Fwd: [wp-discuss] Google Summer of Code 2012

Hi all,

I am very happy to let you know what the below mentioned NRNB project,
Bioclipse and the CDK (again) have found their way into the Google
Summer of Code. The main projects for this GSoC are WikiPathways with
PathVisio and Cytoscape, but there are in total 4 project ideas that
involve these two Blue Obelisk projects.

Two project ideas involve writing Bioclipse plugins, one for
PathVisio, one for the Cytoscape huge graph rendering functionality.
When selecting content in these two widgets, they will pass around
selection events, allowing further detail to be visualized in
Bioclipse's other views.

Two other ideas involve the CDK. One is a plugin for PathVisio showing
molecular properties related to NMR and mass spectrometry
(metabolomics oriented). The other idea is to update the Cytoscape
plugin for visualizing chemical structures which was in fact developed
in a previous GSoC.

I invite all students who want a really cool summer job, to brush up
their programming skills, write a terrific application (there are
limited seats; only the best applications will be accepted; starting
coding and interacting early with developers always helps), and hack
on Bioclipse or the CDK this year in the GSoC 2012!

All project ideas can be found at http://nrnb.org/gsoc/ and also read
the below detail.

With kind regards,

Re: Fwd: [wp-discuss] Google Summer of Code 2012

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Re: [Cdk-user] [wp-discuss] Google Summer of Code 2012

Brillant. And I second what Peter said :)

Kind regards, 

Chris

--
Dr. Christoph Steinbeck
Head of Cheminformatics and Metabolism
European Bioinformatics Institute (EBI)
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD UK
Phone +44 1223 49 2640

What is man but that lofty spirit - that sense of enterprise.
... Kirk, "I, Mudd," stardate 4513.3..

On 18 Mar 2012, at 08:06, Egon Willighagen wrote:

> Hi all,
> 
> I am very happy to let you know what the below mentioned NRNB project,
> Bioclipse and the CDK (again) have found their way into the Google
> Summer of Code. The main projects for this GSoC are WikiPathways with
> PathVisio and Cytoscape, but there are in total 4 project ideas that
> involve these two Blue Obelisk projects.
> 
> Two project ideas involve writing Bioclipse plugins, one for
> PathVisio, one for the Cytoscape huge graph rendering functionality.
> When selecting content in these two widgets, they will pass around
> selection events, allowing further detail to be visualized in
> Bioclipse's other views.
> 
> Two other ideas involve the CDK. One is a plugin for PathVisio showing
> molecular properties related to NMR and mass spectrometry
> (metabolomics oriented). The other idea is to update the Cytoscape
> plugin for visualizing chemical structures which was in fact developed
> in a previous GSoC.
> 
> I invite all students who want a really cool summer job, to brush up
> their programming skills, write a terrific application (there are
> limited seats; only the best applications will be accepted; starting
> coding and interacting early with developers always helps), and hack
> on Bioclipse or the CDK this year in the GSoC 2012!
> 
> All project ideas can be found at http://nrnb.org/gsoc/ and also read
> the below detail.
> 
> With kind regards,
> 
> Egon
> 
> 
> ---------- Forwarded message ----------
> From: Alexander Pico <apico@...>
> Date: Sun, Mar 18, 2012 at 2:35 AM
> Subject: [wp-discuss] Google Summer of Code 2012
> To: wikipathways-discuss <wikipathways-discuss@...>
> 
> 
> As part of NRNB, we will once again be participating in the Google Summer of
> Code (GSoC) program.
> 
> http://nrnb.org/gsoc
> 
> GSoC is a global program that funds student programmers around the world to
> write code for open source projects. This will be our 6th year participating
> and we have a lot of projects to choose from.
> 
> If you are a student interested in coding for our open source projects, then
> check out the link above and apply before April 6th. If you know of any
> students who might be interested, then forward this announcement, mention it
> in the classroom or post the attached flyer.
> 
> http://www.booki.cc/gsocstudentguide/what-is-google-summer-of-code/
> 
> The application period is March 26 - April 6th.  Hop on the discussion
> mailing list and run your ideas by us before applying to improve your
> application.
> 
>  - Alex
> 
> --
> You received this message because you are subscribed to the Google
> Groups "wikipathways-discuss" group.
> To post to this group, send email to wikipathways-discuss@...
> To unsubscribe from this group, send email to
> wikipathways-discuss+unsubscribe@...
> For more options, visit this group at
> http://groups.google.com/group/wikipathways-discuss?hl=en.
> 
> 
> 
> -- 
> Dr E.L. Willighagen
> Postdoctoral Researcher
> Department of Bioinformatics - BiGCaT
> Maastricht University (http://www.bigcat.unimaas.nl/)
> Homepage: http://egonw.github.com/
> LinkedIn: http://se.linkedin.com/in/egonw
> Blog: http://chem-bla-ics.blogspot.com/
> PubList: http://www.citeulike.org/user/egonw/tag/papers
> <GSoC2012Flyer.pdf>------------------------------------------------------------------------------
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BO meeting at ACS, San Diego?

Hi everybody, are then any BO'ers planning to be at the ACS in San
Diego next week? If so is anybody in a meetup? (Monday or Tuesday
nights would be good)

--

-- 
Rajarshi Guha | http://blog.rguha.net
NIH Center for Advancing Translational Science

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Re: Fwd: [wp-discuss] Google Summer of Code 2012

Good for you Egon...that's great news. I am especially interested in the work you are doing on the NMR and
Mass Spec side and would love to contribute expertise, data, APIs as necessary/appropriate to support
the project. As you know I still keep my hand very much in the NMR/MS world - you might be interested in this
recent paper : http://www.springerlink.com/content/e62777217954068m/ re. MS. I am working on some
projects now related to ChemSpider and MS/NMR and it would be good to chat. Maybe there is an opportunity to
connect things up?

Cheers

Antony Williams PhD, FRSC
Learn About.Me
Phone: +1 (919) 201-1516
Email: williamsa@...
Twitter: http://twitter.com/ChemConnector

-----Original Message-----
From: Egon Willighagen [mailto:egon.willighagen@...] 
Sent: Sunday, March 18, 2012 3:07 AM
To: blueobelisk-discuss@...
Subject: [BlueObelisk-discuss] Fwd: [wp-discuss] Google Summer of Code 2012

Hi all,

I am very happy to let you know what the below mentioned NRNB project, Bioclipse and the CDK (again) have
found their way into the Google Summer of Code. The main projects for this GSoC are WikiPathways with
PathVisio and Cytoscape, but there are in total 4 project ideas that involve these two Blue Obelisk projects.

Two project ideas involve writing Bioclipse plugins, one for PathVisio, one for the Cytoscape huge graph
rendering functionality.
When selecting content in these two widgets, they will pass around selection events, allowing further
detail to be visualized in Bioclipse's other views.

Two other ideas involve the CDK. One is a plugin for PathVisio showing molecular properties related to NMR
and mass spectrometry (metabolomics oriented). The other idea is to update the Cytoscape plugin for
visualizing chemical structures which was in fact developed in a previous GSoC.

I invite all students who want a really cool summer job, to brush up their programming skills, write a
terrific application (there are limited seats; only the best applications will be accepted; starting
coding and interacting early with developers always helps), and hack on Bioclipse or the CDK this year in
the GSoC 2012!

All project ideas can be found at http://nrnb.org/gsoc/ and also read the below detail.

With kind regards,

Egon

---------- Forwarded message ----------
From: Alexander Pico <apico@...>
Date: Sun, Mar 18, 2012 at 2:35 AM
Subject: [wp-discuss] Google Summer of Code 2012
To: wikipathways-discuss <wikipathways-discuss@...>

As part of NRNB, we will once again be participating in the Google Summer of Code (GSoC) program.

http://nrnb.org/gsoc

GSoC is a global program that funds student programmers around the world to write code for open source
projects. This will be our 6th year participating and we have a lot of projects to choose from.

If you are a student interested in coding for our open source projects, then check out the link above and
apply before April 6th. If you know of any students who might be interested, then forward this
announcement, mention it in the classroom or post the attached flyer.

http://www.booki.cc/gsocstudentguide/what-is-google-summer-of-code/

The application period is March 26 - April 6th.  Hop on the discussion mailing list and run your ideas by us
before applying to improve your application.

 - Alex

--
You received this message because you are subscribed to the Google Groups "wikipathways-discuss" group.
To post to this group, send email to wikipathways-discuss@...
To unsubscribe from this group, send email to
wikipathways-discuss+unsubscribe@...
For more options, visit this group at
http://groups.google.com/group/wikipathways-discuss?hl=en.

--
Dr E.L. Willighagen
Postdoctoral Researcher
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers

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Re: BO meeting at ACS, San Diego?

I'm not going to be at the ACS meeting, but I'd like to meet up (I
live in San Diego).

Craig

On Sun, Mar 18, 2012 at 6:05 AM, Rajarshi Guha
<rajarshi.guha@...> wrote:
> Hi everybody, are then any BO'ers planning to be at the ACS in San
> Diego next week? If so is anybody in a meetup? (Monday or Tuesday
> nights would be good)
>
> --
> Rajarshi Guha | http://blog.rguha.net
> NIH Center for Advancing Translational Science
>
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Re: BO meeting at ACS, San Diego?

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meetup at San Diego ACS

I won't be at the meeting proper, but I'd like to meet up with
you all.  Monday or Tuesday night is fine with me.

TJ O'Donnell

On Sun, Mar 18, 2012 at 6:05 AM, Rajarshi Guha
<rajarshi.guha@...> wrote:
> Hi everybody, are then any BO'ers planning to be at the ACS in San
> Diego next week? If so is anybody in a meetup? (Monday or Tuesday
> nights would be good)

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Re: BO meeting at ACS, San Diego?

I've put up a wiki page at
https://sourceforge.net/apps/mediawiki/blueobelisk/index.php?title=Spring_ACS_Conference_in_San_Diego

If you have permissions and are interested in attending feel free to
add in your name (or send a message t o the list and I'll add it).

I've taken the liberty of choosing a date and time - if these don't
work we can iterate.

Regarding place - I was hoping a one or more locals could provide suggestions?

On Tue, Mar 20, 2012 at 1:51 PM, Marat Valiev <marat.valiev@...> wrote:
> I would also be interested in meeting people from the group. I will be
> starting up a 3-year project (pending funding decision) at PNNL/EMSL to
> build expert/AI
> system environment for running (bio)molecular simulations with NWChem
> (nwchem-sw.org) and other codes. The emphasis here is not so much on the end
> data but rather on the "correct" procedures to generate data. I just
> subscribed to the list and have only met Markus Hanwell so far. I will be in
> San Diego ACS meeting 3/27 through 3/30.
>
> --
>
> Marat Valiev
>
> Senior Research Scientist
>
> NWCHEM, Molecular Sciences Software Group
>
> Pacific Northwest National Laboratory
>
> 902 Battelle Boulevard
>
> P.O. Box 999, MSIN K8-91
>
> Richland, WA  99352 USA
>
>
>
>
> I just subscribed to the list
>
>
> On Tue, Mar 20, 2012 at 9:18 AM, Craig James <cjames@...> wrote:
>>
>> I'm not going to be at the ACS meeting, but I'd like to meet up (I
>> live in San Diego).
>>
>> Craig
>>
>> On Sun, Mar 18, 2012 at 6:05 AM, Rajarshi Guha <rajarshi.guha@...>
>> wrote:
>> > Hi everybody, are then any BO'ers planning to be at the ACS in San
>> > Diego next week? If so is anybody in a meetup? (Monday or Tuesday
>> > nights would be good)
>> >
>> > --
>> > Rajarshi Guha | http://blog.rguha.net
>> > NIH Center for Advancing Translational Science
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > This SF email is sponsosred by:
>> > Try Windows Azure free for 90 days Click Here
>> > http://p.sf.net/sfu/sfd2d-msazure
>> > _______________________________________________
>> > Blueobelisk-discuss mailing list
>> > Blueobelisk-discuss@...
>> > https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
>>
>>
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>> http://p.sf.net/sfu/sfd2d-msazure
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>> https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
>
>

--

-- 
Rajarshi Guha | http://blog.rguha.net
NIH Center for Advancing Translational Science

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Re: BO meeting at ACS, San Diego?

Regarding a meet-up dinner in San Diego ... only four have indicated
they can make it, and now it turns out my mother is driving down from
Santa Cruz to spend the weekend and Monday with us.  Would Tuesday
work out better for this event?

Craig

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