From cjfields at illinois.edu  Fri Apr  8 09:19:54 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 8 Apr 2011 08:19:54 -0500
Subject: [GSoC] test
Message-ID: <0BD4F3AD-6BC9-43B0-BAB6-814BE112F463@illinois.edu>

<test>
tap tap, is this thing working?
</test>

From p.j.a.cock at googlemail.com  Fri Apr  8 09:36:45 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 8 Apr 2011 14:36:45 +0100
Subject: [GSoC] test
In-Reply-To: <0BD4F3AD-6BC9-43B0-BAB6-814BE112F463@illinois.edu>
References: <0BD4F3AD-6BC9-43B0-BAB6-814BE112F463@illinois.edu>
Message-ID: <BANLkTi=u8ShQEDx6YZXyDB1nM=OA8zW7GQ@mail.gmail.com>

On Fri, Apr 8, 2011 at 2:19 PM, Chris Fields <cjfields at illinois.edu> wrote:
> <test>
> tap tap, is this thing working?
> </test>

Yes :)

From cjfields at illinois.edu  Fri Apr  8 10:20:56 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 8 Apr 2011 09:20:56 -0500
Subject: [GSoC] test
In-Reply-To: <2EA4F074-2384-45CE-9C1F-41ABAC2F45FF@ingm.org>
References: <0BD4F3AD-6BC9-43B0-BAB6-814BE112F463@illinois.edu>
	<BANLkTi=u8ShQEDx6YZXyDB1nM=OA8zW7GQ@mail.gmail.com>
	<2EA4F074-2384-45CE-9C1F-41ABAC2F45FF@ingm.org>
Message-ID: <9E16D4EA-BC8C-4F35-8CD0-10BDBCD67375@illinois.edu>

On Apr 8, 2011, at 9:16 AM, Raoul Bonnal wrote:

> 
> On 08/apr/2011, at 15.36, Peter Cock wrote:
> 
>> On Fri, Apr 8, 2011 at 2:19 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>> <test>
>>> tap tap, is this thing working?
>>> </test>
>> 
>> Yes :)
> LoL Yep
>> _______________________________________________
>> GSoC mailing list
>> GSoC at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/gsoc
> 
> --
> Ra
> 
> linkedin: http://it.linkedin.com/in/raoulbonnal
> twitter: http://twitter.com/ilpuccio
> skype: ilpuccio
> irc.freenode.net: Helius
> github: https://github.com/helios


Cool, just checking.  I'm guessing we need to make sure any prospective mentors sign up.

chris



From bonnal at ingm.org  Fri Apr  8 10:16:24 2011
From: bonnal at ingm.org (Raoul Bonnal)
Date: Fri, 8 Apr 2011 16:16:24 +0200
Subject: [GSoC] test
In-Reply-To: <BANLkTi=u8ShQEDx6YZXyDB1nM=OA8zW7GQ@mail.gmail.com>
References: <0BD4F3AD-6BC9-43B0-BAB6-814BE112F463@illinois.edu>
	<BANLkTi=u8ShQEDx6YZXyDB1nM=OA8zW7GQ@mail.gmail.com>
Message-ID: <2EA4F074-2384-45CE-9C1F-41ABAC2F45FF@ingm.org>


On 08/apr/2011, at 15.36, Peter Cock wrote:

> On Fri, Apr 8, 2011 at 2:19 PM, Chris Fields <cjfields at illinois.edu> wrote:
>> <test>
>> tap tap, is this thing working?
>> </test>
> 
> Yes :)
LoL Yep
> _______________________________________________
> GSoC mailing list
> GSoC at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/gsoc

--
Ra

linkedin: http://it.linkedin.com/in/raoulbonnal
twitter: http://twitter.com/ilpuccio
skype: ilpuccio
irc.freenode.net: Helius
github: https://github.com/helios







From anaryin at gmail.com  Fri Apr  8 12:33:44 2011
From: anaryin at gmail.com (=?UTF-8?Q?Jo=C3=A3o_Rodrigues?=)
Date: Fri, 8 Apr 2011 18:33:44 +0200
Subject: [GSoC] test
In-Reply-To: <9E16D4EA-BC8C-4F35-8CD0-10BDBCD67375@illinois.edu>
References: <0BD4F3AD-6BC9-43B0-BAB6-814BE112F463@illinois.edu>
	<BANLkTi=u8ShQEDx6YZXyDB1nM=OA8zW7GQ@mail.gmail.com>
	<2EA4F074-2384-45CE-9C1F-41ABAC2F45FF@ingm.org>
	<9E16D4EA-BC8C-4F35-8CD0-10BDBCD67375@illinois.edu>
Message-ID: <BANLkTini0iA9dq2ZRbAuMyeS1SDqUtRCvA@mail.gmail.com>

Working here too, what is the purpose of this list again? :x

From rmb32 at cornell.edu  Fri Apr  8 12:56:03 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Fri, 08 Apr 2011 09:56:03 -0700
Subject: [GSoC] test
In-Reply-To: <BANLkTini0iA9dq2ZRbAuMyeS1SDqUtRCvA@mail.gmail.com>
References: <0BD4F3AD-6BC9-43B0-BAB6-814BE112F463@illinois.edu>	<BANLkTi=u8ShQEDx6YZXyDB1nM=OA8zW7GQ@mail.gmail.com>	<2EA4F074-2384-45CE-9C1F-41ABAC2F45FF@ingm.org>	<9E16D4EA-BC8C-4F35-8CD0-10BDBCD67375@illinois.edu>
	<BANLkTini0iA9dq2ZRbAuMyeS1SDqUtRCvA@mail.gmail.com>
Message-ID: <4D9F3E23.9010808@cornell.edu>

On 04/08/2011 09:33 AM, Jo?o Rodrigues wrote:
> Working here too, what is the purpose of this list again? :x

It's for administrative announcements, and general public discussions 
about Open Bioinformatics Foundation GSoC.

With 2011 GSoC starting up now, this list is going to start getting more 
traffic, so if you're not interested in OBF GSoC 2011, you should think 
about unsubscribing using the lists.open-bio.org link at the bottom of 
this email.

Rob

From rmb32 at cornell.edu  Tue May 17 14:02:35 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Tue, 17 May 2011 11:02:35 -0700
Subject: [GSoC] GSoC coding period starts next Monday
Message-ID: <4DD2B83B.1090106@cornell.edu>

Hi all,

The coding period for Google Summer of Code starts this coming Monday.  
Each mentor-student group should be pretty well organized by now, and 
know exactly what they're going to be doing next week.

Each group needs to make sure they have the following in place:

1. Good lines of communication between students and mentors, including 
plans for regular chat or phone meetings.

2. The student needs to have their development environment set up and 
ready to go, so that they'll be ready to be productive from day 1.  Get 
the necessary software, version control checkouts, data sets, and so 
forth.  Don't leave this until the last minute, setting up a development 
environment can be tricky!

3. The student needs to have their blog/wiki/other set up for public 
reports of the project's progress.  Please send the URLs for these to 
me, and I'll construct a page on the OBF GSoC wiki with links to them.

Here's to a fun and productive summer of code!

Best wishes,

Rob

----
Robert Buels
OBF GSoC 2011 Administrator





From to.petr at gmail.com  Wed May 18 04:07:36 2011
From: to.petr at gmail.com (P. Troshin)
Date: Wed, 18 May 2011 09:07:36 +0100
Subject: [GSoC] GSoC coding period starts next Monday
In-Reply-To: <4DD2B83B.1090106@cornell.edu>
References: <4DD2B83B.1090106@cornell.edu>
Message-ID: <BANLkTimud-o6j+57xgBzpbjyz5oBb=NWDA@mail.gmail.com>

Dear Robert,

> 3. The student needs to have their blog/wiki/other set up for public reports
> of the project's progress.  Please send the URLs for these to me, and I'll
> construct a page on the OBF GSoC wiki with links to them.

Thank you for your advice.
The URL for Amino Acid Physico-Chemical Properties Calculation project
is this http://biojava.org/wiki/GSoC:AAPropertiesComputation

Regards,
Peter


On 17 May 2011 19:02, Robert Buels <rmb32 at cornell.edu> wrote:
> Hi all,
>
> The coding period for Google Summer of Code starts this coming Monday. ?Each
> mentor-student group should be pretty well organized by now, and know
> exactly what they're going to be doing next week.
>
> Each group needs to make sure they have the following in place:
>
> 1. Good lines of communication between students and mentors, including plans
> for regular chat or phone meetings.
>
> 2. The student needs to have their development environment set up and ready
> to go, so that they'll be ready to be productive from day 1. ?Get the
> necessary software, version control checkouts, data sets, and so forth.
> ?Don't leave this until the last minute, setting up a development
> environment can be tricky!
>
> 3. The student needs to have their blog/wiki/other set up for public reports
> of the project's progress. ?Please send the URLs for these to me, and I'll
> construct a page on the OBF GSoC wiki with links to them.
>
> Here's to a fun and productive summer of code!
>
> Best wishes,
>
> Rob
>
> ----
> Robert Buels
> OBF GSoC 2011 Administrator
>
>
>
>
> _______________________________________________
> GSoC mailing list
> GSoC at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/gsoc
>


From rmb32 at cornell.edu  Thu May 19 12:07:49 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Thu, 19 May 2011 09:07:49 -0700
Subject: [GSoC] GSoC coding period starts next Monday
In-Reply-To: <4DD2B83B.1090106@cornell.edu>
References: <4DD2B83B.1090106@cornell.edu>
Message-ID: <4DD54055.1020306@cornell.edu>

Reminder: please send me the URLs of your progress report pages Real 
Soon Now.

They need to be up, with some content about how you're starting off, by 
Monday.

Rob



On 05/17/2011 11:02 AM, Robert Buels wrote:
> Hi all,
>
> The coding period for Google Summer of Code starts this coming Monday.
> Each mentor-student group should be pretty well organized by now, and
> know exactly what they're going to be doing next week.
>
> Each group needs to make sure they have the following in place:
>
> 1. Good lines of communication between students and mentors, including
> plans for regular chat or phone meetings.
>
> 2. The student needs to have their development environment set up and
> ready to go, so that they'll be ready to be productive from day 1. Get
> the necessary software, version control checkouts, data sets, and so
> forth. Don't leave this until the last minute, setting up a development
> environment can be tricky!
>
> 3. The student needs to have their blog/wiki/other set up for public
> reports of the project's progress. Please send the URLs for these to me,
> and I'll construct a page on the OBF GSoC wiki with links to them.
>
> Here's to a fun and productive summer of code!
>
> Best wishes,
>
> Rob
>
> ----
> Robert Buels
> OBF GSoC 2011 Administrator
>
>
>
>
> _______________________________________________
> GSoC mailing list
> GSoC at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/gsoc
>


From sheena.scroggins at gmail.com  Sun May 22 19:14:20 2011
From: sheena.scroggins at gmail.com (Sheena Scroggins)
Date: Sun, 22 May 2011 16:14:20 -0700
Subject: [GSoC] GSoC BioPerl Project Page
Message-ID: <BANLkTinq5hPf5wL3oAHFqfPRZPFCN59WaQ@mail.gmail.com>

Hey everyone,


The BioPerl project can be followed at www.techomics.com.

The relevant github links will be posted there soon.

Sheena

From rmb32 at cornell.edu  Mon Jun  6 12:23:02 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Mon, 06 Jun 2011 09:23:02 -0700
Subject: [GSoC] Reminder: frequent updates needed on progress pages
Message-ID: <4DECFEE6.2030708@cornell.edu>

Hi all,

Looking through the project pages, I see that most have not been updated 
in some time.  Justinas and Chuan Hok seem to have been keeping up with 
it, many thanks to them!

For the rest of the projects, please update your pages now.

At minimum, there should be an update to the log every week that reports 
what was done that week.  Ideally, students should use them as a log of 
your progress, struggles, and thoughts throughout the project.

Thanks for all your hard work so far, students and mentors!

Rob

From rmb32 at cornell.edu  Thu Jun 30 09:21:39 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Thu, 30 Jun 2011 06:21:39 -0700
Subject: [GSoC] reminder: mid-term evaluations in 1.5 weeks
Message-ID: <4E0C7863.4030309@cornell.edu>

Hi all,

This is a reminder that GSoC mid-term evaluations are due on July 11, 
which is a little more than a week away.  At the end of this email, I'm 
including the full story on evaluations and how they work.

Hope your projects are going well.  Keep those progress reports up to 
date!  :-)

Rob Buels
OBF GSoC 2011 Administrator


------
EVALUATIONS

(from 
http://www.google-melange.com/document/show/gsoc_program/google/gsoc2011/faqs#evals)


9. How do evaluations work?

Google will pre-publish the evaluation questions for both students and 
mentors. Mentors will fill out mid-term and final evaluations for their 
students via the Google Summer of Code 2011 site. These evaluations will 
be visible in the system to the mentor and the mentoring organization's 
administrator(s). Students will fill out a mid-term and final evaluation 
of their mentors online as well, and their evaluations will only be 
visible in the system to the mentoring organization's administrator(s). 
Program administrators from Google will have access to all evaluation data.

In almost all cases, students will never see their mentor's evaluation 
of their progress, nor will a mentor see a student's evaluation of 
her/his mentorship. However, in the case where the mentoring 
organization's administrator and a student's mentor are one and the 
same, the student's evaluation will be shared with the mentor. If you 
are a student in a situation where your mentor is also your 
organization?s administrator and you would like to discuss an issue with 
the program, please contact the Google Summer of Code program 
administrators. Organization administrators are expected to review 
mid-term and final evaluations and to provide course corrections where 
necessary.

In some cases, Google's program administrators may need to share the 
results of evaluations with the student and mentor, such as to arbitrate 
when payment should not be made. Should this need arise, all parties 
will be notified in advance.


From rmb32 at cornell.edu  Tue Aug 23 13:33:42 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Tue, 23 Aug 2011 10:33:42 -0700
Subject: [GSoC] reminder: final evaluations due Friday
Message-ID: <4E53E476.7080606@cornell.edu>

Hi all,

Students, your projects should now be finished.  Students, please make 
sure you have updated your progress pages with concluding entries and 
final thoughts.  I hope you all enjoyed your summer and learned a lot! 
Please make sure you've given your mentors a BIG thank-you, they have 
some of the hardest jobs in GSoC.

Mentors, final evaluations are due by this Friday, August 26.  Thanks so 
much for your work, it means a lot.  Especially to the students.

Everybody, if you have suggestions or feedback for what aspects of the 
program worked well this year, which things didn't work so well, or 
things we should add for next year, I'm always interested to hear them! 
  Just drop me an email at this same address.

Thank you so much for everything you've done this summer, and here's to 
many more successful years of OBF GSoC in the future!

Rob

-----
Robert Buels
OBF GSoC 2011 Administrator

From p.j.a.cock at googlemail.com  Tue Aug 23 21:59:23 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 24 Aug 2011 02:59:23 +0100
Subject: [GSoC] reminder: final evaluations due Friday
In-Reply-To: <4E53E476.7080606@cornell.edu>
References: <4E53E476.7080606@cornell.edu>
Message-ID: <CAKVJ-_50J5KDTH--5-R+t0qHjKv72woLAYcER=XUb-X95AGYog@mail.gmail.com>

On Tue, Aug 23, 2011 at 6:33 PM, Robert Buels <rmb32 at cornell.edu> wrote:
> Hi all,
>
> Students, your projects should now be finished. ?Students, please make sure
> you have updated your progress pages with concluding entries and final
> thoughts. ?I hope you all enjoyed your summer and learned a lot! Please make
> sure you've given your mentors a BIG thank-you, they have some of the
> hardest jobs in GSoC.
>
> Mentors, final evaluations are due by this Friday, August 26. ?Thanks so
> much for your work, it means a lot. ?Especially to the students.
>
> Everybody, if you have suggestions or feedback for what aspects of the
> program worked well this year, which things didn't work so well, or things
> we should add for next year, I'm always interested to hear them! ?Just drop
> me an email at this same address.
>
> Thank you so much for everything you've done this summer, and here's to many
> more successful years of OBF GSoC in the future!
>
> Rob

Hi Rob,

Thanks for your hard work again this year.

In terms of feedback for the OBF GSoC 2011, my main
observation is that overall it seems there has been less
interaction with the students and the respective community
mailing lists. I have been reassured by mentors, wiki
updates, and code commits that work is going on, but
for next year I think we should insist up front from the
start that students are expected to send a weekly email
report of what they have been doing to the appropriate
mailing list of the host project (e.g. biopython-dev or
bioperl-l), and perhaps CC'd to our GSoC mailing list.
Otherwise it has been hard for non-mentors to follow
what is happening.

This is not intended as a personal criticism of anyone -
just something I think we could do better next year.

Regards,

Peter


From cmzmasek at yahoo.com  Tue Aug 23 22:03:17 2011
From: cmzmasek at yahoo.com (Christian Zmasek)
Date: Tue, 23 Aug 2011 19:03:17 -0700 (PDT)
Subject: [GSoC] reminder: final evaluations due Friday
In-Reply-To: <CAKVJ-_50J5KDTH--5-R+t0qHjKv72woLAYcER=XUb-X95AGYog@mail.gmail.com>
References: <4E53E476.7080606@cornell.edu>
	<CAKVJ-_50J5KDTH--5-R+t0qHjKv72woLAYcER=XUb-X95AGYog@mail.gmail.com>
Message-ID: <1314151397.10878.YahooMailNeo@web38407.mail.mud.yahoo.com>

I totally agree with Peter's points.

Christian



>________________________________
>From: Peter Cock <p.j.a.cock at googlemail.com>
>To: Robert Buels <rmb32 at cornell.edu>
>Cc: OBF GSoC <gsoc at lists.open-bio.org>
>Sent: Wednesday, August 24, 2011 10:59 AM
>Subject: Re: [GSoC] reminder: final evaluations due Friday
>
>On Tue, Aug 23, 2011 at 6:33 PM, Robert Buels <rmb32 at cornell.edu> wrote:
>> Hi all,
>>
>> Students, your projects should now be finished. ?Students, please make sure
>> you have updated your progress pages with concluding entries and final
>> thoughts. ?I hope you all enjoyed your summer and learned a lot! Please make
>> sure you've given your mentors a BIG thank-you, they have some of the
>> hardest jobs in GSoC.
>>
>> Mentors, final evaluations are due by this Friday, August 26. ?Thanks so
>> much for your work, it means a lot. ?Especially to the students.
>>
>> Everybody, if you have suggestions or feedback for what aspects of the
>> program worked well this year, which things didn't work so well, or things
>> we should add for next year, I'm always interested to hear them! ?Just drop
>> me an email at this same address.
>>
>> Thank you so much for everything you've done this summer, and here's to many
>> more successful years of OBF GSoC in the future!
>>
>> Rob
>
>Hi Rob,
>
>Thanks for your hard work again this year.
>
>In terms of feedback for the OBF GSoC 2011, my main
>observation is that overall it seems there has been less
>interaction with the students and the respective community
>mailing lists. I have been reassured by mentors, wiki
>updates, and code commits that work is going on, but
>for next year I think we should insist up front from the
>start that students are expected to send a weekly email
>report of what they have been doing to the appropriate
>mailing list of the host project (e.g. biopython-dev or
>bioperl-l), and perhaps CC'd to our GSoC mailing list.
>Otherwise it has been hard for non-mentors to follow
>what is happening.
>
>This is not intended as a personal criticism of anyone -
>just something I think we could do better next year.
>
>Regards,
>
>Peter
>
>_______________________________________________
>GSoC mailing list
>GSoC at lists.open-bio.org
>http://lists.open-bio.org/mailman/listinfo/gsoc
>
>
>

From cjfields at illinois.edu  Tue Aug 23 22:16:01 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 23 Aug 2011 21:16:01 -0500
Subject: [GSoC] reminder: final evaluations due Friday
In-Reply-To: <1314151397.10878.YahooMailNeo@web38407.mail.mud.yahoo.com>
References: <4E53E476.7080606@cornell.edu>
	<CAKVJ-_50J5KDTH--5-R+t0qHjKv72woLAYcER=XUb-X95AGYog@mail.gmail.com>
	<1314151397.10878.YahooMailNeo@web38407.mail.mud.yahoo.com>
Message-ID: <AB10C27B-BAE5-4381-B0E0-58BD85B7A67E@illinois.edu>

+1

chris

On Aug 23, 2011, at 9:03 PM, Christian Zmasek wrote:

> I totally agree with Peter's points.
> 
> Christian
> 
> 
> 
>> ________________________________
>> From: Peter Cock <p.j.a.cock at googlemail.com>
>> To: Robert Buels <rmb32 at cornell.edu>
>> Cc: OBF GSoC <gsoc at lists.open-bio.org>
>> Sent: Wednesday, August 24, 2011 10:59 AM
>> Subject: Re: [GSoC] reminder: final evaluations due Friday
>> 
>> On Tue, Aug 23, 2011 at 6:33 PM, Robert Buels <rmb32 at cornell.edu> wrote:
>>> Hi all,
>>> 
>>> Students, your projects should now be finished.  Students, please make sure
>>> you have updated your progress pages with concluding entries and final
>>> thoughts.  I hope you all enjoyed your summer and learned a lot! Please make
>>> sure you've given your mentors a BIG thank-you, they have some of the
>>> hardest jobs in GSoC.
>>> 
>>> Mentors, final evaluations are due by this Friday, August 26.  Thanks so
>>> much for your work, it means a lot.  Especially to the students.
>>> 
>>> Everybody, if you have suggestions or feedback for what aspects of the
>>> program worked well this year, which things didn't work so well, or things
>>> we should add for next year, I'm always interested to hear them!  Just drop
>>> me an email at this same address.
>>> 
>>> Thank you so much for everything you've done this summer, and here's to many
>>> more successful years of OBF GSoC in the future!
>>> 
>>> Rob
>> 
>> Hi Rob,
>> 
>> Thanks for your hard work again this year.
>> 
>> In terms of feedback for the OBF GSoC 2011, my main
>> observation is that overall it seems there has been less
>> interaction with the students and the respective community
>> mailing lists. I have been reassured by mentors, wiki
>> updates, and code commits that work is going on, but
>> for next year I think we should insist up front from the
>> start that students are expected to send a weekly email
>> report of what they have been doing to the appropriate
>> mailing list of the host project (e.g. biopython-dev or
>> bioperl-l), and perhaps CC'd to our GSoC mailing list.
>> Otherwise it has been hard for non-mentors to follow
>> what is happening.
>> 
>> This is not intended as a personal criticism of anyone -
>> just something I think we could do better next year.
>> 
>> Regards,
>> 
>> Peter
>> 
>> _______________________________________________
>> GSoC mailing list
>> GSoC at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/gsoc
>> 
>> 
>> 
> _______________________________________________
> GSoC mailing list
> GSoC at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/gsoc



From hlapp at drycafe.net  Tue Aug 23 22:21:52 2011
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Wed, 24 Aug 2011 11:21:52 +0900
Subject: [GSoC] reminder: final evaluations due Friday
In-Reply-To: <1314151397.10878.YahooMailNeo@web38407.mail.mud.yahoo.com>
References: <4E53E476.7080606@cornell.edu>
	<CAKVJ-_50J5KDTH--5-R+t0qHjKv72woLAYcER=XUb-X95AGYog@mail.gmail.com>
	<1314151397.10878.YahooMailNeo@web38407.mail.mud.yahoo.com>
Message-ID: <B6569B44-581C-4F21-A0DA-29017348F905@drycafe.net>

Same here - it has saddened me frankly that the community building  
aspect of GSoC involvement (which in my view is the real motivator  
that makes putting in the mentoring and admin time all worth it in the  
end) has turned into a giant missed opportunity for us this year.

	-hilmar

On Aug 24, 2011, at 11:03 AM, Christian Zmasek wrote:

> I totally agree with Peter's points.
>
> Christian
>
>
>
>> ________________________________
>> From: Peter Cock <p.j.a.cock at googlemail.com>
>> To: Robert Buels <rmb32 at cornell.edu>
>> Cc: OBF GSoC <gsoc at lists.open-bio.org>
>> Sent: Wednesday, August 24, 2011 10:59 AM
>> Subject: Re: [GSoC] reminder: final evaluations due Friday
>>
>> On Tue, Aug 23, 2011 at 6:33 PM, Robert Buels <rmb32 at cornell.edu>  
>> wrote:
>>> Hi all,
>>>
>>> Students, your projects should now be finished.  Students, please  
>>> make sure
>>> you have updated your progress pages with concluding entries and  
>>> final
>>> thoughts.  I hope you all enjoyed your summer and learned a lot!  
>>> Please make
>>> sure you've given your mentors a BIG thank-you, they have some of  
>>> the
>>> hardest jobs in GSoC.
>>>
>>> Mentors, final evaluations are due by this Friday, August 26.   
>>> Thanks so
>>> much for your work, it means a lot.  Especially to the students.
>>>
>>> Everybody, if you have suggestions or feedback for what aspects of  
>>> the
>>> program worked well this year, which things didn't work so well,  
>>> or things
>>> we should add for next year, I'm always interested to hear them!   
>>> Just drop
>>> me an email at this same address.
>>>
>>> Thank you so much for everything you've done this summer, and  
>>> here's to many
>>> more successful years of OBF GSoC in the future!
>>>
>>> Rob
>>
>> Hi Rob,
>>
>> Thanks for your hard work again this year.
>>
>> In terms of feedback for the OBF GSoC 2011, my main
>> observation is that overall it seems there has been less
>> interaction with the students and the respective community
>> mailing lists. I have been reassured by mentors, wiki
>> updates, and code commits that work is going on, but
>> for next year I think we should insist up front from the
>> start that students are expected to send a weekly email
>> report of what they have been doing to the appropriate
>> mailing list of the host project (e.g. biopython-dev or
>> bioperl-l), and perhaps CC'd to our GSoC mailing list.
>> Otherwise it has been hard for non-mentors to follow
>> what is happening.
>>
>> This is not intended as a personal criticism of anyone -
>> just something I think we could do better next year.
>>
>> Regards,
>>
>> Peter
>>
>> _______________________________________________
>> GSoC mailing list
>> GSoC at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/gsoc
>>
>>
>>
> _______________________________________________
> GSoC mailing list
> GSoC at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/gsoc

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





From bonnal at ingm.org  Tue Aug 23 22:53:28 2011
From: bonnal at ingm.org (Raoul Bonnal)
Date: Wed, 24 Aug 2011 11:53:28 +0900
Subject: [GSoC] reminder: final evaluations due Friday
In-Reply-To: <B6569B44-581C-4F21-A0DA-29017348F905@drycafe.net>
Message-ID: <CA7A96B8.4CA2%bonnal@ingm.org>

+1 but
A) I think we need to create some kind of best practices for the students
and select the "well written" proposals as example
B) Schedule mentors meeting during the GSoC, IRC is fine. It was very useful
at the beginning and I want to thanks all the people in particular Chris and
Robert.
C) I'd like to schedule the next GSoC in time, we -BioRuby- need start
thinking to the next GSoC from now. Having a clear plan or road map it's a
must at least for me. Let's pick up the example of this BioHackathon, we can
prototype something here and then decide to use GSoC to improve it.
D) why not create a page on the wiki with our comments and experiences to
identify the BUGS ?

On 24/08/11 11.21, "Hilmar Lapp" <hlapp at drycafe.net> wrote:

> Same here - it has saddened me frankly that the community building
> aspect of GSoC involvement (which in my view is the real motivator
> that makes putting in the mentoring and admin time all worth it in the
> end) has turned into a giant missed opportunity for us this year.
> 
> -hilmar
> 
> On Aug 24, 2011, at 11:03 AM, Christian Zmasek wrote:
> 
>> I totally agree with Peter's points.
>> 
>> Christian
>> 
>> 
>> 
>>> ________________________________
>>> From: Peter Cock <p.j.a.cock at googlemail.com>
>>> To: Robert Buels <rmb32 at cornell.edu>
>>> Cc: OBF GSoC <gsoc at lists.open-bio.org>
>>> Sent: Wednesday, August 24, 2011 10:59 AM
>>> Subject: Re: [GSoC] reminder: final evaluations due Friday
>>> 
>>> On Tue, Aug 23, 2011 at 6:33 PM, Robert Buels <rmb32 at cornell.edu>
>>> wrote:
>>>> Hi all,
>>>> 
>>>> Students, your projects should now be finished.  Students, please
>>>> make sure
>>>> you have updated your progress pages with concluding entries and
>>>> final
>>>> thoughts.  I hope you all enjoyed your summer and learned a lot!
>>>> Please make
>>>> sure you've given your mentors a BIG thank-you, they have some of
>>>> the
>>>> hardest jobs in GSoC.
>>>> 
>>>> Mentors, final evaluations are due by this Friday, August 26.
>>>> Thanks so
>>>> much for your work, it means a lot.  Especially to the students.
>>>> 
>>>> Everybody, if you have suggestions or feedback for what aspects of
>>>> the
>>>> program worked well this year, which things didn't work so well,
>>>> or things
>>>> we should add for next year, I'm always interested to hear them!
>>>> Just drop
>>>> me an email at this same address.
>>>> 
>>>> Thank you so much for everything you've done this summer, and
>>>> here's to many
>>>> more successful years of OBF GSoC in the future!
>>>> 
>>>> Rob
>>> 
>>> Hi Rob,
>>> 
>>> Thanks for your hard work again this year.
>>> 
>>> In terms of feedback for the OBF GSoC 2011, my main
>>> observation is that overall it seems there has been less
>>> interaction with the students and the respective community
>>> mailing lists. I have been reassured by mentors, wiki
>>> updates, and code commits that work is going on, but
>>> for next year I think we should insist up front from the
>>> start that students are expected to send a weekly email
>>> report of what they have been doing to the appropriate
>>> mailing list of the host project (e.g. biopython-dev or
>>> bioperl-l), and perhaps CC'd to our GSoC mailing list.
>>> Otherwise it has been hard for non-mentors to follow
>>> what is happening.
>>> 
>>> This is not intended as a personal criticism of anyone -
>>> just something I think we could do better next year.
>>> 
>>> Regards,
>>> 
>>> Peter
>>> 
>>> _______________________________________________
>>> GSoC mailing list
>>> GSoC at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/gsoc
>>> 
>>> 
>>> 
>> _______________________________________________
>> GSoC mailing list
>> GSoC at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/gsoc



From sheena.scroggins at gmail.com  Wed Aug 24 12:21:07 2011
From: sheena.scroggins at gmail.com (Sheena Scroggins)
Date: Wed, 24 Aug 2011 09:21:07 -0700
Subject: [GSoC] End of GSoC
Message-ID: <CAFUOKQrUPrC8W1k8qBTPgjsdk4d_XSKOMauN2RzXnGzsoRGZjw@mail.gmail.com>

I just wanted to give a GIANT thanks to my mentors on the BioPerl project,
Rob Buels and Chris Fields. They helped me tremendously and we made great
progress on the reorganization.

All of the modules we extracted can be found on github at
https://github.com/bioperl

We used a Dist Zilla plugin bundle, which can also be found there. The steps
used in the process will be outlined on the BioPerl wiki in the upcoming
weeks. The reorganization is off to a great start and by outlining the
workflow I'm hoping others will be able to contribute more easily.

The progress updates were posted at techomics.com during the project,
although they were sporadic. The original outline of the project can be
found there as well.

Thanks again to all the mentors of GSoC, this program wouldn't work without
you!

Sheena

From p.v.troshin at dundee.ac.uk  Thu Aug 25 03:01:31 2011
From: p.v.troshin at dundee.ac.uk (Peter Troshin)
Date: Thu, 25 Aug 2011 08:01:31 +0100
Subject: [GSoC] Fwd: [Biojava-dev] Work completed for
	GSoC:AAPropertiesComputation
In-Reply-To: <CA+rQFrU2_Jz9q=imnR0pxuEj1jQf82Xnrv_qAq09oL7uwJt6Ow@mail.gmail.com>
References: <CA+rQFrU2_Jz9q=imnR0pxuEj1jQf82Xnrv_qAq09oL7uwJt6Ow@mail.gmail.com>
Message-ID: <4E55F34B.6070808@dundee.ac.uk>



-------- Original Message --------
Subject: 	[Biojava-dev] Work completed for GSoC:AAPropertiesComputation
Date: 	Thu, 25 Aug 2011 10:12:43 +0800
From: 	Chuan Hock Koh <kohchuanhock at gmail.com>
To: 	biojava-l at lists.open-bio.org, biojava-dev 
<biojava-dev at lists.open-bio.org>



Hi All,

The Google Summer of Code has come to an end. Please allow me to share with
you what was achieved during this summer by me, Andreas Prlic and Peter
Troshin.

1) A set of APIs to compute Physico-Chemical properties of protein
sequences. Please see CookBook (
http://biojava.org/wiki/BioJava:CookBook:AAPROP:main) on how to use them.
Following is a list of properties that could be generated:

    - Molecular weight
    - Extinction coefficient
    - Instability index
    - Aliphatic index
    - Grand Average of Hydropathy
    - Isoelectric point
    - Amino acid composition


2) A executable jar to do the same thing as point 1. Please see CookBook (
http://biojava.org/wiki/BioJava:CookBook:AAPROP:commandprompt) for examples
on usage.

3) A set of APIs to compute PROFEAT properties of protein sequences. Please
see this paper (
http://nar.oxfordjournals.org/content/34/suppl_2/W32.abstract) for more
details about PROFEAT properties. Also, do see CookBook (
http://biojava.org/wiki/BioJava:CookBook:AAPROP:profeat) on how to use them.

4) Another thing worth noting is that as requested by the BioJava community,
we have enabled the customization for the computing of molecular weight for
point 1 and 2. Please see CookBook (
http://biojava.org/wiki/BioJava:CookBook:AAPROP:xmlfiles) for more
information.

5) Also, a SOAP web service for physico-chemical properties computation
(point 1) was developed within the JABAWS framework for portable web
services (http://www.compbio.dundee.ac.uk/jabaws/). This web service can be
installed on your own computing infrastructure with ease. If you intend to
use this web service, please contact us for further details.

I would continue to improve and work on this package even after this summer.
Therefore, if you have any feedback or comments. Please feel free to drop me
a mail. Thanks!

Regards,
Chuan Hock Koh (aka Ah Fu), Andreas Prlic and Peter Troshin

-- 
http://compbio.ddns.comp.nus.edu.sg/~ChuanHockKoh<http://compbio.ddns.comp.nus.edu.sg/~ChuanHockKoh/index.html>
_______________________________________________
biojava-dev mailing list
biojava-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-dev


From cjfields at illinois.edu  Fri Apr  8 13:19:54 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 8 Apr 2011 08:19:54 -0500
Subject: [GSoC] test
Message-ID: <0BD4F3AD-6BC9-43B0-BAB6-814BE112F463@illinois.edu>

<test>
tap tap, is this thing working?
</test>


From p.j.a.cock at googlemail.com  Fri Apr  8 13:36:45 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 8 Apr 2011 14:36:45 +0100
Subject: [GSoC] test
In-Reply-To: <0BD4F3AD-6BC9-43B0-BAB6-814BE112F463@illinois.edu>
References: <0BD4F3AD-6BC9-43B0-BAB6-814BE112F463@illinois.edu>
Message-ID: <BANLkTi=u8ShQEDx6YZXyDB1nM=OA8zW7GQ@mail.gmail.com>

On Fri, Apr 8, 2011 at 2:19 PM, Chris Fields <cjfields at illinois.edu> wrote:
> <test>
> tap tap, is this thing working?
> </test>

Yes :)


From cjfields at illinois.edu  Fri Apr  8 14:20:56 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 8 Apr 2011 09:20:56 -0500
Subject: [GSoC] test
In-Reply-To: <2EA4F074-2384-45CE-9C1F-41ABAC2F45FF@ingm.org>
References: <0BD4F3AD-6BC9-43B0-BAB6-814BE112F463@illinois.edu>
	<BANLkTi=u8ShQEDx6YZXyDB1nM=OA8zW7GQ@mail.gmail.com>
	<2EA4F074-2384-45CE-9C1F-41ABAC2F45FF@ingm.org>
Message-ID: <9E16D4EA-BC8C-4F35-8CD0-10BDBCD67375@illinois.edu>

On Apr 8, 2011, at 9:16 AM, Raoul Bonnal wrote:

> 
> On 08/apr/2011, at 15.36, Peter Cock wrote:
> 
>> On Fri, Apr 8, 2011 at 2:19 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>> <test>
>>> tap tap, is this thing working?
>>> </test>
>> 
>> Yes :)
> LoL Yep
>> _______________________________________________
>> GSoC mailing list
>> GSoC at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/gsoc
> 
> --
> Ra
> 
> linkedin: http://it.linkedin.com/in/raoulbonnal
> twitter: http://twitter.com/ilpuccio
> skype: ilpuccio
> irc.freenode.net: Helius
> github: https://github.com/helios


Cool, just checking.  I'm guessing we need to make sure any prospective mentors sign up.

chris




From bonnal at ingm.org  Fri Apr  8 14:16:24 2011
From: bonnal at ingm.org (Raoul Bonnal)
Date: Fri, 8 Apr 2011 16:16:24 +0200
Subject: [GSoC] test
In-Reply-To: <BANLkTi=u8ShQEDx6YZXyDB1nM=OA8zW7GQ@mail.gmail.com>
References: <0BD4F3AD-6BC9-43B0-BAB6-814BE112F463@illinois.edu>
	<BANLkTi=u8ShQEDx6YZXyDB1nM=OA8zW7GQ@mail.gmail.com>
Message-ID: <2EA4F074-2384-45CE-9C1F-41ABAC2F45FF@ingm.org>


On 08/apr/2011, at 15.36, Peter Cock wrote:

> On Fri, Apr 8, 2011 at 2:19 PM, Chris Fields <cjfields at illinois.edu> wrote:
>> <test>
>> tap tap, is this thing working?
>> </test>
> 
> Yes :)
LoL Yep
> _______________________________________________
> GSoC mailing list
> GSoC at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/gsoc

--
Ra

linkedin: http://it.linkedin.com/in/raoulbonnal
twitter: http://twitter.com/ilpuccio
skype: ilpuccio
irc.freenode.net: Helius
github: https://github.com/helios








From anaryin at gmail.com  Fri Apr  8 16:33:44 2011
From: anaryin at gmail.com (=?UTF-8?Q?Jo=C3=A3o_Rodrigues?=)
Date: Fri, 8 Apr 2011 18:33:44 +0200
Subject: [GSoC] test
In-Reply-To: <9E16D4EA-BC8C-4F35-8CD0-10BDBCD67375@illinois.edu>
References: <0BD4F3AD-6BC9-43B0-BAB6-814BE112F463@illinois.edu>
	<BANLkTi=u8ShQEDx6YZXyDB1nM=OA8zW7GQ@mail.gmail.com>
	<2EA4F074-2384-45CE-9C1F-41ABAC2F45FF@ingm.org>
	<9E16D4EA-BC8C-4F35-8CD0-10BDBCD67375@illinois.edu>
Message-ID: <BANLkTini0iA9dq2ZRbAuMyeS1SDqUtRCvA@mail.gmail.com>

Working here too, what is the purpose of this list again? :x


From rmb32 at cornell.edu  Fri Apr  8 16:56:03 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Fri, 08 Apr 2011 09:56:03 -0700
Subject: [GSoC] test
In-Reply-To: <BANLkTini0iA9dq2ZRbAuMyeS1SDqUtRCvA@mail.gmail.com>
References: <0BD4F3AD-6BC9-43B0-BAB6-814BE112F463@illinois.edu>	<BANLkTi=u8ShQEDx6YZXyDB1nM=OA8zW7GQ@mail.gmail.com>	<2EA4F074-2384-45CE-9C1F-41ABAC2F45FF@ingm.org>	<9E16D4EA-BC8C-4F35-8CD0-10BDBCD67375@illinois.edu>
	<BANLkTini0iA9dq2ZRbAuMyeS1SDqUtRCvA@mail.gmail.com>
Message-ID: <4D9F3E23.9010808@cornell.edu>

On 04/08/2011 09:33 AM, Jo?o Rodrigues wrote:
> Working here too, what is the purpose of this list again? :x

It's for administrative announcements, and general public discussions 
about Open Bioinformatics Foundation GSoC.

With 2011 GSoC starting up now, this list is going to start getting more 
traffic, so if you're not interested in OBF GSoC 2011, you should think 
about unsubscribing using the lists.open-bio.org link at the bottom of 
this email.

Rob


From rmb32 at cornell.edu  Tue May 17 18:02:35 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Tue, 17 May 2011 11:02:35 -0700
Subject: [GSoC] GSoC coding period starts next Monday
Message-ID: <4DD2B83B.1090106@cornell.edu>

Hi all,

The coding period for Google Summer of Code starts this coming Monday.  
Each mentor-student group should be pretty well organized by now, and 
know exactly what they're going to be doing next week.

Each group needs to make sure they have the following in place:

1. Good lines of communication between students and mentors, including 
plans for regular chat or phone meetings.

2. The student needs to have their development environment set up and 
ready to go, so that they'll be ready to be productive from day 1.  Get 
the necessary software, version control checkouts, data sets, and so 
forth.  Don't leave this until the last minute, setting up a development 
environment can be tricky!

3. The student needs to have their blog/wiki/other set up for public 
reports of the project's progress.  Please send the URLs for these to 
me, and I'll construct a page on the OBF GSoC wiki with links to them.

Here's to a fun and productive summer of code!

Best wishes,

Rob

----
Robert Buels
OBF GSoC 2011 Administrator






From to.petr at gmail.com  Wed May 18 08:07:36 2011
From: to.petr at gmail.com (P. Troshin)
Date: Wed, 18 May 2011 09:07:36 +0100
Subject: [GSoC] GSoC coding period starts next Monday
In-Reply-To: <4DD2B83B.1090106@cornell.edu>
References: <4DD2B83B.1090106@cornell.edu>
Message-ID: <BANLkTimud-o6j+57xgBzpbjyz5oBb=NWDA@mail.gmail.com>

Dear Robert,

> 3. The student needs to have their blog/wiki/other set up for public reports
> of the project's progress.  Please send the URLs for these to me, and I'll
> construct a page on the OBF GSoC wiki with links to them.

Thank you for your advice.
The URL for Amino Acid Physico-Chemical Properties Calculation project
is this http://biojava.org/wiki/GSoC:AAPropertiesComputation

Regards,
Peter


On 17 May 2011 19:02, Robert Buels <rmb32 at cornell.edu> wrote:
> Hi all,
>
> The coding period for Google Summer of Code starts this coming Monday. ?Each
> mentor-student group should be pretty well organized by now, and know
> exactly what they're going to be doing next week.
>
> Each group needs to make sure they have the following in place:
>
> 1. Good lines of communication between students and mentors, including plans
> for regular chat or phone meetings.
>
> 2. The student needs to have their development environment set up and ready
> to go, so that they'll be ready to be productive from day 1. ?Get the
> necessary software, version control checkouts, data sets, and so forth.
> ?Don't leave this until the last minute, setting up a development
> environment can be tricky!
>
> 3. The student needs to have their blog/wiki/other set up for public reports
> of the project's progress. ?Please send the URLs for these to me, and I'll
> construct a page on the OBF GSoC wiki with links to them.
>
> Here's to a fun and productive summer of code!
>
> Best wishes,
>
> Rob
>
> ----
> Robert Buels
> OBF GSoC 2011 Administrator
>
>
>
>
> _______________________________________________
> GSoC mailing list
> GSoC at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/gsoc
>



From rmb32 at cornell.edu  Thu May 19 16:07:49 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Thu, 19 May 2011 09:07:49 -0700
Subject: [GSoC] GSoC coding period starts next Monday
In-Reply-To: <4DD2B83B.1090106@cornell.edu>
References: <4DD2B83B.1090106@cornell.edu>
Message-ID: <4DD54055.1020306@cornell.edu>

Reminder: please send me the URLs of your progress report pages Real 
Soon Now.

They need to be up, with some content about how you're starting off, by 
Monday.

Rob



On 05/17/2011 11:02 AM, Robert Buels wrote:
> Hi all,
>
> The coding period for Google Summer of Code starts this coming Monday.
> Each mentor-student group should be pretty well organized by now, and
> know exactly what they're going to be doing next week.
>
> Each group needs to make sure they have the following in place:
>
> 1. Good lines of communication between students and mentors, including
> plans for regular chat or phone meetings.
>
> 2. The student needs to have their development environment set up and
> ready to go, so that they'll be ready to be productive from day 1. Get
> the necessary software, version control checkouts, data sets, and so
> forth. Don't leave this until the last minute, setting up a development
> environment can be tricky!
>
> 3. The student needs to have their blog/wiki/other set up for public
> reports of the project's progress. Please send the URLs for these to me,
> and I'll construct a page on the OBF GSoC wiki with links to them.
>
> Here's to a fun and productive summer of code!
>
> Best wishes,
>
> Rob
>
> ----
> Robert Buels
> OBF GSoC 2011 Administrator
>
>
>
>
> _______________________________________________
> GSoC mailing list
> GSoC at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/gsoc
>



From sheena.scroggins at gmail.com  Sun May 22 23:14:20 2011
From: sheena.scroggins at gmail.com (Sheena Scroggins)
Date: Sun, 22 May 2011 16:14:20 -0700
Subject: [GSoC] GSoC BioPerl Project Page
Message-ID: <BANLkTinq5hPf5wL3oAHFqfPRZPFCN59WaQ@mail.gmail.com>

Hey everyone,


The BioPerl project can be followed at www.techomics.com.

The relevant github links will be posted there soon.

Sheena


From rmb32 at cornell.edu  Mon Jun  6 16:23:02 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Mon, 06 Jun 2011 09:23:02 -0700
Subject: [GSoC] Reminder: frequent updates needed on progress pages
Message-ID: <4DECFEE6.2030708@cornell.edu>

Hi all,

Looking through the project pages, I see that most have not been updated 
in some time.  Justinas and Chuan Hok seem to have been keeping up with 
it, many thanks to them!

For the rest of the projects, please update your pages now.

At minimum, there should be an update to the log every week that reports 
what was done that week.  Ideally, students should use them as a log of 
your progress, struggles, and thoughts throughout the project.

Thanks for all your hard work so far, students and mentors!

Rob


From rmb32 at cornell.edu  Thu Jun 30 13:21:39 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Thu, 30 Jun 2011 06:21:39 -0700
Subject: [GSoC] reminder: mid-term evaluations in 1.5 weeks
Message-ID: <4E0C7863.4030309@cornell.edu>

Hi all,

This is a reminder that GSoC mid-term evaluations are due on July 11, 
which is a little more than a week away.  At the end of this email, I'm 
including the full story on evaluations and how they work.

Hope your projects are going well.  Keep those progress reports up to 
date!  :-)

Rob Buels
OBF GSoC 2011 Administrator


------
EVALUATIONS

(from 
http://www.google-melange.com/document/show/gsoc_program/google/gsoc2011/faqs#evals)


9. How do evaluations work?

Google will pre-publish the evaluation questions for both students and 
mentors. Mentors will fill out mid-term and final evaluations for their 
students via the Google Summer of Code 2011 site. These evaluations will 
be visible in the system to the mentor and the mentoring organization's 
administrator(s). Students will fill out a mid-term and final evaluation 
of their mentors online as well, and their evaluations will only be 
visible in the system to the mentoring organization's administrator(s). 
Program administrators from Google will have access to all evaluation data.

In almost all cases, students will never see their mentor's evaluation 
of their progress, nor will a mentor see a student's evaluation of 
her/his mentorship. However, in the case where the mentoring 
organization's administrator and a student's mentor are one and the 
same, the student's evaluation will be shared with the mentor. If you 
are a student in a situation where your mentor is also your 
organization?s administrator and you would like to discuss an issue with 
the program, please contact the Google Summer of Code program 
administrators. Organization administrators are expected to review 
mid-term and final evaluations and to provide course corrections where 
necessary.

In some cases, Google's program administrators may need to share the 
results of evaluations with the student and mentor, such as to arbitrate 
when payment should not be made. Should this need arise, all parties 
will be notified in advance.



From rmb32 at cornell.edu  Tue Aug 23 17:33:42 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Tue, 23 Aug 2011 10:33:42 -0700
Subject: [GSoC] reminder: final evaluations due Friday
Message-ID: <4E53E476.7080606@cornell.edu>

Hi all,

Students, your projects should now be finished.  Students, please make 
sure you have updated your progress pages with concluding entries and 
final thoughts.  I hope you all enjoyed your summer and learned a lot! 
Please make sure you've given your mentors a BIG thank-you, they have 
some of the hardest jobs in GSoC.

Mentors, final evaluations are due by this Friday, August 26.  Thanks so 
much for your work, it means a lot.  Especially to the students.

Everybody, if you have suggestions or feedback for what aspects of the 
program worked well this year, which things didn't work so well, or 
things we should add for next year, I'm always interested to hear them! 
  Just drop me an email at this same address.

Thank you so much for everything you've done this summer, and here's to 
many more successful years of OBF GSoC in the future!

Rob

-----
Robert Buels
OBF GSoC 2011 Administrator


From p.j.a.cock at googlemail.com  Wed Aug 24 01:59:23 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 24 Aug 2011 02:59:23 +0100
Subject: [GSoC] reminder: final evaluations due Friday
In-Reply-To: <4E53E476.7080606@cornell.edu>
References: <4E53E476.7080606@cornell.edu>
Message-ID: <CAKVJ-_50J5KDTH--5-R+t0qHjKv72woLAYcER=XUb-X95AGYog@mail.gmail.com>

On Tue, Aug 23, 2011 at 6:33 PM, Robert Buels <rmb32 at cornell.edu> wrote:
> Hi all,
>
> Students, your projects should now be finished. ?Students, please make sure
> you have updated your progress pages with concluding entries and final
> thoughts. ?I hope you all enjoyed your summer and learned a lot! Please make
> sure you've given your mentors a BIG thank-you, they have some of the
> hardest jobs in GSoC.
>
> Mentors, final evaluations are due by this Friday, August 26. ?Thanks so
> much for your work, it means a lot. ?Especially to the students.
>
> Everybody, if you have suggestions or feedback for what aspects of the
> program worked well this year, which things didn't work so well, or things
> we should add for next year, I'm always interested to hear them! ?Just drop
> me an email at this same address.
>
> Thank you so much for everything you've done this summer, and here's to many
> more successful years of OBF GSoC in the future!
>
> Rob

Hi Rob,

Thanks for your hard work again this year.

In terms of feedback for the OBF GSoC 2011, my main
observation is that overall it seems there has been less
interaction with the students and the respective community
mailing lists. I have been reassured by mentors, wiki
updates, and code commits that work is going on, but
for next year I think we should insist up front from the
start that students are expected to send a weekly email
report of what they have been doing to the appropriate
mailing list of the host project (e.g. biopython-dev or
bioperl-l), and perhaps CC'd to our GSoC mailing list.
Otherwise it has been hard for non-mentors to follow
what is happening.

This is not intended as a personal criticism of anyone -
just something I think we could do better next year.

Regards,

Peter



From cmzmasek at yahoo.com  Wed Aug 24 02:03:17 2011
From: cmzmasek at yahoo.com (Christian Zmasek)
Date: Tue, 23 Aug 2011 19:03:17 -0700 (PDT)
Subject: [GSoC] reminder: final evaluations due Friday
In-Reply-To: <CAKVJ-_50J5KDTH--5-R+t0qHjKv72woLAYcER=XUb-X95AGYog@mail.gmail.com>
References: <4E53E476.7080606@cornell.edu>
	<CAKVJ-_50J5KDTH--5-R+t0qHjKv72woLAYcER=XUb-X95AGYog@mail.gmail.com>
Message-ID: <1314151397.10878.YahooMailNeo@web38407.mail.mud.yahoo.com>

I totally agree with Peter's points.

Christian



>________________________________
>From: Peter Cock <p.j.a.cock at googlemail.com>
>To: Robert Buels <rmb32 at cornell.edu>
>Cc: OBF GSoC <gsoc at lists.open-bio.org>
>Sent: Wednesday, August 24, 2011 10:59 AM
>Subject: Re: [GSoC] reminder: final evaluations due Friday
>
>On Tue, Aug 23, 2011 at 6:33 PM, Robert Buels <rmb32 at cornell.edu> wrote:
>> Hi all,
>>
>> Students, your projects should now be finished. ?Students, please make sure
>> you have updated your progress pages with concluding entries and final
>> thoughts. ?I hope you all enjoyed your summer and learned a lot! Please make
>> sure you've given your mentors a BIG thank-you, they have some of the
>> hardest jobs in GSoC.
>>
>> Mentors, final evaluations are due by this Friday, August 26. ?Thanks so
>> much for your work, it means a lot. ?Especially to the students.
>>
>> Everybody, if you have suggestions or feedback for what aspects of the
>> program worked well this year, which things didn't work so well, or things
>> we should add for next year, I'm always interested to hear them! ?Just drop
>> me an email at this same address.
>>
>> Thank you so much for everything you've done this summer, and here's to many
>> more successful years of OBF GSoC in the future!
>>
>> Rob
>
>Hi Rob,
>
>Thanks for your hard work again this year.
>
>In terms of feedback for the OBF GSoC 2011, my main
>observation is that overall it seems there has been less
>interaction with the students and the respective community
>mailing lists. I have been reassured by mentors, wiki
>updates, and code commits that work is going on, but
>for next year I think we should insist up front from the
>start that students are expected to send a weekly email
>report of what they have been doing to the appropriate
>mailing list of the host project (e.g. biopython-dev or
>bioperl-l), and perhaps CC'd to our GSoC mailing list.
>Otherwise it has been hard for non-mentors to follow
>what is happening.
>
>This is not intended as a personal criticism of anyone -
>just something I think we could do better next year.
>
>Regards,
>
>Peter
>
>_______________________________________________
>GSoC mailing list
>GSoC at lists.open-bio.org
>http://lists.open-bio.org/mailman/listinfo/gsoc
>
>
>


From cjfields at illinois.edu  Wed Aug 24 02:16:01 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 23 Aug 2011 21:16:01 -0500
Subject: [GSoC] reminder: final evaluations due Friday
In-Reply-To: <1314151397.10878.YahooMailNeo@web38407.mail.mud.yahoo.com>
References: <4E53E476.7080606@cornell.edu>
	<CAKVJ-_50J5KDTH--5-R+t0qHjKv72woLAYcER=XUb-X95AGYog@mail.gmail.com>
	<1314151397.10878.YahooMailNeo@web38407.mail.mud.yahoo.com>
Message-ID: <AB10C27B-BAE5-4381-B0E0-58BD85B7A67E@illinois.edu>

+1

chris

On Aug 23, 2011, at 9:03 PM, Christian Zmasek wrote:

> I totally agree with Peter's points.
> 
> Christian
> 
> 
> 
>> ________________________________
>> From: Peter Cock <p.j.a.cock at googlemail.com>
>> To: Robert Buels <rmb32 at cornell.edu>
>> Cc: OBF GSoC <gsoc at lists.open-bio.org>
>> Sent: Wednesday, August 24, 2011 10:59 AM
>> Subject: Re: [GSoC] reminder: final evaluations due Friday
>> 
>> On Tue, Aug 23, 2011 at 6:33 PM, Robert Buels <rmb32 at cornell.edu> wrote:
>>> Hi all,
>>> 
>>> Students, your projects should now be finished.  Students, please make sure
>>> you have updated your progress pages with concluding entries and final
>>> thoughts.  I hope you all enjoyed your summer and learned a lot! Please make
>>> sure you've given your mentors a BIG thank-you, they have some of the
>>> hardest jobs in GSoC.
>>> 
>>> Mentors, final evaluations are due by this Friday, August 26.  Thanks so
>>> much for your work, it means a lot.  Especially to the students.
>>> 
>>> Everybody, if you have suggestions or feedback for what aspects of the
>>> program worked well this year, which things didn't work so well, or things
>>> we should add for next year, I'm always interested to hear them!  Just drop
>>> me an email at this same address.
>>> 
>>> Thank you so much for everything you've done this summer, and here's to many
>>> more successful years of OBF GSoC in the future!
>>> 
>>> Rob
>> 
>> Hi Rob,
>> 
>> Thanks for your hard work again this year.
>> 
>> In terms of feedback for the OBF GSoC 2011, my main
>> observation is that overall it seems there has been less
>> interaction with the students and the respective community
>> mailing lists. I have been reassured by mentors, wiki
>> updates, and code commits that work is going on, but
>> for next year I think we should insist up front from the
>> start that students are expected to send a weekly email
>> report of what they have been doing to the appropriate
>> mailing list of the host project (e.g. biopython-dev or
>> bioperl-l), and perhaps CC'd to our GSoC mailing list.
>> Otherwise it has been hard for non-mentors to follow
>> what is happening.
>> 
>> This is not intended as a personal criticism of anyone -
>> just something I think we could do better next year.
>> 
>> Regards,
>> 
>> Peter
>> 
>> _______________________________________________
>> GSoC mailing list
>> GSoC at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/gsoc
>> 
>> 
>> 
> _______________________________________________
> GSoC mailing list
> GSoC at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/gsoc




From hlapp at drycafe.net  Wed Aug 24 02:21:52 2011
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Wed, 24 Aug 2011 11:21:52 +0900
Subject: [GSoC] reminder: final evaluations due Friday
In-Reply-To: <1314151397.10878.YahooMailNeo@web38407.mail.mud.yahoo.com>
References: <4E53E476.7080606@cornell.edu>
	<CAKVJ-_50J5KDTH--5-R+t0qHjKv72woLAYcER=XUb-X95AGYog@mail.gmail.com>
	<1314151397.10878.YahooMailNeo@web38407.mail.mud.yahoo.com>
Message-ID: <B6569B44-581C-4F21-A0DA-29017348F905@drycafe.net>

Same here - it has saddened me frankly that the community building  
aspect of GSoC involvement (which in my view is the real motivator  
that makes putting in the mentoring and admin time all worth it in the  
end) has turned into a giant missed opportunity for us this year.

	-hilmar

On Aug 24, 2011, at 11:03 AM, Christian Zmasek wrote:

> I totally agree with Peter's points.
>
> Christian
>
>
>
>> ________________________________
>> From: Peter Cock <p.j.a.cock at googlemail.com>
>> To: Robert Buels <rmb32 at cornell.edu>
>> Cc: OBF GSoC <gsoc at lists.open-bio.org>
>> Sent: Wednesday, August 24, 2011 10:59 AM
>> Subject: Re: [GSoC] reminder: final evaluations due Friday
>>
>> On Tue, Aug 23, 2011 at 6:33 PM, Robert Buels <rmb32 at cornell.edu>  
>> wrote:
>>> Hi all,
>>>
>>> Students, your projects should now be finished.  Students, please  
>>> make sure
>>> you have updated your progress pages with concluding entries and  
>>> final
>>> thoughts.  I hope you all enjoyed your summer and learned a lot!  
>>> Please make
>>> sure you've given your mentors a BIG thank-you, they have some of  
>>> the
>>> hardest jobs in GSoC.
>>>
>>> Mentors, final evaluations are due by this Friday, August 26.   
>>> Thanks so
>>> much for your work, it means a lot.  Especially to the students.
>>>
>>> Everybody, if you have suggestions or feedback for what aspects of  
>>> the
>>> program worked well this year, which things didn't work so well,  
>>> or things
>>> we should add for next year, I'm always interested to hear them!   
>>> Just drop
>>> me an email at this same address.
>>>
>>> Thank you so much for everything you've done this summer, and  
>>> here's to many
>>> more successful years of OBF GSoC in the future!
>>>
>>> Rob
>>
>> Hi Rob,
>>
>> Thanks for your hard work again this year.
>>
>> In terms of feedback for the OBF GSoC 2011, my main
>> observation is that overall it seems there has been less
>> interaction with the students and the respective community
>> mailing lists. I have been reassured by mentors, wiki
>> updates, and code commits that work is going on, but
>> for next year I think we should insist up front from the
>> start that students are expected to send a weekly email
>> report of what they have been doing to the appropriate
>> mailing list of the host project (e.g. biopython-dev or
>> bioperl-l), and perhaps CC'd to our GSoC mailing list.
>> Otherwise it has been hard for non-mentors to follow
>> what is happening.
>>
>> This is not intended as a personal criticism of anyone -
>> just something I think we could do better next year.
>>
>> Regards,
>>
>> Peter
>>
>> _______________________________________________
>> GSoC mailing list
>> GSoC at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/gsoc
>>
>>
>>
> _______________________________________________
> GSoC mailing list
> GSoC at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/gsoc

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






From bonnal at ingm.org  Wed Aug 24 02:53:28 2011
From: bonnal at ingm.org (Raoul Bonnal)
Date: Wed, 24 Aug 2011 11:53:28 +0900
Subject: [GSoC] reminder: final evaluations due Friday
In-Reply-To: <B6569B44-581C-4F21-A0DA-29017348F905@drycafe.net>
Message-ID: <CA7A96B8.4CA2%bonnal@ingm.org>

+1 but
A) I think we need to create some kind of best practices for the students
and select the "well written" proposals as example
B) Schedule mentors meeting during the GSoC, IRC is fine. It was very useful
at the beginning and I want to thanks all the people in particular Chris and
Robert.
C) I'd like to schedule the next GSoC in time, we -BioRuby- need start
thinking to the next GSoC from now. Having a clear plan or road map it's a
must at least for me. Let's pick up the example of this BioHackathon, we can
prototype something here and then decide to use GSoC to improve it.
D) why not create a page on the wiki with our comments and experiences to
identify the BUGS ?

On 24/08/11 11.21, "Hilmar Lapp" <hlapp at drycafe.net> wrote:

> Same here - it has saddened me frankly that the community building
> aspect of GSoC involvement (which in my view is the real motivator
> that makes putting in the mentoring and admin time all worth it in the
> end) has turned into a giant missed opportunity for us this year.
> 
> -hilmar
> 
> On Aug 24, 2011, at 11:03 AM, Christian Zmasek wrote:
> 
>> I totally agree with Peter's points.
>> 
>> Christian
>> 
>> 
>> 
>>> ________________________________
>>> From: Peter Cock <p.j.a.cock at googlemail.com>
>>> To: Robert Buels <rmb32 at cornell.edu>
>>> Cc: OBF GSoC <gsoc at lists.open-bio.org>
>>> Sent: Wednesday, August 24, 2011 10:59 AM
>>> Subject: Re: [GSoC] reminder: final evaluations due Friday
>>> 
>>> On Tue, Aug 23, 2011 at 6:33 PM, Robert Buels <rmb32 at cornell.edu>
>>> wrote:
>>>> Hi all,
>>>> 
>>>> Students, your projects should now be finished.  Students, please
>>>> make sure
>>>> you have updated your progress pages with concluding entries and
>>>> final
>>>> thoughts.  I hope you all enjoyed your summer and learned a lot!
>>>> Please make
>>>> sure you've given your mentors a BIG thank-you, they have some of
>>>> the
>>>> hardest jobs in GSoC.
>>>> 
>>>> Mentors, final evaluations are due by this Friday, August 26.
>>>> Thanks so
>>>> much for your work, it means a lot.  Especially to the students.
>>>> 
>>>> Everybody, if you have suggestions or feedback for what aspects of
>>>> the
>>>> program worked well this year, which things didn't work so well,
>>>> or things
>>>> we should add for next year, I'm always interested to hear them!
>>>> Just drop
>>>> me an email at this same address.
>>>> 
>>>> Thank you so much for everything you've done this summer, and
>>>> here's to many
>>>> more successful years of OBF GSoC in the future!
>>>> 
>>>> Rob
>>> 
>>> Hi Rob,
>>> 
>>> Thanks for your hard work again this year.
>>> 
>>> In terms of feedback for the OBF GSoC 2011, my main
>>> observation is that overall it seems there has been less
>>> interaction with the students and the respective community
>>> mailing lists. I have been reassured by mentors, wiki
>>> updates, and code commits that work is going on, but
>>> for next year I think we should insist up front from the
>>> start that students are expected to send a weekly email
>>> report of what they have been doing to the appropriate
>>> mailing list of the host project (e.g. biopython-dev or
>>> bioperl-l), and perhaps CC'd to our GSoC mailing list.
>>> Otherwise it has been hard for non-mentors to follow
>>> what is happening.
>>> 
>>> This is not intended as a personal criticism of anyone -
>>> just something I think we could do better next year.
>>> 
>>> Regards,
>>> 
>>> Peter
>>> 
>>> _______________________________________________
>>> GSoC mailing list
>>> GSoC at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/gsoc
>>> 
>>> 
>>> 
>> _______________________________________________
>> GSoC mailing list
>> GSoC at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/gsoc




From sheena.scroggins at gmail.com  Wed Aug 24 16:21:07 2011
From: sheena.scroggins at gmail.com (Sheena Scroggins)
Date: Wed, 24 Aug 2011 09:21:07 -0700
Subject: [GSoC] End of GSoC
Message-ID: <CAFUOKQrUPrC8W1k8qBTPgjsdk4d_XSKOMauN2RzXnGzsoRGZjw@mail.gmail.com>

I just wanted to give a GIANT thanks to my mentors on the BioPerl project,
Rob Buels and Chris Fields. They helped me tremendously and we made great
progress on the reorganization.

All of the modules we extracted can be found on github at
https://github.com/bioperl

We used a Dist Zilla plugin bundle, which can also be found there. The steps
used in the process will be outlined on the BioPerl wiki in the upcoming
weeks. The reorganization is off to a great start and by outlining the
workflow I'm hoping others will be able to contribute more easily.

The progress updates were posted at techomics.com during the project,
although they were sporadic. The original outline of the project can be
found there as well.

Thanks again to all the mentors of GSoC, this program wouldn't work without
you!

Sheena


From p.v.troshin at dundee.ac.uk  Thu Aug 25 07:01:31 2011
From: p.v.troshin at dundee.ac.uk (Peter Troshin)
Date: Thu, 25 Aug 2011 08:01:31 +0100
Subject: [GSoC] Fwd: [Biojava-dev] Work completed for
	GSoC:AAPropertiesComputation
In-Reply-To: <CA+rQFrU2_Jz9q=imnR0pxuEj1jQf82Xnrv_qAq09oL7uwJt6Ow@mail.gmail.com>
References: <CA+rQFrU2_Jz9q=imnR0pxuEj1jQf82Xnrv_qAq09oL7uwJt6Ow@mail.gmail.com>
Message-ID: <4E55F34B.6070808@dundee.ac.uk>



-------- Original Message --------
Subject: 	[Biojava-dev] Work completed for GSoC:AAPropertiesComputation
Date: 	Thu, 25 Aug 2011 10:12:43 +0800
From: 	Chuan Hock Koh <kohchuanhock at gmail.com>
To: 	biojava-l at lists.open-bio.org, biojava-dev 
<biojava-dev at lists.open-bio.org>



Hi All,

The Google Summer of Code has come to an end. Please allow me to share with
you what was achieved during this summer by me, Andreas Prlic and Peter
Troshin.

1) A set of APIs to compute Physico-Chemical properties of protein
sequences. Please see CookBook (
http://biojava.org/wiki/BioJava:CookBook:AAPROP:main) on how to use them.
Following is a list of properties that could be generated:

    - Molecular weight
    - Extinction coefficient
    - Instability index
    - Aliphatic index
    - Grand Average of Hydropathy
    - Isoelectric point
    - Amino acid composition


2) A executable jar to do the same thing as point 1. Please see CookBook (
http://biojava.org/wiki/BioJava:CookBook:AAPROP:commandprompt) for examples
on usage.

3) A set of APIs to compute PROFEAT properties of protein sequences. Please
see this paper (
http://nar.oxfordjournals.org/content/34/suppl_2/W32.abstract) for more
details about PROFEAT properties. Also, do see CookBook (
http://biojava.org/wiki/BioJava:CookBook:AAPROP:profeat) on how to use them.

4) Another thing worth noting is that as requested by the BioJava community,
we have enabled the customization for the computing of molecular weight for
point 1 and 2. Please see CookBook (
http://biojava.org/wiki/BioJava:CookBook:AAPROP:xmlfiles) for more
information.

5) Also, a SOAP web service for physico-chemical properties computation
(point 1) was developed within the JABAWS framework for portable web
services (http://www.compbio.dundee.ac.uk/jabaws/). This web service can be
installed on your own computing infrastructure with ease. If you intend to
use this web service, please contact us for further details.

I would continue to improve and work on this package even after this summer.
Therefore, if you have any feedback or comments. Please feel free to drop me
a mail. Thanks!

Regards,
Chuan Hock Koh (aka Ah Fu), Andreas Prlic and Peter Troshin

-- 
http://compbio.ddns.comp.nus.edu.sg/~ChuanHockKoh<http://compbio.ddns.comp.nus.edu.sg/~ChuanHockKoh/index.html>
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