From p.j.a.cock at googlemail.com  Fri Mar  2 08:49:25 2012
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 2 Mar 2012 13:49:25 +0000
Subject: [BioSQL-l] Update: call for Google Summer of Code project ideas
In-Reply-To: <4F4BADDC.5020905@gmail.com>
References: <4F4BADDC.5020905@gmail.com>
Message-ID: <CAKVJ-_6QU-ZJ1shu2SFoWx+DVCz1=g-cDrSax=eiG0kr752RCQ@mail.gmail.com>

On Mon, Feb 27, 2012 at 4:22 PM, Robert Buels <rbuels at gmail.com> wrote:
> Hi all,
>
> As kindly pointed out by Reece Hart, the previous email I sent out calling
> for Google Summer of Code project ideas, had the wrong due date for project
> ideas in it.
>
> I actually want them to all be in place by Friday, March 2, which is this
> coming Friday.
>
> == Instructions for Wiki Editing ==
>
> For each of the OBF projects that wants to do GSoC again this year, please:
>
> a.) Update the list of project ideas on your project's GSoC page (BioPython,
> BioPerl, BioRuby, etc). ?Add new ones, remove ones that have already been
> done or no longer relevant, etc.
>
> b.) Update the list of project ideas on the main OBF GSoC page
> (http://www.open-bio.org/wiki/Google_Summer_of_Code) to match.
>
> c.) Let me know via email that you have done so and it's ready for Google to
> peruse.
>
> == end instructions ==
>
> Again, please have the updates done by this Friday (March 2). The number and
> quality of the project ideas are part of the evaluation process for whether
> OBF is accepted as a Summer of Code organization again this year, so let's
> come up with some good ones. ?:-)
>
> Rob

Time is short for Rob's deadline ready for the OBF's evaluation, but are
there any BioSQL ideas for GSoC? Assuming we are accepted again,
we can come up with more ideas later.

The only thing I could think of was full support for the SQLite3 schema
(i.e. updating all the BioSQL perl scripts), but that doesn't seem enough
for a whole summer.

Perhaps it could be combined with work on BioPerl-db itself to support
BioSQL on SQLite? Clearly that would require a BioPerl person to mentor it.

Peter


From cjfields at illinois.edu  Fri Mar  2 11:09:23 2012
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 2 Mar 2012 16:09:23 +0000
Subject: [BioSQL-l] [Bioperl-l] Update: call for Google Summer of Code
	project ideas
In-Reply-To: <CAKVJ-_4aKgGq80AVp++mW5Eewyf2ACBXL-PcoUU0J0mQ+h62ZQ@mail.gmail.com>
References: <4F4BAE5B.40309@gmail.com>
	<CAKVJ-_4aKgGq80AVp++mW5Eewyf2ACBXL-PcoUU0J0mQ+h62ZQ@mail.gmail.com>
Message-ID: <3F440BF7-4542-44E7-947D-A77180EC54F9@illinois.edu>

On Mar 2, 2012, at 7:54 AM, Peter Cock wrote:

> On Mon, Feb 27, 2012 at 4:24 PM, Robert Buels <rbuels at gmail.com> wrote:
>> Hi all,
>> 
>> As kindly pointed out by Reece Hart, the previous email I sent out calling
>> for Google Summer of Code project ideas, had the wrong due date for project
>> ideas in it.
>> 
>> I actually want them to all be in place by Friday, March 2, which is this
>> coming Friday.
>> 
>> == Instructions for Wiki Editing ==
>> 
>> For each of the OBF projects that wants to do GSoC again this year, please:
>> 
>> a.) Update the list of project ideas on your project's GSoC page (BioPython,
>> BioPerl, BioRuby, etc).  Add new ones, remove ones that have already been
>> done or no longer relevant, etc.
>> 
>> b.) Update the list of project ideas on the main OBF GSoC page
>> (http://www.open-bio.org/wiki/Google_Summer_of_Code) to match.
>> 
>> c.) Let me know via email that you have done so and it's ready for Google to
>> peruse.
>> 
>> == end instructions ==
>> 
>> Again, please have the updates done by this Friday (March 2). The number and
>> quality of the project ideas are part of the evaluation process for whether
>> OBF is accepted as a Summer of Code organization again this year, so let's
>> come up with some good ones.  :-)
>> 
>> Rob
> 
> Hi all,
> 
> I had a quick look at the BioPerl page (partly for inspiration for Biopython
> projects), and it doesn't seem to have been updated since the 2011 project
> ideas:
> 
> http://bioperl.org/wiki/Google_Summer_of_Code
> 
> Some of those 2011 ideas became actual projects didn't they? If so, can
> any of them be continued as a new project for 2012?
> 
> Over on the BioSQL mailing list I suggested a combined BioSQL+BioPerl
> project idea to support the SQLite schema. Does anyone fancy mentoring
> that?
> 
> Peter

Things have been rather quiet lately, I believe b/c everyone is busy with other $obligations, I myself have been ridiculously busy lately but try to pipe up when I can.  A few of the projects on that page are still legitimate, though, and I think support of SQLite is a good project.  

I would really like to see a somewhat Bio*-agnostic ORM for BioSQL, though.  I know there was an effort for a DBIx::Class-based one a few years back, not sure how far that progressed.

chris



From hlapp at drycafe.net  Fri Mar  2 14:14:53 2012
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Fri, 2 Mar 2012 14:14:53 -0500
Subject: [BioSQL-l] [Bioperl-l] Update: call for Google Summer of Code
	project ideas
In-Reply-To: <3F440BF7-4542-44E7-947D-A77180EC54F9@illinois.edu>
References: <4F4BAE5B.40309@gmail.com>
	<CAKVJ-_4aKgGq80AVp++mW5Eewyf2ACBXL-PcoUU0J0mQ+h62ZQ@mail.gmail.com>
	<3F440BF7-4542-44E7-947D-A77180EC54F9@illinois.edu>
Message-ID: <DA59E2B6-907D-4F5A-9840-22B4705D52B0@drycafe.net>


On Mar 2, 2012, at 11:09 AM, Fields, Christopher J wrote:

> I would really like to see a somewhat Bio*-agnostic ORM for BioSQL, though.  I know there was an effort for a DBIx::Class-based one a few years back, not sure how far that progressed.

Yes, I'd love that too. But I won't have time to formulate anything before some time next week.

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






From rbuels at gmail.com  Tue Mar  6 10:59:56 2012
From: rbuels at gmail.com (Robert Buels)
Date: Tue, 06 Mar 2012 10:59:56 -0500
Subject: [BioSQL-l] Google Summer of Code organization application submitted
Message-ID: <4F56347C.1080202@gmail.com>

Hi all,

I'd like to let you know that I had a look through the GSoC wiki pages 
for the GSoC wiki pages, and they look pretty good.  Thank you very 
much, everyone who worked on them.  I went ahead and submitted our 
application to Google for participation in GSoC 2012.

If you have any more ideas for projects that a Google-funded intern 
might work on this summer, now is the time to add them to the wiki at
http://www.open-bio.org/wiki/Google_Summer_of_Code, and on your 
project's wiki page that is linked from there.  Google will most likely 
be evaluating these ideas within the next couple of days.

If you are interested in helping out with Google Summer of Code this 
year, now is the time to make sure you are listed on your project's wiki 
as a prospective mentor.  Also, please make sure you are a member of 
both the OBF GSoC and OBF GSoC-Mentors email lists[1][2].

The better those project idea pages are, the stronger our case for 
getting Google funding will be.

Thanks a lot for all the hard work you community members have put in so far!

Rob

----
Robert Buels
(prospective) 2012 OBF GSoC Organization Admin


[1] http://lists.open-bio.org/mailman/listinfo/gsoc
[2] http://lists.open-bio.org/mailman/listinfo/gsoc-mentors

From open-bio at wvr7.me.uk  Tue Mar  6 13:44:38 2012
From: open-bio at wvr7.me.uk (Giles Weaver)
Date: Tue, 06 Mar 2012 18:44:38 +0000
Subject: [BioSQL-l] Job opportunity: Head of Bioinformatics at Institute for
	Animal Health (Surrey, UK)
Message-ID: <61678e49fa7f143e3a6f42533da0d745@wvr7.me.uk>

 

Dear All.

Please pass the following onto anyone who may be
interested. Note the closing date is the 16th March (next
Friday!).

Thanks,

Giles

HEAD OF BIOINFORMATICS

DRIVE AND SUPPORT
QUANTITATIVE RESEARCH INTO THE VIRAL DISEASES OF
ANIMALS

?42,769-?47,521
Ref: IRC43544
BASED: INSTITUTE FOR ANIMAL
HEALTH, PIRBRIGHT LABORATORY, SURREY 

Leading the bioinformatics team,
you will provide support to to IAH scientists involved in quantitative
biology, but will also have the opportunity to pursue your own research.
Areas of current interest include modelling of virus evolution and host
immune responses using next-generation sequencing data; _in silico_
analysis of host genetics and genomics data; and learning and predicting
networks of biomolecular interactions from post-genomic data sets. 

In
this high-profile role, you'll be expected to seek funds for new
projects and continue your excellent track record of publication.
Building collaborative research links with other members of IAH is
encouraged. 

Holding a PhD or equivalent in a relevant branch of the
biosciences, you will have experience in a recognised R&D environment.
The ability to develop and manage relational databases is essential, so
we would expect proficiency in MySQL (or similar), languages such as
Perl or Python, and familiarity with R, Bioconductor or another
statistical program. Experience of writing grant applications and
managing staff would be helpful. 

The Institute for Animal Health (IAH)
is an institute of the Biotechnology and Biological Sciences Research
Council (BBSRC). We work to enhance the UK's capability to contain,
control, and eliminate viral diseases in animals through highly
innovative fundamental and applied bioscience. 

Informal enquiries
about the post can be made to Simon Gubbins, Head of Mathematical
Biology (simon.gubbins at iah.ac.uk [1]) 

APPLICATIONS ARE HANDLED BY THE
RCUK SHARED SERVICES CENTRE; TO APPLY PLEASE VISIT OUR JOB BOARD AT
HTTPS://EXT.SSC.RCUK.AC.UK [2] AND COMPLETE AN ONLINE APPLICATION FORM.
APPLICANTS WHO WOULD LIKE TO RECEIVE THIS ADVERT IN AN ALTERNATIVE
FORMAT (E.G. LARGE PRINT, BRAILLE, AUDIO OR HARD COPY), OR WHO ARE
UNABLE TO APPLY ONLINE SHOULD CONTACT US BY TELEPHONE ON 01793 867003,
PLEASE QUOTE REFERENCE NUMBER IRC43544. 

FOR MORE INFORMATION ABOUT THE
IAH GO TO 

CLOSING DATE: 16TH MARCH 2012. 

Links:
------
[1]
mailto:simon.gubbins at iah.ac.uk
[2] https://ext.ssc.rcuk.ac.uk/

From rbuels at gmail.com  Fri Mar 16 15:47:58 2012
From: rbuels at gmail.com (Robert Buels)
Date: Fri, 16 Mar 2012 12:47:58 -0700
Subject: [BioSQL-l] Google Summer of Code is *ON* for OBF projects!
Message-ID: <4F6398EE.4020608@gmail.com>

Hi all,

Great news: Google announced today that the Open Bioinformatics
Foundation has been accepted as a mentoring organization for this
summer's Google Summer of Code!

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

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

For current developers on OBF projects, please consider volunteering to
be a mentor if you have not already, and contribute project ideas.  Just
list your name and project ideas on OBF wiki and on the relevant
project's GSoC wiki page.

Thanks to all who helped make OBF's application to GSoC a success, and
let's have a great, productive summer of code!

Rob Buels
OBF GSoC 2012 Administrator



From p.j.a.cock at googlemail.com  Fri Mar  2 13:49:25 2012
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 2 Mar 2012 13:49:25 +0000
Subject: [BioSQL-l] Update: call for Google Summer of Code project ideas
In-Reply-To: <4F4BADDC.5020905@gmail.com>
References: <4F4BADDC.5020905@gmail.com>
Message-ID: <CAKVJ-_6QU-ZJ1shu2SFoWx+DVCz1=g-cDrSax=eiG0kr752RCQ@mail.gmail.com>

On Mon, Feb 27, 2012 at 4:22 PM, Robert Buels <rbuels at gmail.com> wrote:
> Hi all,
>
> As kindly pointed out by Reece Hart, the previous email I sent out calling
> for Google Summer of Code project ideas, had the wrong due date for project
> ideas in it.
>
> I actually want them to all be in place by Friday, March 2, which is this
> coming Friday.
>
> == Instructions for Wiki Editing ==
>
> For each of the OBF projects that wants to do GSoC again this year, please:
>
> a.) Update the list of project ideas on your project's GSoC page (BioPython,
> BioPerl, BioRuby, etc). ?Add new ones, remove ones that have already been
> done or no longer relevant, etc.
>
> b.) Update the list of project ideas on the main OBF GSoC page
> (http://www.open-bio.org/wiki/Google_Summer_of_Code) to match.
>
> c.) Let me know via email that you have done so and it's ready for Google to
> peruse.
>
> == end instructions ==
>
> Again, please have the updates done by this Friday (March 2). The number and
> quality of the project ideas are part of the evaluation process for whether
> OBF is accepted as a Summer of Code organization again this year, so let's
> come up with some good ones. ?:-)
>
> Rob

Time is short for Rob's deadline ready for the OBF's evaluation, but are
there any BioSQL ideas for GSoC? Assuming we are accepted again,
we can come up with more ideas later.

The only thing I could think of was full support for the SQLite3 schema
(i.e. updating all the BioSQL perl scripts), but that doesn't seem enough
for a whole summer.

Perhaps it could be combined with work on BioPerl-db itself to support
BioSQL on SQLite? Clearly that would require a BioPerl person to mentor it.

Peter



From cjfields at illinois.edu  Fri Mar  2 16:09:23 2012
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 2 Mar 2012 16:09:23 +0000
Subject: [BioSQL-l] [Bioperl-l] Update: call for Google Summer of Code
	project ideas
In-Reply-To: <CAKVJ-_4aKgGq80AVp++mW5Eewyf2ACBXL-PcoUU0J0mQ+h62ZQ@mail.gmail.com>
References: <4F4BAE5B.40309@gmail.com>
	<CAKVJ-_4aKgGq80AVp++mW5Eewyf2ACBXL-PcoUU0J0mQ+h62ZQ@mail.gmail.com>
Message-ID: <3F440BF7-4542-44E7-947D-A77180EC54F9@illinois.edu>

On Mar 2, 2012, at 7:54 AM, Peter Cock wrote:

> On Mon, Feb 27, 2012 at 4:24 PM, Robert Buels <rbuels at gmail.com> wrote:
>> Hi all,
>> 
>> As kindly pointed out by Reece Hart, the previous email I sent out calling
>> for Google Summer of Code project ideas, had the wrong due date for project
>> ideas in it.
>> 
>> I actually want them to all be in place by Friday, March 2, which is this
>> coming Friday.
>> 
>> == Instructions for Wiki Editing ==
>> 
>> For each of the OBF projects that wants to do GSoC again this year, please:
>> 
>> a.) Update the list of project ideas on your project's GSoC page (BioPython,
>> BioPerl, BioRuby, etc).  Add new ones, remove ones that have already been
>> done or no longer relevant, etc.
>> 
>> b.) Update the list of project ideas on the main OBF GSoC page
>> (http://www.open-bio.org/wiki/Google_Summer_of_Code) to match.
>> 
>> c.) Let me know via email that you have done so and it's ready for Google to
>> peruse.
>> 
>> == end instructions ==
>> 
>> Again, please have the updates done by this Friday (March 2). The number and
>> quality of the project ideas are part of the evaluation process for whether
>> OBF is accepted as a Summer of Code organization again this year, so let's
>> come up with some good ones.  :-)
>> 
>> Rob
> 
> Hi all,
> 
> I had a quick look at the BioPerl page (partly for inspiration for Biopython
> projects), and it doesn't seem to have been updated since the 2011 project
> ideas:
> 
> http://bioperl.org/wiki/Google_Summer_of_Code
> 
> Some of those 2011 ideas became actual projects didn't they? If so, can
> any of them be continued as a new project for 2012?
> 
> Over on the BioSQL mailing list I suggested a combined BioSQL+BioPerl
> project idea to support the SQLite schema. Does anyone fancy mentoring
> that?
> 
> Peter

Things have been rather quiet lately, I believe b/c everyone is busy with other $obligations, I myself have been ridiculously busy lately but try to pipe up when I can.  A few of the projects on that page are still legitimate, though, and I think support of SQLite is a good project.  

I would really like to see a somewhat Bio*-agnostic ORM for BioSQL, though.  I know there was an effort for a DBIx::Class-based one a few years back, not sure how far that progressed.

chris




From hlapp at drycafe.net  Fri Mar  2 19:14:53 2012
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Fri, 2 Mar 2012 14:14:53 -0500
Subject: [BioSQL-l] [Bioperl-l] Update: call for Google Summer of Code
	project ideas
In-Reply-To: <3F440BF7-4542-44E7-947D-A77180EC54F9@illinois.edu>
References: <4F4BAE5B.40309@gmail.com>
	<CAKVJ-_4aKgGq80AVp++mW5Eewyf2ACBXL-PcoUU0J0mQ+h62ZQ@mail.gmail.com>
	<3F440BF7-4542-44E7-947D-A77180EC54F9@illinois.edu>
Message-ID: <DA59E2B6-907D-4F5A-9840-22B4705D52B0@drycafe.net>


On Mar 2, 2012, at 11:09 AM, Fields, Christopher J wrote:

> I would really like to see a somewhat Bio*-agnostic ORM for BioSQL, though.  I know there was an effort for a DBIx::Class-based one a few years back, not sure how far that progressed.

Yes, I'd love that too. But I won't have time to formulate anything before some time next week.

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







From rbuels at gmail.com  Tue Mar  6 15:59:56 2012
From: rbuels at gmail.com (Robert Buels)
Date: Tue, 06 Mar 2012 10:59:56 -0500
Subject: [BioSQL-l] Google Summer of Code organization application submitted
Message-ID: <4F56347C.1080202@gmail.com>

Hi all,

I'd like to let you know that I had a look through the GSoC wiki pages 
for the GSoC wiki pages, and they look pretty good.  Thank you very 
much, everyone who worked on them.  I went ahead and submitted our 
application to Google for participation in GSoC 2012.

If you have any more ideas for projects that a Google-funded intern 
might work on this summer, now is the time to add them to the wiki at
http://www.open-bio.org/wiki/Google_Summer_of_Code, and on your 
project's wiki page that is linked from there.  Google will most likely 
be evaluating these ideas within the next couple of days.

If you are interested in helping out with Google Summer of Code this 
year, now is the time to make sure you are listed on your project's wiki 
as a prospective mentor.  Also, please make sure you are a member of 
both the OBF GSoC and OBF GSoC-Mentors email lists[1][2].

The better those project idea pages are, the stronger our case for 
getting Google funding will be.

Thanks a lot for all the hard work you community members have put in so far!

Rob

----
Robert Buels
(prospective) 2012 OBF GSoC Organization Admin


[1] http://lists.open-bio.org/mailman/listinfo/gsoc
[2] http://lists.open-bio.org/mailman/listinfo/gsoc-mentors


From open-bio at wvr7.me.uk  Tue Mar  6 18:44:38 2012
From: open-bio at wvr7.me.uk (Giles Weaver)
Date: Tue, 06 Mar 2012 18:44:38 +0000
Subject: [BioSQL-l] Job opportunity: Head of Bioinformatics at Institute for
	Animal Health (Surrey, UK)
Message-ID: <61678e49fa7f143e3a6f42533da0d745@wvr7.me.uk>

 

Dear All.

Please pass the following onto anyone who may be
interested. Note the closing date is the 16th March (next
Friday!).

Thanks,

Giles

HEAD OF BIOINFORMATICS

DRIVE AND SUPPORT
QUANTITATIVE RESEARCH INTO THE VIRAL DISEASES OF
ANIMALS

?42,769-?47,521
Ref: IRC43544
BASED: INSTITUTE FOR ANIMAL
HEALTH, PIRBRIGHT LABORATORY, SURREY 

Leading the bioinformatics team,
you will provide support to to IAH scientists involved in quantitative
biology, but will also have the opportunity to pursue your own research.
Areas of current interest include modelling of virus evolution and host
immune responses using next-generation sequencing data; _in silico_
analysis of host genetics and genomics data; and learning and predicting
networks of biomolecular interactions from post-genomic data sets. 

In
this high-profile role, you'll be expected to seek funds for new
projects and continue your excellent track record of publication.
Building collaborative research links with other members of IAH is
encouraged. 

Holding a PhD or equivalent in a relevant branch of the
biosciences, you will have experience in a recognised R&D environment.
The ability to develop and manage relational databases is essential, so
we would expect proficiency in MySQL (or similar), languages such as
Perl or Python, and familiarity with R, Bioconductor or another
statistical program. Experience of writing grant applications and
managing staff would be helpful. 

The Institute for Animal Health (IAH)
is an institute of the Biotechnology and Biological Sciences Research
Council (BBSRC). We work to enhance the UK's capability to contain,
control, and eliminate viral diseases in animals through highly
innovative fundamental and applied bioscience. 

Informal enquiries
about the post can be made to Simon Gubbins, Head of Mathematical
Biology (simon.gubbins at iah.ac.uk [1]) 

APPLICATIONS ARE HANDLED BY THE
RCUK SHARED SERVICES CENTRE; TO APPLY PLEASE VISIT OUR JOB BOARD AT
HTTPS://EXT.SSC.RCUK.AC.UK [2] AND COMPLETE AN ONLINE APPLICATION FORM.
APPLICANTS WHO WOULD LIKE TO RECEIVE THIS ADVERT IN AN ALTERNATIVE
FORMAT (E.G. LARGE PRINT, BRAILLE, AUDIO OR HARD COPY), OR WHO ARE
UNABLE TO APPLY ONLINE SHOULD CONTACT US BY TELEPHONE ON 01793 867003,
PLEASE QUOTE REFERENCE NUMBER IRC43544. 

FOR MORE INFORMATION ABOUT THE
IAH GO TO 

CLOSING DATE: 16TH MARCH 2012. 

Links:
------
[1]
mailto:simon.gubbins at iah.ac.uk
[2] https://ext.ssc.rcuk.ac.uk/


From rbuels at gmail.com  Fri Mar 16 19:47:58 2012
From: rbuels at gmail.com (Robert Buels)
Date: Fri, 16 Mar 2012 12:47:58 -0700
Subject: [BioSQL-l] Google Summer of Code is *ON* for OBF projects!
Message-ID: <4F6398EE.4020608@gmail.com>

Hi all,

Great news: Google announced today that the Open Bioinformatics
Foundation has been accepted as a mentoring organization for this
summer's Google Summer of Code!

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

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

For current developers on OBF projects, please consider volunteering to
be a mentor if you have not already, and contribute project ideas.  Just
list your name and project ideas on OBF wiki and on the relevant
project's GSoC wiki page.

Thanks to all who helped make OBF's application to GSoC a success, and
let's have a great, productive summer of code!

Rob Buels
OBF GSoC 2012 Administrator