> [8] - http://goo.gl/2NGfp
>>
>> Cheers,
>> Carol
>>
>> --
>> You received this message because you are subscribed to the Google Groups
>> "Google Summer of Code Mentors Announce List" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to gsoc-mentors-announce+unsubscribe at googlegroups.com.
>> Visit this group at
>> http://groups.google.com/group/gsoc-mentors-announce?hl=en-US.
>> For more options, visit https://groups.google.com/groups/opt_out.
>>
>>
> _______________________________________________
> GSoC mailing list
> GSoC at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/gsoc
>

From hlapp at drycafe.net  Sun Feb 24 11:57:56 2013
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Sun, 24 Feb 2013 11:57:56 -0500
Subject: [GSoC] Fwd: Standardizing Organizations Keywords
References: <CA+3KvkN52yb0qrf8Y4U9EQRNxM1N3kbjhWgjY8h_68aO19oVYw@mail.gmail.com>
Message-ID: <87B7DB03-0F1F-4B8D-9314-8210B27553A5@drycafe.net>

Any other suggestions for adding/fixing DBpedia (= Wikipedia articles) keywords for OBF, or literal string keywords? I'd be happy to add suggestions before I issue a pull request. Alternatively, everyone is of course welcome to fork their own copy and submit a change request.

https://github.com/hlapp/dbpedia-spotlight-gsoc/compare/master...obf-fixes

	-hilmar

Begin forwarded message:

> From: "Pablo N. Mendes" <pablomendes at gmail.com>
> Subject: Re: [GSoC Mentors] Re: Standardizing Organizations Keywords
> Date: February 22, 2013 1:53:11 PM EST
> To: Joel Sherrill <joel.sherrill at gmail.com>
> Cc: Stefan Seefeld <stefan at codesourcery.com>, google-summer-of-code-mentors-list at googlegroups.com, Max Jakob <max.jakob at gmail.com>, Joachim Daiber <daiber.joachim at gmail.com>
> 
> 
> Thanks for the feedback Joel. TL;DR: If the community is interested, we can regenerate better tags and you all can contribute with the necessary fixes/additions.
> 
> As this thread may quickly become unwelcome here, let's move the discussion to our issue tracker?
> https://github.com/pablomendes/dbpedia-spotlight-gsoc/issues
> 
> Now the longer message, answering your questions:
> 
> how could a set of keywords be checked automatically and then the organization admin choose to use them or not.
> 
> Easy! That perks of being among Open Source folks, right? I pointed out in my earlier e-mail the files that our system created automatically [1][2]. All you need to do is to git clone our repo, make the fixes in any text editor and submit a pull request on GitHub. I think it was Jim from Apertium that has already done this for some orgs. We'd be glad to merge the fixes and update our engine.
> 
> But I don't know how to make your engine happy. 
> 
> I can try to help you to understand what is happening there. But first I need to find out which org is yours. After some searching, I figured it must be RTEMS? If not, just let me know. But these are the tags that we have for RTEMS for 2011:
> 
> <http://dbpedia.org/resource/Thread_%28computer_science%29> .
> <http://dbpedia.org/resource/Embedded_system> .
> <http://dbpedia.org/resource/Shapeshifter_%28band%29> .
> <http://dbpedia.org/resource/C%2B%2B> .
> <http://dbpedia.org/resource/POSIX> .
> <http://dbpedia.org/resource/Ada_%28programming_language%29> .
> <http://dbpedia.org/resource/Operating_system>
> 
> Clearly some wrong ones, but also some good ones. So searching for Operating System should definitely have retrieved something. I think that I only loaded the 2012 tags. For 2012, I have no tags for your project at all. This is probably because an error happened in our crawler when processing your page, and we missed those tags. We seem to be able to process it now, as you can see here:
> http://spotlight.dbpedia.org/rest/annotate?url=http://www.rtems.org/wiki/index.php/Open_Projects
> 
> Even better, our new code (result of Jo Daiber's work from GSoC 2012) seems to perform much better:
> http://spotlight.sztaki.hu:2222/rest/annotate?url=http://www.rtems.org/wiki/index.php/Open_Projects
> 
> We can regenerate the tags and have the community helping with some cleanup/additions for their orgs, if anybody is interested.
> 
> Cheers,
> Pablo
> 
> [1] https://raw.github.com/pablomendes/dbpedia-spotlight-gsoc/master/data/gsoc-projects-2011.nt
> [2] https://raw.github.com/pablomendes/dbpedia-spotlight-gsoc/master/data/gsoc-projects-2012.nt
> 
> 
> On Fri, Feb 22, 2013 at 5:08 PM, Joel Sherrill <joel.sherrill at gmail.com> wrote:
> This is very cool!!!  
> 
> It certainly provides more information about the tags but it still suffers from issues like
> me not putting commas between the tags which results gibberish instead of a set
> of Wikipedia pages, various forms of "big data", and strange or useless tags. [1]
> 
> But as a rule, if your tag doesn't match something related at Wikipedia, then 
> it very likely isn't a useful tag. That's a pretty good rule.
> 
> But I don't know how to make your engine happy. Using your search page, I 
> couldn't even find my own project even though we were in both projects. When I
> typed "operating system", I missed a most OS GSOC participants. And when
> I got RTOS, I only got a few closed source products.
> 
> it is too late for 2013, but how could a set of keywords be checked automatically
> and then the organization admin choose to use them or not.
> 
> --joel
> RTEMS
> 
> [1] I am personally interested in the "Awesome_God" project. :)
> 
> On Fri, Feb 22, 2013 at 2:53 AM, Pablo N. Mendes <pablomendes at gmail.com> wrote:
> 
> Well, what about just using Wikipedia pages as topics? All major languages, algorithms, techniques, technologies, etc. are there already. That is the idea of the DBpedia project: use each Wikipedia page as describing a "thing", and subsequently classify these things according to a taxonomy. I don't see why we would need to repeat that work.
> 
> Moreover, our tool (DBpedia Spotlight) has the ability to churn through your "project ideas" pages and suggest DBpedia "tags" based on the content of those pages. Since this information extraction process is automated and tackles a difficult problem, the tool makes mistakes. But, no problem, updating this list should be less work than just creating a taxonomy from scratch and then tagging each project manually.
> 
> By provocation from Jimmy O'Reagan, I sit down together with Max Jakob and hacked something together. Here are the tags that we have extracted for 2011 and 2012 projects:
> https://github.com/pablomendes/dbpedia-spotlight-gsoc/tree/master/data
> 
> We later sit down with Jo Daiber and also prettied up a little search application to help users to find projects and to demonstrate what other advantages you may gain by using DBpedia tags rather than just plain old "string" tags.
> http://spotlight.dbpedia.org/gsoc-searcher/
> 
> The function described there as "Expand" uses some knowledge that we have about the tags to try and model "relatedness", so that we can suggest extra related tags for the students to search.
> 
> Everything was hacked together quickly, so it is still very preliminary. But I think it demonstrates the core ideas, if you are open minded. :)
> 
> What do you think?
> 
> Cheers,
> Pablo
> 
> 
> On Wed, Feb 20, 2013 at 9:59 PM, Stefan Seefeld <stefan at codesourcery.com> wrote:
> On 02/20/2013 03:46 PM, Aaron Meurer wrote:
> > An ideal situation would be if there were some kind of StackOverflow
> > type system where keywords autocompleted against what has already been
> > used, and synonyms could be defined. I don't know if the Melange team
> > has the desire and/or resources to do something like this.
> 
> Indeed, a shared taxonomy would help greatly. And there are a few
> precedents used in the FLOSS world to pick from, such as:
> https://pypi.python.org/pypi?%3Aaction=list_classifiers
> 
> I still struggle understanding why the GSoC (meta-)project needed its
> own web application. It could have picked one with such features already
> in place.
> 
> But that's a separate discussion.
> 
>         Stefan
> 
> --
> Stefan Seefeld
> stefan at codesourcery.com
> 
> 
> 
> -- 
> 
> Pablo N. Mendes
> http://pablomendes.com
> 
> -- 
> You received this message because you are subscribed to the Google Groups "Google Summer of Code Mentors List" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to google-summer-of-code-mentors-list+unsubscribe at googlegroups.com.
> To post to this group, send email to google-summer-of-code-mentors-list at googlegroups.com.
> Visit this group at http://groups.google.com/group/google-summer-of-code-mentors-list?hl=en-US.
> For more options, visit https://groups.google.com/groups/opt_out.
>  
>  
> 
> 
> 
> 
> -- 
> 
> Pablo N. Mendes
> http://pablomendes.com
> 
> -- 
> You received this message because you are subscribed to the Google Groups "Google Summer of Code Mentors List" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to google-summer-of-code-mentors-list+unsubscribe at googlegroups.com.
> To post to this group, send email to google-summer-of-code-mentors-list at googlegroups.com.
> Visit this group at http://groups.google.com/group/google-summer-of-code-mentors-list?hl=en-US.
> For more options, visit https://groups.google.com/groups/opt_out.
>  
>  

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================






From pjotr2010 at thebird.nl  Thu Feb 28 17:13:05 2013
From: pjotr2010 at thebird.nl (Pjotr Prins)
Date: Thu, 28 Feb 2013 23:13:05 +0100
Subject: [GSoC] [GSoC Mentors Announce] Google Summer of Code 2013
In-Reply-To: <5119431F.90100@gmail.com>
References: <CAEkQO61xzGb19SYi2wUVpA8Pe5XHzo+cR6S-9PeyoW_DOfc7JQ@mail.gmail.com>
	<CAKVJ-_56b+oxyAH-PYXTwSDT_KJ5y5tv0AjOEBntuNKsJA_qLw@mail.gmail.com>
	<5119431F.90100@gmail.com>
Message-ID: <20130228221305.GA28817@thebird.nl>

On Mon, Feb 11, 2013 at 02:14:39PM -0500, Robert Buels wrote:
> Hurray!
> 
> Would someone else be interested in being the org admin for OBF this
> year?  Preferably someone who's been an OBF mentor in one of the
> previous years?  I've got a lot of things on my plate.
> 
> If someone else will be the primary, I can certainly volunteer as a backup.
> 
> Rob

Because I think GSoC so important for bioinformatics I volunteer to
take on being the org admin for OBF this year. Chris Fields and Rob
Buels have promised to act as support, backup and conscience. Note
that I view this role as being purely organisational and
administrative. The difficult decisions will be made by OBF board
members. 

Pj.

From hlapp at drycafe.net  Sat Mar  2 20:21:37 2013
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Sat, 2 Mar 2013 20:21:37 -0500
Subject: [GSoC] [OBF-GSoC-Mentors] [GSoC Mentors Announce] Google Summer
	of Code 2013
In-Reply-To: <20130228221305.GA28817@thebird.nl>
References: <CAEkQO61xzGb19SYi2wUVpA8Pe5XHzo+cR6S-9PeyoW_DOfc7JQ@mail.gmail.com>
	<CAKVJ-_56b+oxyAH-PYXTwSDT_KJ5y5tv0AjOEBntuNKsJA_qLw@mail.gmail.com>
	<5119431F.90100@gmail.com> <20130228221305.GA28817@thebird.nl>
Message-ID: <A9A903B2-6D1F-4740-8689-DA5C2F70506F@drycafe.net>


On Feb 28, 2013, at 5:13 PM, Pjotr Prins wrote:

> I volunteer to take on being the org admin for OBF this year.

Awesome & thanks for volunteering!

> Chris Fields and Rob Buels have promised to act as support, backup and conscience.

I'm happy to be asked as well or to chime in on difficult situations.

> Note that I view this role as being purely organisational and administrative. The difficult decisions will be made by OBF board members. 

I'm not sure the Board would be the right body to make those decisions - some of its members aren't or have never been actively involved with GSoC, and so would have limited background.

So I think you should be prepared to make decisions, and that some of these may be difficult. You have common sense, empathy, and good judgment, so I don't see why that should make anyone concerned. It's easy when there's obvious consensus among the mentors, but when there isn't despite attempts to achieve it, someone will have to decide.

I might liken this to BOSC and the Board's relationship to the BOSC Committee Chair. While the Chair may ask the Board for advice, or the Board may ask the Chair to report status, it's the Chair who makes the decisions regarding BOSC, in consultation with others on the committee. 

The Board does give a formal blessing to the BOSC Chair in public session, and if you would like us to start doing the same for the prospective GSoC admin, I'd support that and put it on the agenda for the next public Board meeting.

	-hilmar
-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================






From pjotr2010 at thebird.nl  Sun Mar  3 10:15:05 2013
From: pjotr2010 at thebird.nl (Pjotr Prins)
Date: Sun, 3 Mar 2013 16:15:05 +0100
Subject: [GSoC] [pjotr2010@thebird.nl: GSoC 2013 is ON]
Message-ID: <20130303151505.GA6690@thebird.nl>

Dear project leaders. 

I am sending below announcement to you, to have it forwarded by you to
your mailing lists. Please do so. Also pass this message on to anyone
who might be in some way interested in the OBF/GSoC initiative. To
participate, start by signing up to the soc mailing list at
http://lists.open-bio.org/mailman/listinfo/gsoc

Spread the word!

~~~

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



From pjotr2010 at thebird.nl  Sun Mar  3 06:23:26 2013
From: pjotr2010 at thebird.nl (Pjotr Prins)
Date: Sun, 3 Mar 2013 12:23:26 +0100
Subject: [GSoC] GSoC 2013 is ON
Message-ID: <20130303112326.GA5638@thebird.nl>

Dear project leaders. 

I am sending below announcement to you, to have it forwarded by you to
your mailing lists. Please do so. Also pass this message on to anyone
who might be in some way interested in the OBF/GSoC initiative. To
participate, start by signing up to the soc mailing list at
http://lists.open-bio.org/mailman/listinfo/gsoc

Spread the word!

~~~

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


From pjotr2010 at thebird.nl  Wed Mar 20 17:19:32 2013
From: pjotr2010 at thebird.nl (Pjotr Prins)
Date: Wed, 20 Mar 2013 22:19:32 +0100
Subject: [GSoC] GSoC 2013 is ON
In-Reply-To: <20130303112326.GA5638@thebird.nl>
References: <20130303112326.GA5638@thebird.nl>
Message-ID: <20130320211932.GA23848@thebird.nl>

Heads up! One more week to go for project ideas! Please update

  https://github.com/OBF/GSoC/wiki/Google-Summer-of-Code-2013

with the latest links. And maybe a wakeup call to your lists?

If you are not on the Internet you don't exist. If you are not making
use of GSoC, you might as well be dead ;).

Kidding. But, the more ideas, the better.

Pj.

* March 22nd: Finalise project ideas
* March 29th: Deadline OBF mentoring organisation submission to Google

On Sun, Mar 03, 2013 at 12:23:26PM +0100, Pjotr Prins wrote:
> Dear project leaders. 
> 
> I am sending below announcement to you, to have it forwarded by you to
> your mailing lists. Please do so. Also pass this message on to anyone
> who might be in some way interested in the OBF/GSoC initiative. To
> participate, start by signing up to the soc mailing list at
> http://lists.open-bio.org/mailman/listinfo/gsoc
> 
> Spread the word!
> 
> ~~~
> 
> 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
> 

From pjotr2010 at thebird.nl  Sun Mar 24 03:51:21 2013
From: pjotr2010 at thebird.nl (Pjotr Prins)
Date: Sun, 24 Mar 2013 08:51:21 +0100
Subject: [GSoC] GSoC 2013 is ON
In-Reply-To: <20130320211932.GA23848@thebird.nl>
References: <20130303112326.GA5638@thebird.nl>
	<20130320211932.GA23848@thebird.nl>
Message-ID: <20130324075121.GA7300@thebird.nl>

The GSoC-OBF application has been submitted to Google. The
applications will be reviewed from next week.

So, one week to go for project ideas. Please add at least one link to
your project ideas (page) on either the github page below or the main
OBF GSoC wiki page. I'll combine them in the final stage. Make sure to
show a primary mentor for every idea, and a secondary (backup) mentor.

Thanks,

Pj.

On Wed, Mar 20, 2013 at 10:19:32PM +0100, Pjotr Prins wrote:
> Heads up! One more week to go for project ideas! Please update
> 
>   https://github.com/OBF/GSoC/wiki/Google-Summer-of-Code-2013
> 
> with the latest links. And maybe a wakeup call to your lists?
> 
> If you are not on the Internet you don't exist. If you are not making
> use of GSoC, you might as well be dead ;).
> 
> Kidding. But, the more ideas, the better.
> 
> Pj.
> 
> * March 22nd: Finalise project ideas
> * March 29th: Deadline OBF mentoring organisation submission to Google
> 
> On Sun, Mar 03, 2013 at 12:23:26PM +0100, Pjotr Prins wrote:
> > Dear project leaders. 
> > 
> > I am sending below announcement to you, to have it forwarded by you to
> > your mailing lists. Please do so. Also pass this message on to anyone
> > who might be in some way interested in the OBF/GSoC initiative. To
> > participate, start by signing up to the soc mailing list at
> > http://lists.open-bio.org/mailman/listinfo/gsoc
> > 
> > Spread the word!
> > 
> > ~~~
> > 
> > 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
> > 

From pjotr2010 at thebird.nl  Sat Mar 30 05:22:36 2013
From: pjotr2010 at thebird.nl (Pjotr Prins)
Date: Sat, 30 Mar 2013 10:22:36 +0100
Subject: [GSoC] GSoC 2013 is ON
Message-ID: <20130330092236.GA31459@thebird.nl>

The OBF has submitted the application for being a mentor org in this
year's Google Summer of Code. I have listed all project ideas on:

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

For Biopython (3x), BioRuby (5x) and BioJava (4x) I found project ideas.

The others are missing.

There is still a (rather small) window of opportunity for adding
ideas. Make sure you inform me of additional ones to get them listed
from the main page.

Pj.

From hlapp at drycafe.net  Sat Mar 30 13:41:21 2013
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Sat, 30 Mar 2013 12:41:21 -0500
Subject: [GSoC] GSoC 2013 is ON
In-Reply-To: <20130330092236.GA31459@thebird.nl>
References: <20130330092236.GA31459@thebird.nl>
Message-ID: <1FB4BAB7-E7B2-4AD3-9D8C-A4BF134E66D2@drycafe.net>

I'm assuming "The OBF" is you in this case - thanks & kudos for pulling this together. Now fingers crossed!

-hilmar

Sent with a tap.

On Mar 30, 2013, at 4:22 AM, Pjotr Prins <pjotr2010 at thebird.nl> wrote:

> The OBF has submitted the application for being a mentor org in this
> year's Google Summer of Code. I have listed all project ideas on:
> 
>  http://www.open-bio.org/wiki/Google_Summer_of_Code
> 
> For Biopython (3x), BioRuby (5x) and BioJava (4x) I found project ideas.
> 
> The others are missing.
> 
> There is still a (rather small) window of opportunity for adding
> ideas. Make sure you inform me of additional ones to get them listed
> from the main page.
> 
> Pj.


From cjfields at illinois.edu  Sat Mar 30 18:15:31 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Sat, 30 Mar 2013 22:15:31 +0000
Subject: [GSoC] GSoC 2013 is ON
In-Reply-To: <20130330092236.GA31459@thebird.nl>
References: <20130330092236.GA31459@thebird.nl>
Message-ID: <94avmiklcc69157bvumw54mf.1364681728380@email.android.com>

I'll try adding a few for bioperl tonight.  Been busy this week with family.

Chris


Sent via a capable phone of some make and model


-------- Original message --------
From: Pjotr Prins <pjotr2010 at thebird.nl>
Date: 03/30/2013 4:23 AM (GMT-06:00)
To: Pjotr Prins <pjotr2010 at thebird.nl>
Cc: p.j.a.cock at googlemail.com,"Fields, Christopher J" <cjfields at illinois.edu>,panel at bioruby.org,Andreas Prlic <andreas at sdsc.edu>,hlapp at gmx.net,moeller at debian.org,mark.wilkinson at upm.es,ricepeterm at yahoo.co.uk,ketil at malde.org,jprocter at compbio.dundee.ac.uk,reece at harts.net,chapmanb at 50mail.com,OBF GSoC <gsoc at lists.open-bio.org>
Subject: Re: GSoC 2013 is ON


The OBF has submitted the application for being a mentor org in this
year's Google Summer of Code. I have listed all project ideas on:

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

For Biopython (3x), BioRuby (5x) and BioJava (4x) I found project ideas.

The others are missing.

There is still a (rather small) window of opportunity for adding
ideas. Make sure you inform me of additional ones to get them listed
from the main page.

Pj.


From ketil at malde.org  Tue Apr  2 04:03:58 2013
From: ketil at malde.org (Ketil Malde)
Date: Tue, 02 Apr 2013 10:03:58 +0200
Subject: [GSoC] GSoC 2013 is ON
In-Reply-To: <20130330092236.GA31459@thebird.nl>
References: <20130330092236.GA31459@thebird.nl>
Message-ID: <87r4it8ikx.fsf@nmd999X.imr.no>


[CC everybody including the biohaskell list. Let me know if any of you
want off. :-) ]

Pjotr Prins <pjotr2010 at thebird.nl> writes:

>   http://www.open-bio.org/wiki/Google_Summer_of_Code

> For Biopython (3x), BioRuby (5x) and BioJava (4x) I found project ideas.

> The others are missing.

> There is still a (rather small) window of opportunity for adding
> ideas.

I have one thing that might work well as a SOC project, if the right
student could be found.

Basically, I and a colleague recently developed and published a method
and implementation for more sensitive pairwise alignments.  The paper is
here, I think (PLoS ONE seems to be down atm):
  http://dx.plos.org/10.1371/journal.pone.0054422

I'm really happy about the results, if nothing else, check the SCOP
benchmark.  Although it's difficult to construct a good test case using
more complex methods (training sets for HMMs and whatnot) I don't know
anything that is as good as this.  We're using it for annotation of
genes.

The current implementation is in Haskell, and although it works
correctly, it is a bit slow, and more problematic, it consumes too much
memory (so going multi-threaded, although pretty easy, won't be of any
help).

I would like to make this into a less resource intensive (and thus more
practical) tool, and there are two ways I can think of to go about this:

1) Optimize the Haskell program

2) Reimplement the algorithm (or parts of it) in a different language

Advantages of 1:

* Already have a working program, and the type system makes it easy to
refactor without introducing errors.
* Haskell supports lots of good multi-threading programming models (like
STM)
* I know Haskell pretty well, and will be hopefully be able to mentor.

Disadvantages:

* Haskell has some good debugging tools, but they tend to work really
  poorly for large memory (i.e. it takes a long time to generate
  profiles)
* Needs somebody with a bit (or a lot) of experience optimizing Haskell,
  and good knowledge of high-perf libraries (like vector)

Advantages of 2:

* Easier to get a student with adequate skills.
* More predictable performance models in other languages.
* Easier to compile and install for many users.

Disadvantages:

* Ideally, should know enough Haskell to read and understand the code.
* Likely needs a co-mentor with knowledge of the language in question.

Is this something I could or should submit as a task?

-k
-- 
If I haven't seen further, it is by standing in the footprints of giants

From pjotr2010 at thebird.nl  Tue Apr  2 04:36:52 2013
From: pjotr2010 at thebird.nl (Pjotr Prins)
Date: Tue, 2 Apr 2013 10:36:52 +0200
Subject: [GSoC] GSoC 2013 is ON
In-Reply-To: <87r4it8ikx.fsf@nmd999X.imr.no>
References: <20130330092236.GA31459@thebird.nl> <87r4it8ikx.fsf@nmd999X.imr.no>
Message-ID: <20130402083652.GA9504@thebird.nl>

Great idea. Can you format it as a project idea on your Wiki - take
the other ideas as an example. You can leave the two options open and
see what student reacts to.

BTW We only have the 'right' students :). The selection process is
pretty strong.

There is some ongoing discussion about core and non-core OBF projects,
but I think since BioHaskell is going strong there will be little
against adding one project idea. If it brings a really competent
student we all gain.

There is a meeting between GSoC and the OBF board on the 9th, right
after we get or do not get accepted as a mentoring organisation. I'll
make a case for inclusion of your project idea into the program.

Adding it to the wiki will help.

Pj.

On Tue, Apr 02, 2013 at 10:03:58AM +0200, Ketil Malde wrote:
> 
> [CC everybody including the biohaskell list. Let me know if any of you
> want off. :-) ]
> 
> Pjotr Prins <pjotr2010 at thebird.nl> writes:
> 
> >   http://www.open-bio.org/wiki/Google_Summer_of_Code
> 
> > For Biopython (3x), BioRuby (5x) and BioJava (4x) I found project ideas.
> 
> > The others are missing.
> 
> > There is still a (rather small) window of opportunity for adding
> > ideas.
> 
> I have one thing that might work well as a SOC project, if the right
> student could be found.
> 
> Basically, I and a colleague recently developed and published a method
> and implementation for more sensitive pairwise alignments.  The paper is
> here, I think (PLoS ONE seems to be down atm):
>   http://dx.plos.org/10.1371/journal.pone.0054422
> 
> I'm really happy about the results, if nothing else, check the SCOP
> benchmark.  Although it's difficult to construct a good test case using
> more complex methods (training sets for HMMs and whatnot) I don't know
> anything that is as good as this.  We're using it for annotation of
> genes.
> 
> The current implementation is in Haskell, and although it works
> correctly, it is a bit slow, and more problematic, it consumes too much
> memory (so going multi-threaded, although pretty easy, won't be of any
> help).
> 
> I would like to make this into a less resource intensive (and thus more
> practical) tool, and there are two ways I can think of to go about this:
> 
> 1) Optimize the Haskell program
> 
> 2) Reimplement the algorithm (or parts of it) in a different language
> 
> Advantages of 1:
> 
> * Already have a working program, and the type system makes it easy to
> refactor without introducing errors.
> * Haskell supports lots of good multi-threading programming models (like
> STM)
> * I know Haskell pretty well, and will be hopefully be able to mentor.
> 
> Disadvantages:
> 
> * Haskell has some good debugging tools, but they tend to work really
>   poorly for large memory (i.e. it takes a long time to generate
>   profiles)
> * Needs somebody with a bit (or a lot) of experience optimizing Haskell,
>   and good knowledge of high-perf libraries (like vector)
> 
> Advantages of 2:
> 
> * Easier to get a student with adequate skills.
> * More predictable performance models in other languages.
> * Easier to compile and install for many users.
> 
> Disadvantages:
> 
> * Ideally, should know enough Haskell to read and understand the code.
> * Likely needs a co-mentor with knowledge of the language in question.
> 
> Is this something I could or should submit as a task?
> 
> -k
> -- 
> If I haven't seen further, it is by standing in the footprints of giants

From ketil at malde.org  Thu Apr  4 07:29:32 2013
From: ketil at malde.org (Ketil Malde)
Date: Thu, 04 Apr 2013 13:29:32 +0200
Subject: [GSoC] GSoC 2013 is ON
In-Reply-To: <20130402083652.GA9504@thebird.nl>
References: <20130330092236.GA31459@thebird.nl>,
	<87r4it8ikx.fsf@nmd999X.imr.no>, <20130402083652.GA9504@thebird.nl>
Message-ID: <874nfm7cv7.fsf@nmd999X.imr.no>


Pjotr Prins <pjotr2010 at thebird.nl> writes:

> Great idea. Can you format it as a project idea on your Wiki - take
> the other ideas as an example.

I've added the link with just a quick rehash of my email text.

-k
-- 
If I haven't seen further, it is by standing in the footprints of giants

From pjotr2010 at thebird.nl  Mon Apr  8 16:13:46 2013
From: pjotr2010 at thebird.nl (Pjotr Prins)
Date: Mon, 8 Apr 2013 22:13:46 +0200
Subject: [GSoC] GSoC 2013 is ON
In-Reply-To: <20130320211932.GA23848@thebird.nl>
References: <20130303112326.GA5638@thebird.nl>
	<20130320211932.GA23848@thebird.nl>
Message-ID: <20130408201346.GA3054@thebird.nl>

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.

On Wed, Mar 20, 2013 at 10:19:32PM +0100, Pjotr Prins wrote:
> Heads up! One more week to go for project ideas! Please update
> 
>   https://github.com/OBF/GSoC/wiki/Google-Summer-of-Code-2013
> 
> with the latest links. And maybe a wakeup call to your lists?
> 
> If you are not on the Internet you don't exist. If you are not making
> use of GSoC, you might as well be dead ;).
> 
> Kidding. But, the more ideas, the better.
> 
> Pj.
> 
> * March 22nd: Finalise project ideas
> * March 29th: Deadline OBF mentoring organisation submission to Google
> 
> On Sun, Mar 03, 2013 at 12:23:26PM +0100, Pjotr Prins wrote:
> > Dear project leaders. 
> > 
> > I am sending below announcement to you, to have it forwarded by you to
> > your mailing lists. Please do so. Also pass this message on to anyone
> > who might be in some way interested in the OBF/GSoC initiative. To
> > participate, start by signing up to the soc mailing list at
> > http://lists.open-bio.org/mailman/listinfo/gsoc
> > 
> > Spread the word!
> > 
> > ~~~
> > 
> > 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
> > 

From p.j.a.cock at googlemail.com  Mon Apr  8 16:28:29 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 8 Apr 2013 21:28:29 +0100
Subject: [GSoC] GSoC 2013 is ON
In-Reply-To: <20130408201346.GA3054@thebird.nl>
References: <20130303112326.GA5638@thebird.nl>
	<20130320211932.GA23848@thebird.nl>
	<20130408201346.GA3054@thebird.nl>
Message-ID: <CAKVJ-_5rt_OWBp5dmw0YP8-sCoRx9Uuc1Pc9aAG2AwPZTjQ-Yw@mail.gmail.com>

Thanks Pjotr,

Dang. That was unexpected. Looking back we could have
done a better job highlighting what previous projects had
achieved (although I think we were getting better at that),
but otherwise I am struggling to guess what the cause
was - beyond your suggestion that things are simply
increasingly competitive.

We'll need to send out some sort of public announcement
(email & posted to blog), your email below does highlight some
positives. Do we know if NESCent was accepted? Or any
other relevant organisations with which we might partner
for one or two projects?

Peter

On Monday, April 8, 2013, Pjotr Prins wrote:

> 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.
>
> On Wed, Mar 20, 2013 at 10:19:32PM +0100, Pjotr Prins wrote:
> > Heads up! One more week to go for project ideas! Please update
> >
> >   https://github.com/OBF/GSoC/wiki/Google-Summer-of-Code-2013
> >
> > with the latest links. And maybe a wakeup call to your lists?
> >
> > If you are not on the Internet you don't exist. If you are not making
> > use of GSoC, you might as well be dead ;).
> >
> > Kidding. But, the more ideas, the better.
> >
> > Pj.
> >
> > * March 22nd: Finalise project ideas
> > * March 29th: Deadline OBF mentoring organisation submission to Google
> >
> > On Sun, Mar 03, 2013 at 12:23:26PM +0100, Pjotr Prins wrote:
> > > Dear project leaders.
> > >
> > > I am sending below announcement to you, to have it forwarded by you to
> > > your mailing lists. Please do so. Also pass this message on to anyone
> > > who might be in some way interested in the OBF/GSoC initiative. To
> > > participate, start by signing up to the soc mailing list at
> > > http://lists.open-bio.org/mailman/listinfo/gsoc
> > >
> > > Spread the word!
> > >
> > > ~~~
> > >
> > > 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 <javascript:;>
> > >
> > > 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
> > >
>

From hlapp at drycafe.net  Mon Apr  8 16:51:01 2013
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Mon, 8 Apr 2013 16:51:01 -0400
Subject: [GSoC] GSoC 2013 is ON
In-Reply-To: <CAKVJ-_5rt_OWBp5dmw0YP8-sCoRx9Uuc1Pc9aAG2AwPZTjQ-Yw@mail.gmail.com>
References: <20130303112326.GA5638@thebird.nl>
	<20130320211932.GA23848@thebird.nl>
	<20130408201346.GA3054@thebird.nl>
	<CAKVJ-_5rt_OWBp5dmw0YP8-sCoRx9Uuc1Pc9aAG2AwPZTjQ-Yw@mail.gmail.com>
Message-ID: <A9491C4B-8DE2-43AA-BD9E-67A43FF3B03B@drycafe.net>


On Apr 8, 2013, at 4:28 PM, Peter Cock wrote:

> Do we know if NESCent was accepted? 


Yes, they were. -hilmar

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================





From john.woods at marcottelab.org  Mon Apr  8 16:58:45 2013
From: john.woods at marcottelab.org (John Woods)
Date: Mon, 8 Apr 2013 15:58:45 -0500
Subject: [GSoC] GSoC 2013 is ON
In-Reply-To: <20130408201346.GA3054@thebird.nl>
References: <20130303112326.GA5638@thebird.nl>
	<20130320211932.GA23848@thebird.nl>
	<20130408201346.GA3054@thebird.nl>
Message-ID: <CAPkCRRuffbwq9oTPPCoCZmbJ43QC4hUp6nALtU6iOQR04eVe-A@mail.gmail.com>

(+John Prince, +Carlos Agarie)

Hey Pjotr,

First of all, I'm so sorry to hear you all didn't get it. I've learned so
much about running our fellowship programs from how well you all manage
your GSOC students.

I just learned that SciRuby did get accepted, which was quite honestly a
tiny bit surprising for me (we've definitely been rejected before).

Would you all be willing to get involved with our Summer of Code efforts?
We're a bit short on mentors, and I think there's room for us to adopt some
of your more general-science-y projects.

John


On Mon, Apr 8, 2013 at 3:13 PM, Pjotr Prins <pjotr2010 at thebird.nl> wrote:

> 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.
>
> On Wed, Mar 20, 2013 at 10:19:32PM +0100, Pjotr Prins wrote:
> > Heads up! One more week to go for project ideas! Please update
> >
> >   https://github.com/OBF/GSoC/wiki/Google-Summer-of-Code-2013
> >
> > with the latest links. And maybe a wakeup call to your lists?
> >
> > If you are not on the Internet you don't exist. If you are not making
> > use of GSoC, you might as well be dead ;).
> >
> > Kidding. But, the more ideas, the better.
> >
> > Pj.
> >
> > * March 22nd: Finalise project ideas
> > * March 29th: Deadline OBF mentoring organisation submission to Google
> >
> > On Sun, Mar 03, 2013 at 12:23:26PM +0100, Pjotr Prins wrote:
> > > Dear project leaders.
> > >
> > > I am sending below announcement to you, to have it forwarded by you to
> > > your mailing lists. Please do so. Also pass this message on to anyone
> > > who might be in some way interested in the OBF/GSoC initiative. To
> > > participate, start by signing up to the soc mailing list at
> > > http://lists.open-bio.org/mailman/listinfo/gsoc
> > >
> > > Spread the word!
> > >
> > > ~~~
> > >
> > > 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
> > >
> _______________________________________________
> GSoC mailing list
> GSoC at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/gsoc
>

From cjfields at illinois.edu  Mon Apr  8 16:55:25 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 8 Apr 2013 20:55:25 +0000
Subject: [GSoC] GSoC 2013 is ON
In-Reply-To: <A9491C4B-8DE2-43AA-BD9E-67A43FF3B03B@drycafe.net>
References: <20130303112326.GA5638@thebird.nl>
	<20130320211932.GA23848@thebird.nl> <20130408201346.GA3054@thebird.nl>
	<CAKVJ-_5rt_OWBp5dmw0YP8-sCoRx9Uuc1Pc9aAG2AwPZTjQ-Yw@mail.gmail.com>
	<A9491C4B-8DE2-43AA-BD9E-67A43FF3B03B@drycafe.net>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DD325A@CHIMBX5.ad.uillinois.edu>

On Apr 8, 2013, at 3:51 PM, Hilmar Lapp <hlapp at drycafe.net>
 wrote:

> 
> On Apr 8, 2013, at 4:28 PM, Peter Cock wrote:
> 
>> Do we know if NESCent was accepted? 
> 
> Yes, they were. -hilmar

Not sure if GMOD resubmitted this year; Scott Cain would know.  Will ask him?

chris

From jprocter at compbio.dundee.ac.uk  Mon Apr  8 22:14:18 2013
From: jprocter at compbio.dundee.ac.uk (Jim Procter)
Date: Tue, 09 Apr 2013 12:14:18 +1000
Subject: [GSoC] GSoC 2013 is ON
In-Reply-To: <CAPkCRRuffbwq9oTPPCoCZmbJ43QC4hUp6nALtU6iOQR04eVe-A@mail.gmail.com>
References: <20130303112326.GA5638@thebird.nl>
	<20130320211932.GA23848@thebird.nl>
	<20130408201346.GA3054@thebird.nl>
	<CAPkCRRuffbwq9oTPPCoCZmbJ43QC4hUp6nALtU6iOQR04eVe-A@mail.gmail.com>
Message-ID: <5163797A.3090208@compbio.dundee.ac.uk>

Hi.

This does suck, but as you said, Pjotr - it suggests competition for 
resources from FLOSS philanthropists is now very fierce - which is a 
Good Thing, but also a less good thing if writing GSoC org applications 
become as much work as grant applications, with the same low acceptance 
rate.

In the case of OBF I'm not quite sure why it didn't make the cut, so a 
post-mortem might be informative. For this year, though - it is 
definitely worth looking at bio/sci related GSoC orgs that did make the 
cut to see if an OBF project might fit there, or even applying for 
alternate sources of internship funding. Does anyone feel like starting 
a page to organise this kind of information on the OBF wiki ?

I did a quick analysis of the list in Melange and a random survey of 
tweets, and it looks like around 20 of the 121 orgs listed as of 3am 
UTC are science related. As to the ones that didn't make it - there are 
some surprises, such as Drupal, VLC, and RockPlayer - but I couldn't 
get a definite list together. At least one comment suggested the number 
of accepted orgs is less this year - I guess we'll see something in the 
announcements later on... since the bottom line will be whether the 
total number of student slots is less.

Jim.

On Tue Apr  9 06:58:45 2013, John Woods wrote:
> (+John Prince, +Carlos Agarie)
>
> Hey Pjotr,
>
> First of all, I'm so sorry to hear you all didn't get it. I've learned
> so much about running our fellowship programs from how well you all
> manage your GSOC students.
>
> I just learned that SciRuby did get accepted, which was quite honestly
> a tiny bit surprising for me (we've definitely been rejected before).
>
> Would you all be willing to get involved with our Summer of Code
> efforts? We're a bit short on mentors, and I think there's room for us
> to adopt some of your more general-science-y projects.
>
> John
>
>
> On Mon, Apr 8, 2013 at 3:13 PM, Pjotr Prins <pjotr2010 at thebird.nl
> <mailto:pjotr2010 at thebird.nl>> wrote:
>
>     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.
>
>     On Wed, Mar 20, 2013 at 10:19:32PM +0100, Pjotr Prins wrote:
>     > Heads up! One more week to go for project ideas! Please update
>     >
>     > https://github.com/OBF/GSoC/wiki/Google-Summer-of-Code-2013
>     >
>     > with the latest links. And maybe a wakeup call to your lists?
>     >
>     > If you are not on the Internet you don't exist. If you are not
>     making
>     > use of GSoC, you might as well be dead ;).
>     >
>     > Kidding. But, the more ideas, the better.
>     >
>     > Pj.
>     >
>     > * March 22nd: Finalise project ideas
>     > * March 29th: Deadline OBF mentoring organisation submission to
>     Google
>     >
>     > On Sun, Mar 03, 2013 at 12:23:26PM +0100, Pjotr Prins wrote:
>     > > Dear project leaders.
>     > >
>     > > I am sending below announcement to you, to have it forwarded
>     by you to
>     > > your mailing lists. Please do so. Also pass this message on to
>     anyone
>     > > who might be in some way interested in the OBF/GSoC initiative. To
>     > > participate, start by signing up to the soc mailing list at
>     > > http://lists.open-bio.org/mailman/listinfo/gsoc
>     > >
>     > > Spread the word!
>     > >
>     > > ~~~
>     > >
>     > > 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
>     <mailto: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
>     > >
>     _______________________________________________
>     GSoC mailing list
>     GSoC at lists.open-bio.org <mailto:GSoC at lists.open-bio.org>
>     http://lists.open-bio.org/mailman/listinfo/gsoc
>
>



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: [GSoC] 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 steffen_moeller at gmx.de  Tue Apr  9 05:32:57 2013
From: steffen_moeller at gmx.de (=?UTF-8?Q?=22Steffen_M=C3=B6ller=22?=)
Date: Tue, 9 Apr 2013 11:32:57 +0200 (CEST)
Subject: [GSoC] GSoC 2013 is ON
In-Reply-To: <5163797A.3090208@compbio.dundee.ac.uk>
References: <20130303112326.GA5638@thebird.nl>
	<20130320211932.GA23848@thebird.nl> <20130408201346.GA3054@thebird.nl>
	<CAPkCRRuffbwq9oTPPCoCZmbJ43QC4hUp6nALtU6iOQR04eVe-A@mail.gmail.com>,
	<5163797A.3090208@compbio.dundee.ac.uk>
Message-ID: <trinity-022153dc-869e-47ff-9bef-b7c79a5d6911-1365499977647@3capp-gmx-bs44>

An HTML attachment was scrubbed...
URL: <http://lists.open-bio.org/pipermail/gsoc/attachments/20130409/d24a50ff/attachment.html>

From p.j.a.cock at googlemail.com  Tue Apr  9 06:34:37 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Tue, 9 Apr 2013 11:34:37 +0100
Subject: [GSoC] OBF not accepted for GSoC 2013
In-Reply-To: <CAKVJ-_6-+nyJk+7tp5YOyy7i7N7GtkRswZ_2Vs0uTuqGEV4wWQ@mail.gmail.com>
References: <CAKVJ-_6-+nyJk+7tp5YOyy7i7N7GtkRswZ_2Vs0uTuqGEV4wWQ@mail.gmail.com>
Message-ID: <CAKVJ-_4dB_uHQ=52-9D8WT+KCkyYk0jg6hPq15kE_SK3fWQimw@mail.gmail.com>

In a mass-email Peter wrote:
> 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.
> ...

Sorry Rob - "Rob Buels". Is is worth sending a correction to all
the mailing lists?

Peter

From rbuels at gmail.com  Tue Apr  9 13:41:15 2013
From: rbuels at gmail.com (Robert Buels)
Date: Tue, 09 Apr 2013 13:41:15 -0400
Subject: [GSoC] OBF not accepted for GSoC 2013
In-Reply-To: <CAKVJ-_4dB_uHQ=52-9D8WT+KCkyYk0jg6hPq15kE_SK3fWQimw@mail.gmail.com>
References: <CAKVJ-_6-+nyJk+7tp5YOyy7i7N7GtkRswZ_2Vs0uTuqGEV4wWQ@mail.gmail.com>
	<CAKVJ-_4dB_uHQ=52-9D8WT+KCkyYk0jg6hPq15kE_SK3fWQimw@mail.gmail.com>
Message-ID: <516452BB.3060202@gmail.com>

LOL no, not worth it.

You'll get your comeuppance at the DBCLS hackathon, anyway.  ;-)


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 04/09/2013 06:34 AM, Peter Cock wrote:
> Sorry Rob - "Rob Buels". Is is worth sending a correction to all
> the mailing lists?

From scott at scottcain.net  Tue Apr  9 06:57:40 2013
From: scott at scottcain.net (Scott Cain)
Date: Tue, 9 Apr 2013 11:57:40 +0100
Subject: [GSoC] [Bioperl-l] OBF not accepted for GSoC 2013
In-Reply-To: <CAKVJ-_6-+nyJk+7tp5YOyy7i7N7GtkRswZ_2Vs0uTuqGEV4wWQ@mail.gmail.com>
References: <CAKVJ-_6-+nyJk+7tp5YOyy7i7N7GtkRswZ_2Vs0uTuqGEV4wWQ@mail.gmail.com>
Message-ID: <3155B235-4068-491C-B611-1117EF1B5C50@scottcain.net>

Hi all, 

I was certainly surprised the the openbio application wasn't accepted; completion must be very tight. I just want to point out another bio project for inclined students: the Genome Informatics project is a GSoC collaboration of several well known projects, including GMOD (chado, gbrowse, jbrowse), Reactome, and Galaxy. For more information, see:

  http://gmod.org/wiki/GSoC

Thanks,
Scott


Sent from my iPhone

On Apr 9, 2013, at 11:20 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> 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.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From l.m.timmermans at students.uu.nl  Tue Apr  9 08:24:24 2013
From: l.m.timmermans at students.uu.nl (Leon Timmermans)
Date: Tue, 9 Apr 2013 14:24:24 +0200
Subject: [GSoC] [Bioperl-l] OBF not accepted for GSoC 2013
In-Reply-To: <CAKVJ-_6-+nyJk+7tp5YOyy7i7N7GtkRswZ_2Vs0uTuqGEV4wWQ@mail.gmail.com>
References: <CAKVJ-_6-+nyJk+7tp5YOyy7i7N7GtkRswZ_2Vs0uTuqGEV4wWQ@mail.gmail.com>
Message-ID: <CAC1jpXC=WuUU3Vx-psQds=yyje8r0XAFHiJVnZB2KxrxWY+_8w@mail.gmail.com>

On Tue, Apr 9, 2013 at 12:20 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> 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.

Something similar happened to The Perl Foundation last year, so we
asked them why? We had been a well-performing organization (100%
success rate in the preceding year) that put a lot of effort in our
submission and had a solid community behind us.

The answer was not quite what we expected. It had little to do with
the quality of the application, but everything with them wanting new
blood in the SOC. The same had happened to other projects I'm told.

Leon

From hlapp at drycafe.net  Tue Apr  9 07:47:22 2013
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Tue, 9 Apr 2013 07:47:22 -0400
Subject: [GSoC] GSoC 2013 is ON
In-Reply-To: <5163797A.3090208@compbio.dundee.ac.uk>
References: <20130303112326.GA5638@thebird.nl>
	<20130320211932.GA23848@thebird.nl>
	<20130408201346.GA3054@thebird.nl>
	<CAPkCRRuffbwq9oTPPCoCZmbJ43QC4hUp6nALtU6iOQR04eVe-A@mail.gmail.com>
	<5163797A.3090208@compbio.dundee.ac.uk>
Message-ID: <9B1CEC1A-0839-43C0-AFBA-334BF4F3D459@drycafe.net>

Wasn't the number of orgs last year around 180? That would mean that the total number of accepted orgs is almost unchanged. However, the announcement on the Google blog says that they accepted more than 40 new projects. Since the number of accepted orgs for sure didn't rise, this must mean that around 40 projects turned over, or almost 1 in every 4.

-hilmar

Sent with a tap.

On Apr 8, 2013, at 10:14 PM, Jim Procter <jprocter at compbio.dundee.ac.uk> wrote:

> Hi.
> 
> This does suck, but as you said, Pjotr - it suggests competition for resources from FLOSS philanthropists is now very fierce - which is a Good Thing, but also a less good thing if writing GSoC org applications become as much work as grant applications, with the same low acceptance rate.
> 
> In the case of OBF I'm not quite sure why it didn't make the cut, so a post-mortem might be informative. For this year, though - it is definitely worth looking at bio/sci related GSoC orgs that did make the cut to see if an OBF project might fit there, or even applying for alternate sources of internship funding. Does anyone feel like starting a page to organise this kind of information on the OBF wiki ?
> 
> I did a quick analysis of the list in Melange and a random survey of tweets, and it looks like around 20 of the 121 orgs listed as of 3am UTC are science related. As to the ones that didn't make it - there are some surprises, such as Drupal, VLC, and RockPlayer - but I couldn't get a definite list together. At least one comment suggested the number of accepted orgs is less this year - I guess we'll see something in the announcements later on... since the bottom line will be whether the total number of student slots is less.
> 
> Jim.
> 
> On Tue Apr  9 06:58:45 2013, John Woods wrote:
>> (+John Prince, +Carlos Agarie)
>> 
>> Hey Pjotr,
>> 
>> First of all, I'm so sorry to hear you all didn't get it. I've learned
>> so much about running our fellowship programs from how well you all
>> manage your GSOC students.
>> 
>> I just learned that SciRuby did get accepted, which was quite honestly
>> a tiny bit surprising for me (we've definitely been rejected before).
>> 
>> Would you all be willing to get involved with our Summer of Code
>> efforts? We're a bit short on mentors, and I think there's room for us
>> to adopt some of your more general-science-y projects.
>> 
>> John
>> 
>> 
>> On Mon, Apr 8, 2013 at 3:13 PM, Pjotr Prins <pjotr2010 at thebird.nl
>> <mailto:pjotr2010 at thebird.nl>> wrote:
>> 
>>    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.
>> 
>>    On Wed, Mar 20, 2013 at 10:19:32PM +0100, Pjotr Prins wrote:
>>    > Heads up! One more week to go for project ideas! Please update
>>    >
>>    > https://github.com/OBF/GSoC/wiki/Google-Summer-of-Code-2013
>>    >
>>    > with the latest links. And maybe a wakeup call to your lists?
>>    >
>>    > If you are not on the Internet you don't exist. If you are not
>>    making
>>    > use of GSoC, you might as well be dead ;).
>>    >
>>    > Kidding. But, the more ideas, the better.
>>    >
>>    > Pj.
>>    >
>>    > * March 22nd: Finalise project ideas
>>    > * March 29th: Deadline OBF mentoring organisation submission to
>>    Google
>>    >
>>    > On Sun, Mar 03, 2013 at 12:23:26PM +0100, Pjotr Prins wrote:
>>    > > Dear project leaders.
>>    > >
>>    > > I am sending below announcement to you, to have it forwarded
>>    by you to
>>    > > your mailing lists. Please do so. Also pass this message on to
>>    anyone
>>    > > who might be in some way interested in the OBF/GSoC initiative. To
>>    > > participate, start by signing up to the soc mailing list at
>>    > > http://lists.open-bio.org/mailman/listinfo/gsoc
>>    > >
>>    > > Spread the word!
>>    > >
>>    > > ~~~
>>    > >
>>    > > 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
>>    <mailto: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
>>    > >
>>    _______________________________________________
>>    GSoC mailing list
>>    GSoC at lists.open-bio.org <mailto:GSoC at lists.open-bio.org>
>>    http://lists.open-bio.org/mailman/listinfo/gsoc
>> 
>> 
> 
> 


From p.j.a.cock at googlemail.com  Tue Apr  9 15:00:29 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Tue, 9 Apr 2013 20:00:29 +0100
Subject: [GSoC] GSoC 2013 is ON
In-Reply-To: <9B1CEC1A-0839-43C0-AFBA-334BF4F3D459@drycafe.net>
References: <20130303112326.GA5638@thebird.nl>
	<20130320211932.GA23848@thebird.nl>
	<20130408201346.GA3054@thebird.nl>
	<CAPkCRRuffbwq9oTPPCoCZmbJ43QC4hUp6nALtU6iOQR04eVe-A@mail.gmail.com>
	<5163797A.3090208@compbio.dundee.ac.uk>
	<9B1CEC1A-0839-43C0-AFBA-334BF4F3D459@drycafe.net>
Message-ID: <CAKVJ-_447qQmoAL9h7GN79E=FkRYwnACUxCGYW4cyyP4O8BM1A@mail.gmail.com>

On Tue, Apr 9, 2013 at 12:47 PM, Hilmar Lapp <hlapp at drycafe.net> wrote:
> Wasn't the number of orgs last year around 180? That would
> mean that the total number of accepted orgs is almost unchanged.

Yes, i checked and its been just under 180 for the last few years.

> However, the announcement on the Google blog says that
> they accepted more than 40 new projects. Since the number
> of accepted orgs for sure didn't rise, this must mean that
> around 40 projects turned over, or almost 1 in every 4.
>
> -hilmar

It does seem Google are trying to cover different ground but
with a fixed budget - and this year we were one of the unlucky
organisations (but not alone in this respect).

Peter

From pjotr2010 at thebird.nl  Thu Apr 11 02:13:04 2013
From: pjotr2010 at thebird.nl (Pjotr Prins)
Date: Thu, 11 Apr 2013 08:13:04 +0200
Subject: [GSoC] GSoC 2013 is ON
In-Reply-To: <CAKVJ-_447qQmoAL9h7GN79E=FkRYwnACUxCGYW4cyyP4O8BM1A@mail.gmail.com>
References: <20130303112326.GA5638@thebird.nl>
	<20130320211932.GA23848@thebird.nl>
	<20130408201346.GA3054@thebird.nl>
	<CAPkCRRuffbwq9oTPPCoCZmbJ43QC4hUp6nALtU6iOQR04eVe-A@mail.gmail.com>
	<5163797A.3090208@compbio.dundee.ac.uk>
	<9B1CEC1A-0839-43C0-AFBA-334BF4F3D459@drycafe.net>
	<CAKVJ-_447qQmoAL9h7GN79E=FkRYwnACUxCGYW4cyyP4O8BM1A@mail.gmail.com>
Message-ID: <20130411061304.GA14038@thebird.nl>

SciRuby has been so kind to allow us to merge some BioRuby project
ideas into their GSoC organisation. I suggest every project could try
that. Having experienced mentors is an asset to any organisation.

Pj.

On Tue, Apr 09, 2013 at 08:00:29PM +0100, Peter Cock wrote:
> On Tue, Apr 9, 2013 at 12:47 PM, Hilmar Lapp <hlapp at drycafe.net> wrote:
> > Wasn't the number of orgs last year around 180? That would
> > mean that the total number of accepted orgs is almost unchanged.
> 
> Yes, i checked and its been just under 180 for the last few years.
> 
> > However, the announcement on the Google blog says that
> > they accepted more than 40 new projects. Since the number
> > of accepted orgs for sure didn't rise, this must mean that
> > around 40 projects turned over, or almost 1 in every 4.
> >
> > -hilmar
> 
> It does seem Google are trying to cover different ground but
> with a fixed budget - and this year we were one of the unlucky
> organisations (but not alone in this respect).
> 
> Peter
> _______________________________________________
> GSoC mailing list
> GSoC at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/gsoc

From p.j.a.cock at googlemail.com  Thu Apr 11 05:11:57 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 11 Apr 2013 10:11:57 +0100
Subject: [GSoC] GSoC 2013 is ON
In-Reply-To: <20130411061304.GA14038@thebird.nl>
References: <20130303112326.GA5638@thebird.nl>
	<20130320211932.GA23848@thebird.nl>
	<20130408201346.GA3054@thebird.nl>
	<CAPkCRRuffbwq9oTPPCoCZmbJ43QC4hUp6nALtU6iOQR04eVe-A@mail.gmail.com>
	<5163797A.3090208@compbio.dundee.ac.uk>
	<9B1CEC1A-0839-43C0-AFBA-334BF4F3D459@drycafe.net>
	<CAKVJ-_447qQmoAL9h7GN79E=FkRYwnACUxCGYW4cyyP4O8BM1A@mail.gmail.com>
	<20130411061304.GA14038@thebird.nl>
Message-ID: <CAKVJ-_54KH9KiZrDZF9+9RgjZYokZ8Jfe-nZ0M-6x4ebftyZCw@mail.gmail.com>

On Thu, Apr 11, 2013 at 7:13 AM, Pjotr Prins <pjotr2010 at thebird.nl> wrote:
> SciRuby has been so kind to allow us to merge some BioRuby project
> ideas into their GSoC organisation. I suggest every project could try
> that. Having experienced mentors is an asset to any organisation.
>
> Pj.

That's good news.

Similarly Eric has been in touch with NESCent about some of the
phylogenetic project ideas we'd come up with for Biopython (we'd
partnered with them for GSoC before the OBF started applying).

I have tried emailing the Python Software Foundation (PSF)
contact - they are also acting as a GSoC umbrella organisation,
but have not had a reply yet.

Peter

(The CC list is quite long - are some of these potential
mentors not on the OBF's gsoc at lists.open-bio.org list?)

From cjfields at illinois.edu  Thu Apr 11 11:08:04 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 11 Apr 2013 15:08:04 +0000
Subject: [GSoC] GSoC 2013 is ON
In-Reply-To: <CAKVJ-_54KH9KiZrDZF9+9RgjZYokZ8Jfe-nZ0M-6x4ebftyZCw@mail.gmail.com>
References: <20130303112326.GA5638@thebird.nl>
	<20130320211932.GA23848@thebird.nl> <20130408201346.GA3054@thebird.nl>
	<CAPkCRRuffbwq9oTPPCoCZmbJ43QC4hUp6nALtU6iOQR04eVe-A@mail.gmail.com>
	<5163797A.3090208@compbio.dundee.ac.uk>
	<9B1CEC1A-0839-43C0-AFBA-334BF4F3D459@drycafe.net>
	<CAKVJ-_447qQmoAL9h7GN79E=FkRYwnACUxCGYW4cyyP4O8BM1A@mail.gmail.com>
	<20130411061304.GA14038@thebird.nl>
	<CAKVJ-_54KH9KiZrDZF9+9RgjZYokZ8Jfe-nZ0M-6x4ebftyZCw@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DD77BA@CHIMBX5.ad.uillinois.edu>

On Apr 11, 2013, at 4:11 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Thu, Apr 11, 2013 at 7:13 AM, Pjotr Prins <pjotr2010 at thebird.nl> wrote:
>> SciRuby has been so kind to allow us to merge some BioRuby project
>> ideas into their GSoC organisation. I suggest every project could try
>> that. Having experienced mentors is an asset to any organisation.
>> 
>> Pj.
> 
> That's good news.
> 
> Similarly Eric has been in touch with NESCent about some of the
> phylogenetic project ideas we'd come up with for Biopython (we'd
> partnered with them for GSoC before the OBF started applying).
> 
> I have tried emailing the Python Software Foundation (PSF)
> contact - they are also acting as a GSoC umbrella organisation,
> but have not had a reply yet.
> 
> Peter
> 
> (The CC list is quite long - are some of these potential
> mentors not on the OBF's gsoc at lists.open-bio.org list?)

Scott Cain (GMOD, aka 'Genome Informatics') also indicated students can submit project proposals to them as well.

chris



From p.j.a.cock at googlemail.com  Mon Feb 11 19:08:13 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 11 Feb 2013 19:08:13 +0000
Subject: [GSoC] [GSoC Mentors Announce] Google Summer of Code 2013
In-Reply-To: <CAEkQO61xzGb19SYi2wUVpA8Pe5XHzo+cR6S-9PeyoW_DOfc7JQ@mail.gmail.com>
References: <CAEkQO61xzGb19SYi2wUVpA8Pe5XHzo+cR6S-9PeyoW_DOfc7JQ@mail.gmail.com>
Message-ID: <CAKVJ-_56b+oxyAH-PYXTwSDT_KJ5y5tv0AjOEBntuNKsJA_qLw@mail.gmail.com>

Good news everyone, GSoC 2013 is happening :)

Hopefully the OBF will be accepted to take part once again.

Peter

On Mon, Feb 11, 2013 at 7:02 PM, Carol Smith <carols at google.com> wrote:
> Hi GSoC mentors and org admins,
>
> We've announced that we're doing Google Summer of Code 2013 [1]. Yay!
>
> If you would like to help spread the word about GSoC, we have presentations
> [2], logos [3], and flyers [4] for you to use. Please host meetups, tell
> your friends and colleagues about the program, go to conferences, talk to
> people about the program, and just generally do all the awesome
> word-of-mouth stuff you do every year to promote the program.
>
> The GSoC calendar, FAQ, and events timeline have all been updated with this
> year's important dates, so please refer to those for the milestones for this
> year's program. NB: the normal timeline for the program has been modified
> for this year. You'll probably want to examine the dates closely to make
> sure you know when important things are happening.
>
> Please consider translating the presentations and/or flyers into your native
> language and submitting them directly to me to post on the wiki.
> Localization for our material is integral to reaching the widest possible
> audience around the world. If you decide to translate a flyer, please fill
> out our form to request a thank you gift for your effort. [5]
>
> If you decide to host a meetup, please email me to let me know the date,
> time, and location so I can put it on the GSoC calendar. Also, remember to
> take pictures at your meetup and write up a blog post for our blog using our
> provided template for formatting [6]. If you need promotional items for your
> attendees, please fill out our form [7] to request some; we're happy to send
> some along. We can provide up to about 25 pens, notebooks, or stickers
> and/or a few t-shirts. Please keep in mind, though, that shipping
> restrictions and timeline vary country-to-country; request items early to
> make sure they get there on time! If you have questions about hosting
> meetups, please see the section in our FAQ [8].
>
> Please also consider applying to participate as an organization again this
> year or maybe joining as a mentor for your favorite organization if they are
> selected this year.
>
> We rely on you for your help for the success of this program, so thank you
> in advance for all the work you do!
>
> [1] -
> http://google-opensource.blogspot.com/2013/02/flip-bits-not-burgers-google-summer-of.html
> [2] -
> http://code.google.com/p/google-summer-of-code/wiki/ProgramPresentations
> [3] - http://code.google.com/p/google-summer-of-code/wiki/GsocLogos
> [4] - http://code.google.com/p/google-summer-of-code/wiki/GsocFlyers
> [5] - http://goo.gl/gEHDO
> [6] - http://goo.gl/wbZrt
> [7] - http://goo.gl/0BsR8
> [8] - http://goo.gl/2NGfp
>
> Cheers,
> Carol
>
> --
> You received this message because you are subscribed to the Google Groups
> "Google Summer of Code Mentors Announce List" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to gsoc-mentors-announce+unsubscribe at googlegroups.com.
> Visit this group at
> http://groups.google.com/group/gsoc-mentors-announce?hl=en-US.
> For more options, visit https://groups.google.com/groups/opt_out.
>
>


From rbuels at gmail.com  Mon Feb 11 19:14:39 2013
From: rbuels at gmail.com (Robert Buels)
Date: Mon, 11 Feb 2013 14:14:39 -0500
Subject: [GSoC] [GSoC Mentors Announce] Google Summer of Code 2013
In-Reply-To: <CAKVJ-_56b+oxyAH-PYXTwSDT_KJ5y5tv0AjOEBntuNKsJA_qLw@mail.gmail.com>
References: <CAEkQO61xzGb19SYi2wUVpA8Pe5XHzo+cR6S-9PeyoW_DOfc7JQ@mail.gmail.com>
	<CAKVJ-_56b+oxyAH-PYXTwSDT_KJ5y5tv0AjOEBntuNKsJA_qLw@mail.gmail.com>
Message-ID: <5119431F.90100@gmail.com>

Hurray!

Would someone else be interested in being the org admin for OBF this 
year?  Preferably someone who's been an OBF mentor in one of the 
previous years?  I've got a lot of things on my plate.

If someone else will be the primary, I can certainly volunteer as a backup.

Rob



On 02/11/2013 02:08 PM, Peter Cock wrote:
> Good news everyone, GSoC 2013 is happening :)
>
> Hopefully the OBF will be accepted to take part once again.
>
> Peter
>
> On Mon, Feb 11, 2013 at 7:02 PM, Carol Smith <carols at google.com> wrote:
>> Hi GSoC mentors and org admins,
>>
>> We've announced that we're doing Google Summer of Code 2013 [1]. Yay!
>>
>> If you would like to help spread the word about GSoC, we have presentations
>> [2], logos [3], and flyers [4] for you to use. Please host meetups, tell
>> your friends and colleagues about the program, go to conferences, talk to
>> people about the program, and just generally do all the awesome
>> word-of-mouth stuff you do every year to promote the program.
>>
>> The GSoC calendar, FAQ, and events timeline have all been updated with this
>> year's important dates, so please refer to those for the milestones for this
>> year's program. NB: the normal timeline for the program has been modified
>> for this year. You'll probably want to examine the dates closely to make
>> sure you know when important things are happening.
>>
>> Please consider translating the presentations and/or flyers into your native
>> language and submitting them directly to me to post on the wiki.
>> Localization for our material is integral to reaching the widest possible
>> audience around the world. If you decide to translate a flyer, please fill
>> out our form to request a thank you gift for your effort. [5]
>>
>> If you decide to host a meetup, please email me to let me know the date,
>> time, and location so I can put it on the GSoC calendar. Also, remember to
>> take pictures at your meetup and write up a blog post for our blog using our
>> provided template for formatting [6]. If you need promotional items for your
>> attendees, please fill out our form [7] to request some; we're happy to send
>> some along. We can provide up to about 25 pens, notebooks, or stickers
>> and/or a few t-shirts. Please keep in mind, though, that shipping
>> restrictions and timeline vary country-to-country; request items early to
>> make sure they get there on time! If you have questions about hosting
>> meetups, please see the section in our FAQ [8].
>>
>> Please also consider applying to participate as an organization again this
>> year or maybe joining as a mentor for your favorite organization if they are
>> selected this year.
>>
>> We rely on you for your help for the success of this program, so thank you
>> in advance for all the work you do!
>>
>> [1] -
>> http://google-opensource.blogspot.com/2013/02/flip-bits-not-burgers-google-summer-of.html
>> [2] -
>> http://code.google.com/p/google-summer-of-code/wiki/ProgramPresentations
>> [3] - http://code.google.com/p/google-summer-of-code/wiki/GsocLogos
>> [4] - http://code.google.com/p/google-summer-of-code/wiki/GsocFlyers
>> [5] - http://goo.gl/gEHDO
>> [6] - http://goo.gl/wbZrt
>> [7] - http://goo.gl/0BsR8
>> [8] - http://goo.gl/2NGfp
>>
>> Cheers,
>> Carol
>>
>> --
>> You received this message because you are subscribed to the Google Groups
>> "Google Summer of Code Mentors Announce List" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to gsoc-mentors-announce+unsubscribe at googlegroups.com.
>> Visit this group at
>> http://groups.google.com/group/gsoc-mentors-announce?hl=en-US.
>> For more options, visit https://groups.google.com/groups/opt_out.
>>
>>
> _______________________________________________
> GSoC mailing list
> GSoC at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/gsoc
>


From hlapp at drycafe.net  Sun Feb 24 16:57:56 2013
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Sun, 24 Feb 2013 11:57:56 -0500
Subject: [GSoC] Fwd: Standardizing Organizations Keywords
References: <CA+3KvkN52yb0qrf8Y4U9EQRNxM1N3kbjhWgjY8h_68aO19oVYw@mail.gmail.com>
Message-ID: <87B7DB03-0F1F-4B8D-9314-8210B27553A5@drycafe.net>

Any other suggestions for adding/fixing DBpedia (= Wikipedia articles) keywords for OBF, or literal string keywords? I'd be happy to add suggestions before I issue a pull request. Alternatively, everyone is of course welcome to fork their own copy and submit a change request.

https://github.com/hlapp/dbpedia-spotlight-gsoc/compare/master...obf-fixes

	-hilmar

Begin forwarded message:

> From: "Pablo N. Mendes" <pablomendes at gmail.com>
> Subject: Re: [GSoC Mentors] Re: Standardizing Organizations Keywords
> Date: February 22, 2013 1:53:11 PM EST
> To: Joel Sherrill <joel.sherrill at gmail.com>
> Cc: Stefan Seefeld <stefan at codesourcery.com>, google-summer-of-code-mentors-list at googlegroups.com, Max Jakob <max.jakob at gmail.com>, Joachim Daiber <daiber.joachim at gmail.com>
> 
> 
> Thanks for the feedback Joel. TL;DR: If the community is interested, we can regenerate better tags and you all can contribute with the necessary fixes/additions.
> 
> As this thread may quickly become unwelcome here, let's move the discussion to our issue tracker?
> https://github.com/pablomendes/dbpedia-spotlight-gsoc/issues
> 
> Now the longer message, answering your questions:
> 
> how could a set of keywords be checked automatically and then the organization admin choose to use them or not.
> 
> Easy! That perks of being among Open Source folks, right? I pointed out in my earlier e-mail the files that our system created automatically [1][2]. All you need to do is to git clone our repo, make the fixes in any text editor and submit a pull request on GitHub. I think it was Jim from Apertium that has already done this for some orgs. We'd be glad to merge the fixes and update our engine.
> 
> But I don't know how to make your engine happy. 
> 
> I can try to help you to understand what is happening there. But first I need to find out which org is yours. After some searching, I figured it must be RTEMS? If not, just let me know. But these are the tags that we have for RTEMS for 2011:
> 
> <http://dbpedia.org/resource/Thread_%28computer_science%29> .
> <http://dbpedia.org/resource/Embedded_system> .
> <http://dbpedia.org/resource/Shapeshifter_%28band%29> .
> <http://dbpedia.org/resource/C%2B%2B> .
> <http://dbpedia.org/resource/POSIX> .
> <http://dbpedia.org/resource/Ada_%28programming_language%29> .
> <http://dbpedia.org/resource/Operating_system>
> 
> Clearly some wrong ones, but also some good ones. So searching for Operating System should definitely have retrieved something. I think that I only loaded the 2012 tags. For 2012, I have no tags for your project at all. This is probably because an error happened in our crawler when processing your page, and we missed those tags. We seem to be able to process it now, as you can see here:
> http://spotlight.dbpedia.org/rest/annotate?url=http://www.rtems.org/wiki/index.php/Open_Projects
> 
> Even better, our new code (result of Jo Daiber's work from GSoC 2012) seems to perform much better:
> http://spotlight.sztaki.hu:2222/rest/annotate?url=http://www.rtems.org/wiki/index.php/Open_Projects
> 
> We can regenerate the tags and have the community helping with some cleanup/additions for their orgs, if anybody is interested.
> 
> Cheers,
> Pablo
> 
> [1] https://raw.github.com/pablomendes/dbpedia-spotlight-gsoc/master/data/gsoc-projects-2011.nt
> [2] https://raw.github.com/pablomendes/dbpedia-spotlight-gsoc/master/data/gsoc-projects-2012.nt
> 
> 
> On Fri, Feb 22, 2013 at 5:08 PM, Joel Sherrill <joel.sherrill at gmail.com> wrote:
> This is very cool!!!  
> 
> It certainly provides more information about the tags but it still suffers from issues like
> me not putting commas between the tags which results gibberish instead of a set
> of Wikipedia pages, various forms of "big data", and strange or useless tags. [1]
> 
> But as a rule, if your tag doesn't match something related at Wikipedia, then 
> it very likely isn't a useful tag. That's a pretty good rule.
> 
> But I don't know how to make your engine happy. Using your search page, I 
> couldn't even find my own project even though we were in both projects. When I
> typed "operating system", I missed a most OS GSOC participants. And when
> I got RTOS, I only got a few closed source products.
> 
> it is too late for 2013, but how could a set of keywords be checked automatically
> and then the organization admin choose to use them or not.
> 
> --joel
> RTEMS
> 
> [1] I am personally interested in the "Awesome_God" project. :)
> 
> On Fri, Feb 22, 2013 at 2:53 AM, Pablo N. Mendes <pablomendes at gmail.com> wrote:
> 
> Well, what about just using Wikipedia pages as topics? All major languages, algorithms, techniques, technologies, etc. are there already. That is the idea of the DBpedia project: use each Wikipedia page as describing a "thing", and subsequently classify these things according to a taxonomy. I don't see why we would need to repeat that work.
> 
> Moreover, our tool (DBpedia Spotlight) has the ability to churn through your "project ideas" pages and suggest DBpedia "tags" based on the content of those pages. Since this information extraction process is automated and tackles a difficult problem, the tool makes mistakes. But, no problem, updating this list should be less work than just creating a taxonomy from scratch and then tagging each project manually.
> 
> By provocation from Jimmy O'Reagan, I sit down together with Max Jakob and hacked something together. Here are the tags that we have extracted for 2011 and 2012 projects:
> https://github.com/pablomendes/dbpedia-spotlight-gsoc/tree/master/data
> 
> We later sit down with Jo Daiber and also prettied up a little search application to help users to find projects and to demonstrate what other advantages you may gain by using DBpedia tags rather than just plain old "string" tags.
> http://spotlight.dbpedia.org/gsoc-searcher/
> 
> The function described there as "Expand" uses some knowledge that we have about the tags to try and model "relatedness", so that we can suggest extra related tags for the students to search.
> 
> Everything was hacked together quickly, so it is still very preliminary. But I think it demonstrates the core ideas, if you are open minded. :)
> 
> What do you think?
> 
> Cheers,
> Pablo
> 
> 
> On Wed, Feb 20, 2013 at 9:59 PM, Stefan Seefeld <stefan at codesourcery.com> wrote:
> On 02/20/2013 03:46 PM, Aaron Meurer wrote:
> > An ideal situation would be if there were some kind of StackOverflow
> > type system where keywords autocompleted against what has already been
> > used, and synonyms could be defined. I don't know if the Melange team
> > has the desire and/or resources to do something like this.
> 
> Indeed, a shared taxonomy would help greatly. And there are a few
> precedents used in the FLOSS world to pick from, such as:
> https://pypi.python.org/pypi?%3Aaction=list_classifiers
> 
> I still struggle understanding why the GSoC (meta-)project needed its
> own web application. It could have picked one with such features already
> in place.
> 
> But that's a separate discussion.
> 
>         Stefan
> 
> --
> Stefan Seefeld
> stefan at codesourcery.com
> 
> 
> 
> -- 
> 
> Pablo N. Mendes
> http://pablomendes.com
> 
> -- 
> You received this message because you are subscribed to the Google Groups "Google Summer of Code Mentors List" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to google-summer-of-code-mentors-list+unsubscribe at googlegroups.com.
> To post to this group, send email to google-summer-of-code-mentors-list at googlegroups.com.
> Visit this group at http://groups.google.com/group/google-summer-of-code-mentors-list?hl=en-US.
> For more options, visit https://groups.google.com/groups/opt_out.
>  
>  
> 
> 
> 
> 
> -- 
> 
> Pablo N. Mendes
> http://pablomendes.com
> 
> -- 
> You received this message because you are subscribed to the Google Groups "Google Summer of Code Mentors List" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to google-summer-of-code-mentors-list+unsubscribe at googlegroups.com.
> To post to this group, send email to google-summer-of-code-mentors-list at googlegroups.com.
> Visit this group at http://groups.google.com/group/google-summer-of-code-mentors-list?hl=en-US.
> For more options, visit https://groups.google.com/groups/opt_out.
>  
>  

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================







From pjotr2010 at thebird.nl  Thu Feb 28 22:13:05 2013
From: pjotr2010 at thebird.nl (Pjotr Prins)
Date: Thu, 28 Feb 2013 23:13:05 +0100
Subject: [GSoC] [GSoC Mentors Announce] Google Summer of Code 2013
In-Reply-To: <5119431F.90100@gmail.com>
References: <CAEkQO61xzGb19SYi2wUVpA8Pe5XHzo+cR6S-9PeyoW_DOfc7JQ@mail.gmail.com>
	<CAKVJ-_56b+oxyAH-PYXTwSDT_KJ5y5tv0AjOEBntuNKsJA_qLw@mail.gmail.com>
	<5119431F.90100@gmail.com>
Message-ID: <20130228221305.GA28817@thebird.nl>

On Mon, Feb 11, 2013 at 02:14:39PM -0500, Robert Buels wrote:
> Hurray!
> 
> Would someone else be interested in being the org admin for OBF this
> year?  Preferably someone who's been an OBF mentor in one of the
> previous years?  I've got a lot of things on my plate.
> 
> If someone else will be the primary, I can certainly volunteer as a backup.
> 
> Rob

Because I think GSoC so important for bioinformatics I volunteer to
take on being the org admin for OBF this year. Chris Fields and Rob
Buels have promised to act as support, backup and conscience. Note
that I view this role as being purely organisational and
administrative. The difficult decisions will be made by OBF board
members. 

Pj.


From hlapp at drycafe.net  Sun Mar  3 01:21:37 2013
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Sat, 2 Mar 2013 20:21:37 -0500
Subject: [GSoC] [OBF-GSoC-Mentors] [GSoC Mentors Announce] Google Summer
	of Code 2013
In-Reply-To: <20130228221305.GA28817@thebird.nl>
References: <CAEkQO61xzGb19SYi2wUVpA8Pe5XHzo+cR6S-9PeyoW_DOfc7JQ@mail.gmail.com>
	<CAKVJ-_56b+oxyAH-PYXTwSDT_KJ5y5tv0AjOEBntuNKsJA_qLw@mail.gmail.com>
	<5119431F.90100@gmail.com> <20130228221305.GA28817@thebird.nl>
Message-ID: <A9A903B2-6D1F-4740-8689-DA5C2F70506F@drycafe.net>


On Feb 28, 2013, at 5:13 PM, Pjotr Prins wrote:

> I volunteer to take on being the org admin for OBF this year.

Awesome & thanks for volunteering!

> Chris Fields and Rob Buels have promised to act as support, backup and conscience.

I'm happy to be asked as well or to chime in on difficult situations.

> Note that I view this role as being purely organisational and administrative. The difficult decisions will be made by OBF board members. 

I'm not sure the Board would be the right body to make those decisions - some of its members aren't or have never been actively involved with GSoC, and so would have limited background.

So I think you should be prepared to make decisions, and that some of these may be difficult. You have common sense, empathy, and good judgment, so I don't see why that should make anyone concerned. It's easy when there's obvious consensus among the mentors, but when there isn't despite attempts to achieve it, someone will have to decide.

I might liken this to BOSC and the Board's relationship to the BOSC Committee Chair. While the Chair may ask the Board for advice, or the Board may ask the Chair to report status, it's the Chair who makes the decisions regarding BOSC, in consultation with others on the committee. 

The Board does give a formal blessing to the BOSC Chair in public session, and if you would like us to start doing the same for the prospective GSoC admin, I'd support that and put it on the agenda for the next public Board meeting.

	-hilmar
-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================







From pjotr2010 at thebird.nl  Sun Mar  3 15:15:05 2013
From: pjotr2010 at thebird.nl (Pjotr Prins)
Date: Sun, 3 Mar 2013 16:15:05 +0100
Subject: [GSoC] [pjotr2010@thebird.nl: GSoC 2013 is ON]
Message-ID: <20130303151505.GA6690@thebird.nl>

Dear project leaders. 

I am sending below announcement to you, to have it forwarded by you to
your mailing lists. Please do so. Also pass this message on to anyone
who might be in some way interested in the OBF/GSoC initiative. To
participate, start by signing up to the soc mailing list at
http://lists.open-bio.org/mailman/listinfo/gsoc

Spread the word!

~~~

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




From pjotr2010 at thebird.nl  Sun Mar  3 11:23:26 2013
From: pjotr2010 at thebird.nl (Pjotr Prins)
Date: Sun, 3 Mar 2013 12:23:26 +0100
Subject: [GSoC] GSoC 2013 is ON
Message-ID: <20130303112326.GA5638@thebird.nl>

Dear project leaders. 

I am sending below announcement to you, to have it forwarded by you to
your mailing lists. Please do so. Also pass this message on to anyone
who might be in some way interested in the OBF/GSoC initiative. To
participate, start by signing up to the soc mailing list at
http://lists.open-bio.org/mailman/listinfo/gsoc

Spread the word!

~~~

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



From pjotr2010 at thebird.nl  Wed Mar 20 21:19:32 2013
From: pjotr2010 at thebird.nl (Pjotr Prins)
Date: Wed, 20 Mar 2013 22:19:32 +0100
Subject: [GSoC] GSoC 2013 is ON
In-Reply-To: <20130303112326.GA5638@thebird.nl>
References: <20130303112326.GA5638@thebird.nl>
Message-ID: <20130320211932.GA23848@thebird.nl>

Heads up! One more week to go for project ideas! Please update

  https://github.com/OBF/GSoC/wiki/Google-Summer-of-Code-2013

with the latest links. And maybe a wakeup call to your lists?

If you are not on the Internet you don't exist. If you are not making
use of GSoC, you might as well be dead ;).

Kidding. But, the more ideas, the better.

Pj.

* March 22nd: Finalise project ideas
* March 29th: Deadline OBF mentoring organisation submission to Google

On Sun, Mar 03, 2013 at 12:23:26PM +0100, Pjotr Prins wrote:
> Dear project leaders. 
> 
> I am sending below announcement to you, to have it forwarded by you to
> your mailing lists. Please do so. Also pass this message on to anyone
> who might be in some way interested in the OBF/GSoC initiative. To
> participate, start by signing up to the soc mailing list at
> http://lists.open-bio.org/mailman/listinfo/gsoc
> 
> Spread the word!
> 
> ~~~
> 
> 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
> 


From pjotr2010 at thebird.nl  Sun Mar 24 07:51:21 2013
From: pjotr2010 at thebird.nl (Pjotr Prins)
Date: Sun, 24 Mar 2013 08:51:21 +0100
Subject: [GSoC] GSoC 2013 is ON
In-Reply-To: <20130320211932.GA23848@thebird.nl>
References: <20130303112326.GA5638@thebird.nl>
	<20130320211932.GA23848@thebird.nl>
Message-ID: <20130324075121.GA7300@thebird.nl>

The GSoC-OBF application has been submitted to Google. The
applications will be reviewed from next week.

So, one week to go for project ideas. Please add at least one link to
your project ideas (page) on either the github page below or the main
OBF GSoC wiki page. I'll combine them in the final stage. Make sure to
show a primary mentor for every idea, and a secondary (backup) mentor.

Thanks,

Pj.

On Wed, Mar 20, 2013 at 10:19:32PM +0100, Pjotr Prins wrote:
> Heads up! One more week to go for project ideas! Please update
> 
>   https://github.com/OBF/GSoC/wiki/Google-Summer-of-Code-2013
> 
> with the latest links. And maybe a wakeup call to your lists?
> 
> If you are not on the Internet you don't exist. If you are not making
> use of GSoC, you might as well be dead ;).
> 
> Kidding. But, the more ideas, the better.
> 
> Pj.
> 
> * March 22nd: Finalise project ideas
> * March 29th: Deadline OBF mentoring organisation submission to Google
> 
> On Sun, Mar 03, 2013 at 12:23:26PM +0100, Pjotr Prins wrote:
> > Dear project leaders. 
> > 
> > I am sending below announcement to you, to have it forwarded by you to
> > your mailing lists. Please do so. Also pass this message on to anyone
> > who might be in some way interested in the OBF/GSoC initiative. To
> > participate, start by signing up to the soc mailing list at
> > http://lists.open-bio.org/mailman/listinfo/gsoc
> > 
> > Spread the word!
> > 
> > ~~~
> > 
> > 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
> > 


From pjotr2010 at thebird.nl  Sat Mar 30 09:22:36 2013
From: pjotr2010 at thebird.nl (Pjotr Prins)
Date: Sat, 30 Mar 2013 10:22:36 +0100
Subject: [GSoC] GSoC 2013 is ON
Message-ID: <20130330092236.GA31459@thebird.nl>

The OBF has submitted the application for being a mentor org in this
year's Google Summer of Code. I have listed all project ideas on:

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

For Biopython (3x), BioRuby (5x) and BioJava (4x) I found project ideas.

The others are missing.

There is still a (rather small) window of opportunity for adding
ideas. Make sure you inform me of additional ones to get them listed
from the main page.

Pj.


From hlapp at drycafe.net  Sat Mar 30 17:41:21 2013
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Sat, 30 Mar 2013 12:41:21 -0500
Subject: [GSoC] GSoC 2013 is ON
In-Reply-To: <20130330092236.GA31459@thebird.nl>
References: <20130330092236.GA31459@thebird.nl>
Message-ID: <1FB4BAB7-E7B2-4AD3-9D8C-A4BF134E66D2@drycafe.net>

I'm assuming "The OBF" is you in this case - thanks & kudos for pulling this together. Now fingers crossed!

-hilmar

Sent with a tap.

On Mar 30, 2013, at 4:22 AM, Pjotr Prins <pjotr2010 at thebird.nl> wrote:

> The OBF has submitted the application for being a mentor org in this
> year's Google Summer of Code. I have listed all project ideas on:
> 
>  http://www.open-bio.org/wiki/Google_Summer_of_Code
> 
> For Biopython (3x), BioRuby (5x) and BioJava (4x) I found project ideas.
> 
> The others are missing.
> 
> There is still a (rather small) window of opportunity for adding
> ideas. Make sure you inform me of additional ones to get them listed
> from the main page.
> 
> Pj.



From cjfields at illinois.edu  Sat Mar 30 22:15:31 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Sat, 30 Mar 2013 22:15:31 +0000
Subject: [GSoC] GSoC 2013 is ON
In-Reply-To: <20130330092236.GA31459@thebird.nl>
References: <20130330092236.GA31459@thebird.nl>
Message-ID: <94avmiklcc69157bvumw54mf.1364681728380@email.android.com>

I'll try adding a few for bioperl tonight.  Been busy this week with family.

Chris


Sent via a capable phone of some make and model


-------- Original message --------
From: Pjotr Prins <pjotr2010 at thebird.nl>
Date: 03/30/2013 4:23 AM (GMT-06:00)
To: Pjotr Prins <pjotr2010 at thebird.nl>
Cc: p.j.a.cock at googlemail.com,"Fields, Christopher J" <cjfields at illinois.edu>,panel at bioruby.org,Andreas Prlic <andreas at sdsc.edu>,hlapp at gmx.net,moeller at debian.org,mark.wilkinson at upm.es,ricepeterm at yahoo.co.uk,ketil at malde.org,jprocter at compbio.dundee.ac.uk,reece at harts.net,chapmanb at 50mail.com,OBF GSoC <gsoc at lists.open-bio.org>
Subject: Re: GSoC 2013 is ON


The OBF has submitted the application for being a mentor org in this
year's Google Summer of Code. I have listed all project ideas on:

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

For Biopython (3x), BioRuby (5x) and BioJava (4x) I found project ideas.

The others are missing.

There is still a (rather small) window of opportunity for adding
ideas. Make sure you inform me of additional ones to get them listed
from the main page.

Pj.



From ketil at malde.org  Tue Apr  2 08:03:58 2013
From: ketil at malde.org (Ketil Malde)
Date: Tue, 02 Apr 2013 10:03:58 +0200
Subject: [GSoC] GSoC 2013 is ON
In-Reply-To: <20130330092236.GA31459@thebird.nl>
References: <20130330092236.GA31459@thebird.nl>
Message-ID: <87r4it8ikx.fsf@nmd999X.imr.no>


[CC everybody including the biohaskell list. Let me know if any of you
want off. :-) ]

Pjotr Prins <pjotr2010 at thebird.nl> writes:

>   http://www.open-bio.org/wiki/Google_Summer_of_Code

> For Biopython (3x), BioRuby (5x) and BioJava (4x) I found project ideas.

> The others are missing.

> There is still a (rather small) window of opportunity for adding
> ideas.

I have one thing that might work well as a SOC project, if the right
student could be found.

Basically, I and a colleague recently developed and published a method
and implementation for more sensitive pairwise alignments.  The paper is
here, I think (PLoS ONE seems to be down atm):
  http://dx.plos.org/10.1371/journal.pone.0054422

I'm really happy about the results, if nothing else, check the SCOP
benchmark.  Although it's difficult to construct a good test case using
more complex methods (training sets for HMMs and whatnot) I don't know
anything that is as good as this.  We're using it for annotation of
genes.

The current implementation is in Haskell, and although it works
correctly, it is a bit slow, and more problematic, it consumes too much
memory (so going multi-threaded, although pretty easy, won't be of any
help).

I would like to make this into a less resource intensive (and thus more
practical) tool, and there are two ways I can think of to go about this:

1) Optimize the Haskell program

2) Reimplement the algorithm (or parts of it) in a different language

Advantages of 1:

* Already have a working program, and the type system makes it easy to
refactor without introducing errors.
* Haskell supports lots of good multi-threading programming models (like
STM)
* I know Haskell pretty well, and will be hopefully be able to mentor.

Disadvantages:

* Haskell has some good debugging tools, but they tend to work really
  poorly for large memory (i.e. it takes a long time to generate
  profiles)
* Needs somebody with a bit (or a lot) of experience optimizing Haskell,
  and good knowledge of high-perf libraries (like vector)

Advantages of 2:

* Easier to get a student with adequate skills.
* More predictable performance models in other languages.
* Easier to compile and install for many users.

Disadvantages:

* Ideally, should know enough Haskell to read and understand the code.
* Likely needs a co-mentor with knowledge of the language in question.

Is this something I could or should submit as a task?

-k
-- 
If I haven't seen further, it is by standing in the footprints of giants


From pjotr2010 at thebird.nl  Tue Apr  2 08:36:52 2013
From: pjotr2010 at thebird.nl (Pjotr Prins)
Date: Tue, 2 Apr 2013 10:36:52 +0200
Subject: [GSoC] GSoC 2013 is ON
In-Reply-To: <87r4it8ikx.fsf@nmd999X.imr.no>
References: <20130330092236.GA31459@thebird.nl> <87r4it8ikx.fsf@nmd999X.imr.no>
Message-ID: <20130402083652.GA9504@thebird.nl>

Great idea. Can you format it as a project idea on your Wiki - take
the other ideas as an example. You can leave the two options open and
see what student reacts to.

BTW We only have the 'right' students :). The selection process is
pretty strong.

There is some ongoing discussion about core and non-core OBF projects,
but I think since BioHaskell is going strong there will be little
against adding one project idea. If it brings a really competent
student we all gain.

There is a meeting between GSoC and the OBF board on the 9th, right
after we get or do not get accepted as a mentoring organisation. I'll
make a case for inclusion of your project idea into the program.

Adding it to the wiki will help.

Pj.

On Tue, Apr 02, 2013 at 10:03:58AM +0200, Ketil Malde wrote:
> 
> [CC everybody including the biohaskell list. Let me know if any of you
> want off. :-) ]
> 
> Pjotr Prins <pjotr2010 at thebird.nl> writes:
> 
> >   http://www.open-bio.org/wiki/Google_Summer_of_Code
> 
> > For Biopython (3x), BioRuby (5x) and BioJava (4x) I found project ideas.
> 
> > The others are missing.
> 
> > There is still a (rather small) window of opportunity for adding
> > ideas.
> 
> I have one thing that might work well as a SOC project, if the right
> student could be found.
> 
> Basically, I and a colleague recently developed and published a method
> and implementation for more sensitive pairwise alignments.  The paper is
> here, I think (PLoS ONE seems to be down atm):
>   http://dx.plos.org/10.1371/journal.pone.0054422
> 
> I'm really happy about the results, if nothing else, check the SCOP
> benchmark.  Although it's difficult to construct a good test case using
> more complex methods (training sets for HMMs and whatnot) I don't know
> anything that is as good as this.  We're using it for annotation of
> genes.
> 
> The current implementation is in Haskell, and although it works
> correctly, it is a bit slow, and more problematic, it consumes too much
> memory (so going multi-threaded, although pretty easy, won't be of any
> help).
> 
> I would like to make this into a less resource intensive (and thus more
> practical) tool, and there are two ways I can think of to go about this:
> 
> 1) Optimize the Haskell program
> 
> 2) Reimplement the algorithm (or parts of it) in a different language
> 
> Advantages of 1:
> 
> * Already have a working program, and the type system makes it easy to
> refactor without introducing errors.
> * Haskell supports lots of good multi-threading programming models (like
> STM)
> * I know Haskell pretty well, and will be hopefully be able to mentor.
> 
> Disadvantages:
> 
> * Haskell has some good debugging tools, but they tend to work really
>   poorly for large memory (i.e. it takes a long time to generate
>   profiles)
> * Needs somebody with a bit (or a lot) of experience optimizing Haskell,
>   and good knowledge of high-perf libraries (like vector)
> 
> Advantages of 2:
> 
> * Easier to get a student with adequate skills.
> * More predictable performance models in other languages.
> * Easier to compile and install for many users.
> 
> Disadvantages:
> 
> * Ideally, should know enough Haskell to read and understand the code.
> * Likely needs a co-mentor with knowledge of the language in question.
> 
> Is this something I could or should submit as a task?
> 
> -k
> -- 
> If I haven't seen further, it is by standing in the footprints of giants


From ketil at malde.org  Thu Apr  4 11:29:32 2013
From: ketil at malde.org (Ketil Malde)
Date: Thu, 04 Apr 2013 13:29:32 +0200
Subject: [GSoC] GSoC 2013 is ON
In-Reply-To: <20130402083652.GA9504@thebird.nl>
References: <20130330092236.GA31459@thebird.nl>,
	<87r4it8ikx.fsf@nmd999X.imr.no>, <20130402083652.GA9504@thebird.nl>
Message-ID: <874nfm7cv7.fsf@nmd999X.imr.no>


Pjotr Prins <pjotr2010 at thebird.nl> writes:

> Great idea. Can you format it as a project idea on your Wiki - take
> the other ideas as an example.

I've added the link with just a quick rehash of my email text.

-k
-- 
If I haven't seen further, it is by standing in the footprints of giants


From pjotr2010 at thebird.nl  Mon Apr  8 20:13:46 2013
From: pjotr2010 at thebird.nl (Pjotr Prins)
Date: Mon, 8 Apr 2013 22:13:46 +0200
Subject: [GSoC] GSoC 2013 is ON
In-Reply-To: <20130320211932.GA23848@thebird.nl>
References: <20130303112326.GA5638@thebird.nl>
	<20130320211932.GA23848@thebird.nl>
Message-ID: <20130408201346.GA3054@thebird.nl>

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.

On Wed, Mar 20, 2013 at 10:19:32PM +0100, Pjotr Prins wrote:
> Heads up! One more week to go for project ideas! Please update
> 
>   https://github.com/OBF/GSoC/wiki/Google-Summer-of-Code-2013
> 
> with the latest links. And maybe a wakeup call to your lists?
> 
> If you are not on the Internet you don't exist. If you are not making
> use of GSoC, you might as well be dead ;).
> 
> Kidding. But, the more ideas, the better.
> 
> Pj.
> 
> * March 22nd: Finalise project ideas
> * March 29th: Deadline OBF mentoring organisation submission to Google
> 
> On Sun, Mar 03, 2013 at 12:23:26PM +0100, Pjotr Prins wrote:
> > Dear project leaders. 
> > 
> > I am sending below announcement to you, to have it forwarded by you to
> > your mailing lists. Please do so. Also pass this message on to anyone
> > who might be in some way interested in the OBF/GSoC initiative. To
> > participate, start by signing up to the soc mailing list at
> > http://lists.open-bio.org/mailman/listinfo/gsoc
> > 
> > Spread the word!
> > 
> > ~~~
> > 
> > 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
> > 


From p.j.a.cock at googlemail.com  Mon Apr  8 20:28:29 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 8 Apr 2013 21:28:29 +0100
Subject: [GSoC] GSoC 2013 is ON
In-Reply-To: <20130408201346.GA3054@thebird.nl>
References: <20130303112326.GA5638@thebird.nl>
	<20130320211932.GA23848@thebird.nl>
	<20130408201346.GA3054@thebird.nl>
Message-ID: <CAKVJ-_5rt_OWBp5dmw0YP8-sCoRx9Uuc1Pc9aAG2AwPZTjQ-Yw@mail.gmail.com>

Thanks Pjotr,

Dang. That was unexpected. Looking back we could have
done a better job highlighting what previous projects had
achieved (although I think we were getting better at that),
but otherwise I am struggling to guess what the cause
was - beyond your suggestion that things are simply
increasingly competitive.

We'll need to send out some sort of public announcement
(email & posted to blog), your email below does highlight some
positives. Do we know if NESCent was accepted? Or any
other relevant organisations with which we might partner
for one or two projects?

Peter

On Monday, April 8, 2013, Pjotr Prins wrote:

> 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.
>
> On Wed, Mar 20, 2013 at 10:19:32PM +0100, Pjotr Prins wrote:
> > Heads up! One more week to go for project ideas! Please update
> >
> >   https://github.com/OBF/GSoC/wiki/Google-Summer-of-Code-2013
> >
> > with the latest links. And maybe a wakeup call to your lists?
> >
> > If you are not on the Internet you don't exist. If you are not making
> > use of GSoC, you might as well be dead ;).
> >
> > Kidding. But, the more ideas, the better.
> >
> > Pj.
> >
> > * March 22nd: Finalise project ideas
> > * March 29th: Deadline OBF mentoring organisation submission to Google
> >
> > On Sun, Mar 03, 2013 at 12:23:26PM +0100, Pjotr Prins wrote:
> > > Dear project leaders.
> > >
> > > I am sending below announcement to you, to have it forwarded by you to
> > > your mailing lists. Please do so. Also pass this message on to anyone
> > > who might be in some way interested in the OBF/GSoC initiative. To
> > > participate, start by signing up to the soc mailing list at
> > > http://lists.open-bio.org/mailman/listinfo/gsoc
> > >
> > > Spread the word!
> > >
> > > ~~~
> > >
> > > 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 <javascript:;>
> > >
> > > 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
> > >
>


From hlapp at drycafe.net  Mon Apr  8 20:51:01 2013
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Mon, 8 Apr 2013 16:51:01 -0400
Subject: [GSoC] GSoC 2013 is ON
In-Reply-To: <CAKVJ-_5rt_OWBp5dmw0YP8-sCoRx9Uuc1Pc9aAG2AwPZTjQ-Yw@mail.gmail.com>
References: <20130303112326.GA5638@thebird.nl>
	<20130320211932.GA23848@thebird.nl>
	<20130408201346.GA3054@thebird.nl>
	<CAKVJ-_5rt_OWBp5dmw0YP8-sCoRx9Uuc1Pc9aAG2AwPZTjQ-Yw@mail.gmail.com>
Message-ID: <A9491C4B-8DE2-43AA-BD9E-67A43FF3B03B@drycafe.net>


On Apr 8, 2013, at 4:28 PM, Peter Cock wrote:

> Do we know if NESCent was accepted? 


Yes, they were. -hilmar

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================






From john.woods at marcottelab.org  Mon Apr  8 20:58:45 2013
From: john.woods at marcottelab.org (John Woods)
Date: Mon, 8 Apr 2013 15:58:45 -0500
Subject: [GSoC] GSoC 2013 is ON
In-Reply-To: <20130408201346.GA3054@thebird.nl>
References: <20130303112326.GA5638@thebird.nl>
	<20130320211932.GA23848@thebird.nl>
	<20130408201346.GA3054@thebird.nl>
Message-ID: <CAPkCRRuffbwq9oTPPCoCZmbJ43QC4hUp6nALtU6iOQR04eVe-A@mail.gmail.com>

(+John Prince, +Carlos Agarie)

Hey Pjotr,

First of all, I'm so sorry to hear you all didn't get it. I've learned so
much about running our fellowship programs from how well you all manage
your GSOC students.

I just learned that SciRuby did get accepted, which was quite honestly a
tiny bit surprising for me (we've definitely been rejected before).

Would you all be willing to get involved with our Summer of Code efforts?
We're a bit short on mentors, and I think there's room for us to adopt some
of your more general-science-y projects.

John


On Mon, Apr 8, 2013 at 3:13 PM, Pjotr Prins <pjotr2010 at thebird.nl> wrote:

> 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.
>
> On Wed, Mar 20, 2013 at 10:19:32PM +0100, Pjotr Prins wrote:
> > Heads up! One more week to go for project ideas! Please update
> >
> >   https://github.com/OBF/GSoC/wiki/Google-Summer-of-Code-2013
> >
> > with the latest links. And maybe a wakeup call to your lists?
> >
> > If you are not on the Internet you don't exist. If you are not making
> > use of GSoC, you might as well be dead ;).
> >
> > Kidding. But, the more ideas, the better.
> >
> > Pj.
> >
> > * March 22nd: Finalise project ideas
> > * March 29th: Deadline OBF mentoring organisation submission to Google
> >
> > On Sun, Mar 03, 2013 at 12:23:26PM +0100, Pjotr Prins wrote:
> > > Dear project leaders.
> > >
> > > I am sending below announcement to you, to have it forwarded by you to
> > > your mailing lists. Please do so. Also pass this message on to anyone
> > > who might be in some way interested in the OBF/GSoC initiative. To
> > > participate, start by signing up to the soc mailing list at
> > > http://lists.open-bio.org/mailman/listinfo/gsoc
> > >
> > > Spread the word!
> > >
> > > ~~~
> > >
> > > 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
> > >
> _______________________________________________
> GSoC mailing list
> GSoC at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/gsoc
>


From cjfields at illinois.edu  Mon Apr  8 20:55:25 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 8 Apr 2013 20:55:25 +0000
Subject: [GSoC] GSoC 2013 is ON
In-Reply-To: <A9491C4B-8DE2-43AA-BD9E-67A43FF3B03B@drycafe.net>
References: <20130303112326.GA5638@thebird.nl>
	<20130320211932.GA23848@thebird.nl> <20130408201346.GA3054@thebird.nl>
	<CAKVJ-_5rt_OWBp5dmw0YP8-sCoRx9Uuc1Pc9aAG2AwPZTjQ-Yw@mail.gmail.com>
	<A9491C4B-8DE2-43AA-BD9E-67A43FF3B03B@drycafe.net>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DD325A@CHIMBX5.ad.uillinois.edu>

On Apr 8, 2013, at 3:51 PM, Hilmar Lapp <hlapp at drycafe.net>
 wrote:

> 
> On Apr 8, 2013, at 4:28 PM, Peter Cock wrote:
> 
>> Do we know if NESCent was accepted? 
> 
> Yes, they were. -hilmar

Not sure if GMOD resubmitted this year; Scott Cain would know.  Will ask him?

chris


From jprocter at compbio.dundee.ac.uk  Tue Apr  9 02:14:18 2013
From: jprocter at compbio.dundee.ac.uk (Jim Procter)
Date: Tue, 09 Apr 2013 12:14:18 +1000
Subject: [GSoC] GSoC 2013 is ON
In-Reply-To: <CAPkCRRuffbwq9oTPPCoCZmbJ43QC4hUp6nALtU6iOQR04eVe-A@mail.gmail.com>
References: <20130303112326.GA5638@thebird.nl>
	<20130320211932.GA23848@thebird.nl>
	<20130408201346.GA3054@thebird.nl>
	<CAPkCRRuffbwq9oTPPCoCZmbJ43QC4hUp6nALtU6iOQR04eVe-A@mail.gmail.com>
Message-ID: <5163797A.3090208@compbio.dundee.ac.uk>

Hi.

This does suck, but as you said, Pjotr - it suggests competition for 
resources from FLOSS philanthropists is now very fierce - which is a 
Good Thing, but also a less good thing if writing GSoC org applications 
become as much work as grant applications, with the same low acceptance 
rate.

In the case of OBF I'm not quite sure why it didn't make the cut, so a 
post-mortem might be informative. For this year, though - it is 
definitely worth looking at bio/sci related GSoC orgs that did make the 
cut to see if an OBF project might fit there, or even applying for 
alternate sources of internship funding. Does anyone feel like starting 
a page to organise this kind of information on the OBF wiki ?

I did a quick analysis of the list in Melange and a random survey of 
tweets, and it looks like around 20 of the 121 orgs listed as of 3am 
UTC are science related. As to the ones that didn't make it - there are 
some surprises, such as Drupal, VLC, and RockPlayer - but I couldn't 
get a definite list together. At least one comment suggested the number 
of accepted orgs is less this year - I guess we'll see something in the 
announcements later on... since the bottom line will be whether the 
total number of student slots is less.

Jim.

On Tue Apr  9 06:58:45 2013, John Woods wrote:
> (+John Prince, +Carlos Agarie)
>
> Hey Pjotr,
>
> First of all, I'm so sorry to hear you all didn't get it. I've learned
> so much about running our fellowship programs from how well you all
> manage your GSOC students.
>
> I just learned that SciRuby did get accepted, which was quite honestly
> a tiny bit surprising for me (we've definitely been rejected before).
>
> Would you all be willing to get involved with our Summer of Code
> efforts? We're a bit short on mentors, and I think there's room for us
> to adopt some of your more general-science-y projects.
>
> John
>
>
> On Mon, Apr 8, 2013 at 3:13 PM, Pjotr Prins <pjotr2010 at thebird.nl
> <mailto:pjotr2010 at thebird.nl>> wrote:
>
>     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.
>
>     On Wed, Mar 20, 2013 at 10:19:32PM +0100, Pjotr Prins wrote:
>     > Heads up! One more week to go for project ideas! Please update
>     >
>     > https://github.com/OBF/GSoC/wiki/Google-Summer-of-Code-2013
>     >
>     > with the latest links. And maybe a wakeup call to your lists?
>     >
>     > If you are not on the Internet you don't exist. If you are not
>     making
>     > use of GSoC, you might as well be dead ;).
>     >
>     > Kidding. But, the more ideas, the better.
>     >
>     > Pj.
>     >
>     > * March 22nd: Finalise project ideas
>     > * March 29th: Deadline OBF mentoring organisation submission to
>     Google
>     >
>     > On Sun, Mar 03, 2013 at 12:23:26PM +0100, Pjotr Prins wrote:
>     > > Dear project leaders.
>     > >
>     > > I am sending below announcement to you, to have it forwarded
>     by you to
>     > > your mailing lists. Please do so. Also pass this message on to
>     anyone
>     > > who might be in some way interested in the OBF/GSoC initiative. To
>     > > participate, start by signing up to the soc mailing list at
>     > > http://lists.open-bio.org/mailman/listinfo/gsoc
>     > >
>     > > Spread the word!
>     > >
>     > > ~~~
>     > >
>     > > 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
>     <mailto: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
>     > >
>     _______________________________________________
>     GSoC mailing list
>     GSoC at lists.open-bio.org <mailto:GSoC at lists.open-bio.org>
>     http://lists.open-bio.org/mailman/listinfo/gsoc
>
>




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: [GSoC] 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 steffen_moeller at gmx.de  Tue Apr  9 09:32:57 2013
From: steffen_moeller at gmx.de (=?UTF-8?Q?=22Steffen_M=C3=B6ller=22?=)
Date: Tue, 9 Apr 2013 11:32:57 +0200 (CEST)
Subject: [GSoC] GSoC 2013 is ON
In-Reply-To: <5163797A.3090208@compbio.dundee.ac.uk>
References: <20130303112326.GA5638@thebird.nl>
	<20130320211932.GA23848@thebird.nl> <20130408201346.GA3054@thebird.nl>
	<CAPkCRRuffbwq9oTPPCoCZmbJ43QC4hUp6nALtU6iOQR04eVe-A@mail.gmail.com>,
	<5163797A.3090208@compbio.dundee.ac.uk>
Message-ID: <trinity-022153dc-869e-47ff-9bef-b7c79a5d6911-1365499977647@3capp-gmx-bs44>

An HTML attachment was scrubbed...
URL: <http://lists.open-bio.org/pipermail/gsoc/attachments/20130409/d24a50ff/attachment-0002.html>

From p.j.a.cock at googlemail.com  Tue Apr  9 10:34:37 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Tue, 9 Apr 2013 11:34:37 +0100
Subject: [GSoC] OBF not accepted for GSoC 2013
In-Reply-To: <CAKVJ-_6-+nyJk+7tp5YOyy7i7N7GtkRswZ_2Vs0uTuqGEV4wWQ@mail.gmail.com>
References: <CAKVJ-_6-+nyJk+7tp5YOyy7i7N7GtkRswZ_2Vs0uTuqGEV4wWQ@mail.gmail.com>
Message-ID: <CAKVJ-_4dB_uHQ=52-9D8WT+KCkyYk0jg6hPq15kE_SK3fWQimw@mail.gmail.com>

In a mass-email Peter wrote:
> 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.
> ...

Sorry Rob - "Rob Buels". Is is worth sending a correction to all
the mailing lists?

Peter


From rbuels at gmail.com  Tue Apr  9 17:41:15 2013
From: rbuels at gmail.com (Robert Buels)
Date: Tue, 09 Apr 2013 13:41:15 -0400
Subject: [GSoC] OBF not accepted for GSoC 2013
In-Reply-To: <CAKVJ-_4dB_uHQ=52-9D8WT+KCkyYk0jg6hPq15kE_SK3fWQimw@mail.gmail.com>
References: <CAKVJ-_6-+nyJk+7tp5YOyy7i7N7GtkRswZ_2Vs0uTuqGEV4wWQ@mail.gmail.com>
	<CAKVJ-_4dB_uHQ=52-9D8WT+KCkyYk0jg6hPq15kE_SK3fWQimw@mail.gmail.com>
Message-ID: <516452BB.3060202@gmail.com>

LOL no, not worth it.

You'll get your comeuppance at the DBCLS hackathon, anyway.  ;-)


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 04/09/2013 06:34 AM, Peter Cock wrote:
> Sorry Rob - "Rob Buels". Is is worth sending a correction to all
> the mailing lists?


From scott at scottcain.net  Tue Apr  9 10:57:40 2013
From: scott at scottcain.net (Scott Cain)
Date: Tue, 9 Apr 2013 11:57:40 +0100
Subject: [GSoC] [Bioperl-l] OBF not accepted for GSoC 2013
In-Reply-To: <CAKVJ-_6-+nyJk+7tp5YOyy7i7N7GtkRswZ_2Vs0uTuqGEV4wWQ@mail.gmail.com>
References: <CAKVJ-_6-+nyJk+7tp5YOyy7i7N7GtkRswZ_2Vs0uTuqGEV4wWQ@mail.gmail.com>
Message-ID: <3155B235-4068-491C-B611-1117EF1B5C50@scottcain.net>

Hi all, 

I was certainly surprised the the openbio application wasn't accepted; completion must be very tight. I just want to point out another bio project for inclined students: the Genome Informatics project is a GSoC collaboration of several well known projects, including GMOD (chado, gbrowse, jbrowse), Reactome, and Galaxy. For more information, see:

  http://gmod.org/wiki/GSoC

Thanks,
Scott


Sent from my iPhone

On Apr 9, 2013, at 11:20 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> 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.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From l.m.timmermans at students.uu.nl  Tue Apr  9 12:24:24 2013
From: l.m.timmermans at students.uu.nl (Leon Timmermans)
Date: Tue, 9 Apr 2013 14:24:24 +0200
Subject: [GSoC] [Bioperl-l] OBF not accepted for GSoC 2013
In-Reply-To: <CAKVJ-_6-+nyJk+7tp5YOyy7i7N7GtkRswZ_2Vs0uTuqGEV4wWQ@mail.gmail.com>
References: <CAKVJ-_6-+nyJk+7tp5YOyy7i7N7GtkRswZ_2Vs0uTuqGEV4wWQ@mail.gmail.com>
Message-ID: <CAC1jpXC=WuUU3Vx-psQds=yyje8r0XAFHiJVnZB2KxrxWY+_8w@mail.gmail.com>

On Tue, Apr 9, 2013 at 12:20 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> 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.

Something similar happened to The Perl Foundation last year, so we
asked them why? We had been a well-performing organization (100%
success rate in the preceding year) that put a lot of effort in our
submission and had a solid community behind us.

The answer was not quite what we expected. It had little to do with
the quality of the application, but everything with them wanting new
blood in the SOC. The same had happened to other projects I'm told.

Leon


From hlapp at drycafe.net  Tue Apr  9 11:47:22 2013
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Tue, 9 Apr 2013 07:47:22 -0400
Subject: [GSoC] GSoC 2013 is ON
In-Reply-To: <5163797A.3090208@compbio.dundee.ac.uk>
References: <20130303112326.GA5638@thebird.nl>
	<20130320211932.GA23848@thebird.nl>
	<20130408201346.GA3054@thebird.nl>
	<CAPkCRRuffbwq9oTPPCoCZmbJ43QC4hUp6nALtU6iOQR04eVe-A@mail.gmail.com>
	<5163797A.3090208@compbio.dundee.ac.uk>
Message-ID: <9B1CEC1A-0839-43C0-AFBA-334BF4F3D459@drycafe.net>

Wasn't the number of orgs last year around 180? That would mean that the total number of accepted orgs is almost unchanged. However, the announcement on the Google blog says that they accepted more than 40 new projects. Since the number of accepted orgs for sure didn't rise, this must mean that around 40 projects turned over, or almost 1 in every 4.

-hilmar

Sent with a tap.

On Apr 8, 2013, at 10:14 PM, Jim Procter <jprocter at compbio.dundee.ac.uk> wrote:

> Hi.
> 
> This does suck, but as you said, Pjotr - it suggests competition for resources from FLOSS philanthropists is now very fierce - which is a Good Thing, but also a less good thing if writing GSoC org applications become as much work as grant applications, with the same low acceptance rate.
> 
> In the case of OBF I'm not quite sure why it didn't make the cut, so a post-mortem might be informative. For this year, though - it is definitely worth looking at bio/sci related GSoC orgs that did make the cut to see if an OBF project might fit there, or even applying for alternate sources of internship funding. Does anyone feel like starting a page to organise this kind of information on the OBF wiki ?
> 
> I did a quick analysis of the list in Melange and a random survey of tweets, and it looks like around 20 of the 121 orgs listed as of 3am UTC are science related. As to the ones that didn't make it - there are some surprises, such as Drupal, VLC, and RockPlayer - but I couldn't get a definite list together. At least one comment suggested the number of accepted orgs is less this year - I guess we'll see something in the announcements later on... since the bottom line will be whether the total number of student slots is less.
> 
> Jim.
> 
> On Tue Apr  9 06:58:45 2013, John Woods wrote:
>> (+John Prince, +Carlos Agarie)
>> 
>> Hey Pjotr,
>> 
>> First of all, I'm so sorry to hear you all didn't get it. I've learned
>> so much about running our fellowship programs from how well you all
>> manage your GSOC students.
>> 
>> I just learned that SciRuby did get accepted, which was quite honestly
>> a tiny bit surprising for me (we've definitely been rejected before).
>> 
>> Would you all be willing to get involved with our Summer of Code
>> efforts? We're a bit short on mentors, and I think there's room for us
>> to adopt some of your more general-science-y projects.
>> 
>> John
>> 
>> 
>> On Mon, Apr 8, 2013 at 3:13 PM, Pjotr Prins <pjotr2010 at thebird.nl
>> <mailto:pjotr2010 at thebird.nl>> wrote:
>> 
>>    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.
>> 
>>    On Wed, Mar 20, 2013 at 10:19:32PM +0100, Pjotr Prins wrote:
>>    > Heads up! One more week to go for project ideas! Please update
>>    >
>>    > https://github.com/OBF/GSoC/wiki/Google-Summer-of-Code-2013
>>    >
>>    > with the latest links. And maybe a wakeup call to your lists?
>>    >
>>    > If you are not on the Internet you don't exist. If you are not
>>    making
>>    > use of GSoC, you might as well be dead ;).
>>    >
>>    > Kidding. But, the more ideas, the better.
>>    >
>>    > Pj.
>>    >
>>    > * March 22nd: Finalise project ideas
>>    > * March 29th: Deadline OBF mentoring organisation submission to
>>    Google
>>    >
>>    > On Sun, Mar 03, 2013 at 12:23:26PM +0100, Pjotr Prins wrote:
>>    > > Dear project leaders.
>>    > >
>>    > > I am sending below announcement to you, to have it forwarded
>>    by you to
>>    > > your mailing lists. Please do so. Also pass this message on to
>>    anyone
>>    > > who might be in some way interested in the OBF/GSoC initiative. To
>>    > > participate, start by signing up to the soc mailing list at
>>    > > http://lists.open-bio.org/mailman/listinfo/gsoc
>>    > >
>>    > > Spread the word!
>>    > >
>>    > > ~~~
>>    > >
>>    > > 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
>>    <mailto: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
>>    > >
>>    _______________________________________________
>>    GSoC mailing list
>>    GSoC at lists.open-bio.org <mailto:GSoC at lists.open-bio.org>
>>    http://lists.open-bio.org/mailman/listinfo/gsoc
>> 
>> 
> 
> 



From p.j.a.cock at googlemail.com  Tue Apr  9 19:00:29 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Tue, 9 Apr 2013 20:00:29 +0100
Subject: [GSoC] GSoC 2013 is ON
In-Reply-To: <9B1CEC1A-0839-43C0-AFBA-334BF4F3D459@drycafe.net>
References: <20130303112326.GA5638@thebird.nl>
	<20130320211932.GA23848@thebird.nl>
	<20130408201346.GA3054@thebird.nl>
	<CAPkCRRuffbwq9oTPPCoCZmbJ43QC4hUp6nALtU6iOQR04eVe-A@mail.gmail.com>
	<5163797A.3090208@compbio.dundee.ac.uk>
	<9B1CEC1A-0839-43C0-AFBA-334BF4F3D459@drycafe.net>
Message-ID: <CAKVJ-_447qQmoAL9h7GN79E=FkRYwnACUxCGYW4cyyP4O8BM1A@mail.gmail.com>

On Tue, Apr 9, 2013 at 12:47 PM, Hilmar Lapp <hlapp at drycafe.net> wrote:
> Wasn't the number of orgs last year around 180? That would
> mean that the total number of accepted orgs is almost unchanged.

Yes, i checked and its been just under 180 for the last few years.

> However, the announcement on the Google blog says that
> they accepted more than 40 new projects. Since the number
> of accepted orgs for sure didn't rise, this must mean that
> around 40 projects turned over, or almost 1 in every 4.
>
> -hilmar

It does seem Google are trying to cover different ground but
with a fixed budget - and this year we were one of the unlucky
organisations (but not alone in this respect).

Peter


From pjotr2010 at thebird.nl  Thu Apr 11 06:13:04 2013
From: pjotr2010 at thebird.nl (Pjotr Prins)
Date: Thu, 11 Apr 2013 08:13:04 +0200
Subject: [GSoC] GSoC 2013 is ON
In-Reply-To: <CAKVJ-_447qQmoAL9h7GN79E=FkRYwnACUxCGYW4cyyP4O8BM1A@mail.gmail.com>
References: <20130303112326.GA5638@thebird.nl>
	<20130320211932.GA23848@thebird.nl>
	<20130408201346.GA3054@thebird.nl>
	<CAPkCRRuffbwq9oTPPCoCZmbJ43QC4hUp6nALtU6iOQR04eVe-A@mail.gmail.com>
	<5163797A.3090208@compbio.dundee.ac.uk>
	<9B1CEC1A-0839-43C0-AFBA-334BF4F3D459@drycafe.net>
	<CAKVJ-_447qQmoAL9h7GN79E=FkRYwnACUxCGYW4cyyP4O8BM1A@mail.gmail.com>
Message-ID: <20130411061304.GA14038@thebird.nl>

SciRuby has been so kind to allow us to merge some BioRuby project
ideas into their GSoC organisation. I suggest every project could try
that. Having experienced mentors is an asset to any organisation.

Pj.

On Tue, Apr 09, 2013 at 08:00:29PM +0100, Peter Cock wrote:
> On Tue, Apr 9, 2013 at 12:47 PM, Hilmar Lapp <hlapp at drycafe.net> wrote:
> > Wasn't the number of orgs last year around 180? That would
> > mean that the total number of accepted orgs is almost unchanged.
> 
> Yes, i checked and its been just under 180 for the last few years.
> 
> > However, the announcement on the Google blog says that
> > they accepted more than 40 new projects. Since the number
> > of accepted orgs for sure didn't rise, this must mean that
> > around 40 projects turned over, or almost 1 in every 4.
> >
> > -hilmar
> 
> It does seem Google are trying to cover different ground but
> with a fixed budget - and this year we were one of the unlucky
> organisations (but not alone in this respect).
> 
> Peter
> _______________________________________________
> GSoC mailing list
> GSoC at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/gsoc


From p.j.a.cock at googlemail.com  Thu Apr 11 09:11:57 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 11 Apr 2013 10:11:57 +0100
Subject: [GSoC] GSoC 2013 is ON
In-Reply-To: <20130411061304.GA14038@thebird.nl>
References: <20130303112326.GA5638@thebird.nl>
	<20130320211932.GA23848@thebird.nl>
	<20130408201346.GA3054@thebird.nl>
	<CAPkCRRuffbwq9oTPPCoCZmbJ43QC4hUp6nALtU6iOQR04eVe-A@mail.gmail.com>
	<5163797A.3090208@compbio.dundee.ac.uk>
	<9B1CEC1A-0839-43C0-AFBA-334BF4F3D459@drycafe.net>
	<CAKVJ-_447qQmoAL9h7GN79E=FkRYwnACUxCGYW4cyyP4O8BM1A@mail.gmail.com>
	<20130411061304.GA14038@thebird.nl>
Message-ID: <CAKVJ-_54KH9KiZrDZF9+9RgjZYokZ8Jfe-nZ0M-6x4ebftyZCw@mail.gmail.com>

On Thu, Apr 11, 2013 at 7:13 AM, Pjotr Prins <pjotr2010 at thebird.nl> wrote:
> SciRuby has been so kind to allow us to merge some BioRuby project
> ideas into their GSoC organisation. I suggest every project could try
> that. Having experienced mentors is an asset to any organisation.
>
> Pj.

That's good news.

Similarly Eric has been in touch with NESCent about some of the
phylogenetic project ideas we'd come up with for Biopython (we'd
partnered with them for GSoC before the OBF started applying).

I have tried emailing the Python Software Foundation (PSF)
contact - they are also acting as a GSoC umbrella organisation,
but have not had a reply yet.

Peter

(The CC list is quite long - are some of these potential
mentors not on the OBF's gsoc at lists.open-bio.org list?)


From cjfields at illinois.edu  Thu Apr 11 15:08:04 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 11 Apr 2013 15:08:04 +0000
Subject: [GSoC] GSoC 2013 is ON
In-Reply-To: <CAKVJ-_54KH9KiZrDZF9+9RgjZYokZ8Jfe-nZ0M-6x4ebftyZCw@mail.gmail.com>
References: <20130303112326.GA5638@thebird.nl>
	<20130320211932.GA23848@thebird.nl> <20130408201346.GA3054@thebird.nl>
	<CAPkCRRuffbwq9oTPPCoCZmbJ43QC4hUp6nALtU6iOQR04eVe-A@mail.gmail.com>
	<5163797A.3090208@compbio.dundee.ac.uk>
	<9B1CEC1A-0839-43C0-AFBA-334BF4F3D459@drycafe.net>
	<CAKVJ-_447qQmoAL9h7GN79E=FkRYwnACUxCGYW4cyyP4O8BM1A@mail.gmail.com>
	<20130411061304.GA14038@thebird.nl>
	<CAKVJ-_54KH9KiZrDZF9+9RgjZYokZ8Jfe-nZ0M-6x4ebftyZCw@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DD77BA@CHIMBX5.ad.uillinois.edu>

On Apr 11, 2013, at 4:11 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Thu, Apr 11, 2013 at 7:13 AM, Pjotr Prins <pjotr2010 at thebird.nl> wrote:
>> SciRuby has been so kind to allow us to merge some BioRuby project
>> ideas into their GSoC organisation. I suggest every project could try
>> that. Having experienced mentors is an asset to any organisation.
>> 
>> Pj.
> 
> That's good news.
> 
> Similarly Eric has been in touch with NESCent about some of the
> phylogenetic project ideas we'd come up with for Biopython (we'd
> partnered with them for GSoC before the OBF started applying).
> 
> I have tried emailing the Python Software Foundation (PSF)
> contact - they are also acting as a GSoC umbrella organisation,
> but have not had a reply yet.
> 
> Peter
> 
> (The CC list is quite long - are some of these potential
> mentors not on the OBF's gsoc at lists.open-bio.org list?)

Scott Cain (GMOD, aka 'Genome Informatics') also indicated students can submit project proposals to them as well.

chris