gmane.science.chemistry.blue-obelisk

Re: Looking for collaborators in Scala project

Peter Murray-Rust — 2013-04-24T13:37:19


I  am very interested in developing a Scala engine for CML - probably a cut
down version from the complete JUMBO6 . DaveMR (copied) has created a Scala
engine for MathML to integrate maths with chemistry.


JUMBO has a wide range of tests so it should be possible to use them to
test the scala engine.



It will be very interesting to see how this works.

Looking for collaborators in Scala project

Stefan Hoeck — 2013-04-24T08:13:38

Dear all

I am an organic chemist at the Zurich University of Applied Sciences. A
couple of months ago we published an article in the Journal of
Cheminformatics about the beginnings of a purely functional cheminformatics
toolkit written in Scala (the article can be found here:
http://www.jcheminf.com/content/4/1/38/abstract). So far, this toolkit only
supports SMILES parsing and representing molecules in a basic, immutable
graph data structure. I am now looking for people interested in pushing
this project forward. The toolkit, which we called 'chemf', is open-source
(the source code is hosted on github: https://github.com/stefan-hoeck/chemf)
but it hasn't seen much activity lately since so far I have been the only
person working on it.

So, I am looking for people helping me implement the typical algorithms
needed for a fully fledged cheminformatics toolkit in a purely functional,
referentially transparent way. The algorithms may be implemented in an
imperative style in the background, but they need to be d

Re: Database question

Geoffrey Hutchison — 2013-04-09T16:38:39

It depends on how big you intend to grow this database, but you can stick to flat-file organization for many things (e.g., hundreds or thousands of groups). I’d organize the functional groups into SMARTS, which can be used with many toolkits.

Hope that helps,
-Geoff

---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoffh-fYq5UfK3d1k< at >public.gmane.org
web: http://hutchison.chem.pitt.edu/


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Database question

Alex Gorbounov — 2013-04-08T17:09:08

Hello, all,

I would like to design a database to support group contribution methods. Since the model is the primary focus of this project at the moment, I only need a primitive DB, with main requirement of being able to represent the groups correctly. If anyone can offer any tips, thoughts, references, links; those would be highly appreciated.

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Re: dinner at ACS meeting in New Orleans?

Robert Hanson — 2013-04-03T18:32:57

suberb idea!!


On Wed, Apr 3, 2013 at 12:35 PM, Egon Willighagen <
egon.willighagen-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org> wrote:

Re: dinner at ACS meeting in New Orleans?

Egon Willighagen — 2013-04-03T17:35:07

Yeah, that should work for me too, I think.

Egon

--
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: Dinner at ACS NOLA

Noel O'Boyle — 2013-04-03T11:40:37

Yes - you are very welcome. Keep an eye on the list for the details.

- Noel

On 2 April 2013 14:16, Jess Barilone <jessica.barilone-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org> wrote:

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Re: Dinner at ACS NOLA

Peter Murray-Rust — 2013-04-03T11:30:41


BTW you included a whole digest in your mail and it bounced as too large -
cheers.

P.

Re: dinner at ACS meeting in New Orleans?

Rajarshi Guha — 2013-04-03T11:13:40

Works for me


On Wed, Apr 3, 2013 at 4:35 AM, Noel O'Boyle <baoilleach-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org> wrote:

Re: dinner at ACS meeting in New Orleans?

Noel O'Boyle — 2013-04-03T08:35:52

Actually, Monday is looking less attractive now for me too. How
about...any day except Monday? :-)

Sunday after CINF reception?

- Noel

On 3 April 2013 02:37, Egon Willighagen <egon.willighagen-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org> wrote:

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Re: dinner at ACS meeting in New Orleans?

Egon Willighagen — 2013-04-03T01:37:24

I think I am expected to show up at the Sci-Mix meeting that night
with two posters... I would join around 10pm for a drink.

Egon

--
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: Dinner at ACS NOLA

Jess Barilone — 2013-04-02T13:16:06

Hi Everyone,
I am new to the blue obelisk list serv, I was wondering if I could join you all for dinner/drinks in New Orleans. Where and when is everyone meeting?

Cheers,
Jessica 

Undergraduate Student 
Department of Chemistry
University of Southern Maine

On Apr 2, 2013, at 7:58 AM, blueobelisk-discuss-request-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f< at >public.gmane.org wrote:


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Re: dinner at ACS meeting in New Orleans?

Rajarshi Guha — 2013-04-02T11:58:07

Oops. Yes Monday

On Tue, Apr 2, 2013 at 7:54 AM, Noel O'Boyle <baoilleach-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org> wrote:

Re: dinner at ACS meeting in New Orleans?

Noel O'Boyle — 2013-04-02T11:54:29

Is that Monday? Either way. Sounds good.

On 2 April 2013 12:41, Rajarshi Guha <rajarshi.guha-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org> wrote:

------------------------------------------------------------------------------
Own the Future-Intel(R) Level Up Game Demo Contest 2013
Rise to greatness in Intel's independent game demo contest. Compete 
for recognition, cash, and the chance to get your game on Steam. 
$5K grand prize plus 10 genre and skill prizes. Submit your demo 
by 6/6/13. http://altfarm.mediaplex.com/ad/ck/12124-176961-30367-2

Re: dinner at ACS meeting in New Orleans?

Rajarshi Guha — 2013-04-02T11:41:37

Any suggestions on where and when to meet? My vote is

7:45pm, at the Convention Center

As for places to sit, chat, eat and drink, I'm not a local, so not
very familiar. Some interesting ones, all a few blocks from the
convention center:

http://rootnola.com/
http://www.riomarseafood.com/
http://www.cochonrestaurant.com/

for a bar style stting theres a Gordon Biersch close by, or for more
local flavor http://www.districtnola.com/


On Wed, Mar 6, 2013 at 10:52 AM, Egon Willighagen
<egon.willighagen-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org> wrote:

Re: dinner at ACS meeting in New Orleans?

Robert Hanson — 2013-03-20T22:04:13

ps --  if you haven't been following the Jmol list, maybe you don't know,
but we have a fully functional JavaScript-only version of Jmol now. Totally
optimized, compartmentalized, and language-localized duplicate of Jmol but
without Java. And it's speed is reasonably good. Best of all, all the
development is done in Java still. See
http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm  - reads PyMOL session
files, too!

Bob



On Wed, Mar 20, 2013 at 4:52 PM, Robert Hanson <hansonr-MGnxaD/BIt43uPMLIKxrzw< at >public.gmane.org> wrote:

Re: dinner at ACS meeting in New Orleans?

Robert Hanson — 2013-03-20T21:52:42

I will be there just Sat - Tuesday. Either a late dinner Sunday (8 pm) or
anytime Monday would work for me. Very eager to reconnect with my favorite
group!

Bob



On Thu, Mar 7, 2013 at 2:53 AM, John P. Overington <jpo-jcUp+/l53Jxaa/9Udqfwiw< at >public.gmane.org> wrote:

Invitation to present at ACS Indianapolis on Exchangeable Data Formats

Antony Williams — 2013-03-14T04:56:30

Blue Obelisk members,
I am not sure whether any of you intend to attend the ACS Indianapolis meeting in the fall? If so, can I suggest that you might have some valuable comments and presentations for the session that Bob Lancashire and I are co-chairing. The title is below
Session Code:

CINF013

Session Title:

Exchangeable Molecular and Analytical Data Formats and Their Importance in Facilitating Data Exchange


If you have a presentation that you believe might fit into the session please do join us. The deadline for submissions is March 18th. Thanks

Antony Williams PhD, FRSC

Phone: +1 (919) 201-1516
Email: williamsa-LFlALxTm1og< at >public.gmane.org<mailto:williamsa-LFlALxTm1og< at >public.gmane.org>
My LinkedIn Profile: http://www.linkedin.com/in/antonywilliams/
My ScientistsDB page: www.scientistsdb.com/index.php?title=Antony_John_Williams<http://www.scientistsdb.com/index.php?title=Antony_John_Williams>
My ORCID ID: http://orcid.org/0000-0002-2668-4821
My Blog: www.chemconnector.com<http://www.chemconnector.co

Re: dinner at ACS meeting in New Orleans?

Julien Thibault — 2013-03-07T16:20:31

I'd be happy to meet with you guys.

~Julien

Re: dinner at ACS meeting in New Orleans?

John P. Overington — 2013-03-07T08:53:27

I'll be there too.

    jpo

--
John P. Overington, BSc PhD MBCS FRSC C.Chem.

Head of Chemistry and Molecular Systems Resources
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire
CB10 1SD 
United Kingdom

mail: jpo-jcUp+/l53Jxaa/9Udqfwiw< at >public.gmane.org                       admin: kholmes-jcUp+/l53Jxaa/9Udqfwiw< at >public.gmane.org
phone: +44-1223-492666            skype: john.overington                  twitter: < at >chembl








On 6 Mar 2013, at 15:52, Egon Willighagen <egon.willighagen-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org> wrote:


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Re: dinner at ACS meeting in New Orleans?

Noel O'Boyle — 2013-03-06T15:59:05

Me too.

On 6 March 2013 15:55, Rajarshi Guha <rajarshi.guha-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org> wrote:

------------------------------------------------------------------------------
Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester  
Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the  
endpoint security space. For insight on selecting the right partner to 
tackle endpoint security challenges, access the full report. 
http://p.sf.net/sfu/symantec-dev2dev