[BlueObelisk-discuss] Best wishes from the COD team!

[Saulius Gražulis]

Dear colleagues,

during the two very exciting weeks of hacking with Peter Murray-Rust, in
Vilnius, he suggested that I join the Blue Obelisk community and the
mailing list.

Let me introduce myself: I am currently heading the Vilnius team of the
Crystallography Open Database, and maintain the database site at the
Vilnius University Institute of Biotechnology
(http://www.crystallography.net). As such, I am very interested in
(co)-developing free software for chemistry and crystallography, and
sharing data. You are cordially invited to use COD, to download COD and
to contribute to its development if you wish.

Another project which we have started recently, and which I would like
to discuss and coordinate with you, is the Theoretical Crystallography
Open Database (TCOD, http://www.crystallography.net/tcod/). After our
successful development of COD (which contains experimental crystal
structures), and after several requests from a community, we have
started TCOD to collect published structures, computed using DFT and
other methods.

Peter has told me that the NWChem group, who is present on this mailing
list :), has done a large work in developing ontologies to describe
various computational methods and encode (meta)data in CML. It seems to
me like a good idea to join our efforts, to make a set of descriptions
and quality criteria endorsed by computational community, and to have a
comprehensive representation of computation results in TCOD.

I'm looking forward to hear from you!

Sincerely,
Saulius

P.S. In a short while, I'll post another message regarding presentation
of TCOD at the IUCr 2014 Congress in Montreal.

[Peter Murray-Rust]

Post by Saulius Gražulis
Dear colleagues,
during the two very exciting weeks of hacking with Peter Murray-Rust, in
Vilnius, he suggested that I join the Blue Obelisk community and the
mailing list.

And I awarded Saulius a Blue Obelisk in recognition of the massive
contribution to chemical Open Data that COD has made. We are about to see
this expand even further.

Let me introduce myself: I am currently heading the Vilnius team of the

Post by Saulius Gražulis
Crystallography Open Database, and maintain the database site at the
Vilnius University Institute of Biotechnology
(http://www.crystallography.net). As such, I am very interested in
(co)-developing free software for chemistry and crystallography, and
sharing data. You are cordially invited to use COD, to download COD and
to contribute to its development if you wish.
Saulius and colleagues have built a superb server which can update

crystallography on a daily basis and publish it to the whole world. There
is also a strong tradition of COD members reviewing structures and I have
seen some structures with several curatorial events.

Another project which we have started recently, and which I would like

Post by Saulius Gražulis
to discuss and coordinate with you, is the Theoretical Crystallography
Open Database (TCOD, http://www.crystallography.net/tcod/). After our
successful development of COD (which contains experimental crystal
structures), and after several requests from a community, we have
started TCOD to collect published structures, computed using DFT and
other methods.
This should be of great value to those who either compute crystal

structures for predictive purpose or to compute properties.

Post by Saulius Gražulis
Peter has told me that the NWChem group, who is present on this mailing
list :), has done a large work in developing ontologies to describe
various computational methods and encode (meta)data in CML. It seems to
me like a good idea to join our efforts, to make a set of descriptions
and quality criteria endorsed by computational community, and to have a
comprehensive representation of computation results in TCOD.
The BO community is indebted to all authors of fully Open source code

(FLOSS) of which NWChem is one. The NWChem community has also been
presented with an obelisk because of not only open-sourcing the code but
their commitment to community development of vocabularies.

Post by Saulius Gražulis
I'm looking forward to hear from you!
Sincerely,
Saulius
Note that we have transferred the CrystalEye data and software to Vilnius

so that it will be continually enhanced by Nick Day's great work on
extracting molecules from crystal structures and adding chemistry with
software.

P

[Karol M. Langner]

Hi everyone,

Post by Peter Murray-Rust

Post by Saulius Gražulis
Dear colleagues,
during the two very exciting weeks of hacking with Peter Murray-Rust, in
Vilnius, he suggested that I join the Blue Obelisk community and the
mailing list.

And I awarded Saulius a Blue Obelisk in recognition of the massive
contribution to chemical Open Data that COD has made. We are about to see
this expand even further.

Welcome Saulius! Although I am myself not a frequent author on this mailing list,
I've noticed COD before and liek it!

Post by Peter Murray-Rust

Post by Saulius Gražulis
Peter has told me that the NWChem group, who is present on this mailing
list :), has done a large work in developing ontologies to describe
various computational methods and encode (meta)data in CML. It seems to
me like a good idea to join our efforts, to make a set of descriptions
and quality criteria endorsed by computational community, and to have a
comprehensive representation of computation results in TCOD.
The BO community is indebted to all authors of fully Open source code

(FLOSS) of which NWChem is one. The NWChem community has also been
presented with an obelisk because of not only open-sourcing the code but
their commitment to community development of vocabularies.

@Peter and others: does NWChem write CML? I was planning to do some work
on a NWChem parser in cclib (which will export CML itself), but if NWChem
already writes CML that would not be a priority.

Cheers,
Karol

[Peter Murray-Rust]

On Mon, Feb 10, 2014 at 6:45 PM, Karol M. Langner

Post by Karol M. Langner
Hi everyone,
@Peter and others: does NWChem write CML? I was planning to do some work
on a NWChem parser in cclib (which will export CML itself), but if NWChem
already writes CML that would not be a priority.

Bert de Jong will be able to tell you the exact poisition - but it's in
the pipeline.

I have written logfile2CML parsers for about 10 compchem codes and they are
in http://bitbucket.org/petermr/jumbo-converters. Their goal is to extract
all information from logfiles into semantic form.

Bert is coordinating the effort to create vocabularies for compchem

(Bert - what is your new email address??)

Post by Karol M. Langner
Cheers,
Karol
--
written by Karol M. Langner
Mon Feb 10 13:40:55 EST 2014

[Karol M. Langner]

Post by Peter Murray-Rust
On Mon, Feb 10, 2014 at 6:45 PM, Karol M. Langner

Post by Karol M. Langner
Hi everyone,
@Peter and others: does NWChem write CML? I was planning to do some work
on a NWChem parser in cclib (which will export CML itself), but if NWChem
already writes CML that would not be a priority.

Bert de Jong will be able to tell you the exact poisition - but it's in
the pipeline.
I have written logfile2CML parsers for about 10 compchem codes and they are
in http://bitbucket.org/petermr/jumbo-converters. Their goal is to extract
all information from logfiles into semantic form.
Bert is coordinating the effort to create vocabularies for compchem
(Bert - what is your new email address??)

Thanks Peter, I've contacted Saulius off-list.

[Robert Hanson]

Saulius,

Welcome!

Do you know about all the cool crystallographic capabilities of Jmol?
Latest is incommensurately modulated structures.

Let's talk!

Bob Hanson

Post by Saulius Gražulis
Dear colleagues,
during the two very exciting weeks of hacking with Peter Murray-Rust, in
Vilnius, he suggested that I join the Blue Obelisk community and the
mailing list.
Let me introduce myself: I am currently heading the Vilnius team of the
Crystallography Open Database, and maintain the database site at the
Vilnius University Institute of Biotechnology
(http://www.crystallography.net). As such, I am very interested in
(co)-developing free software for chemistry and crystallography, and
sharing data. You are cordially invited to use COD, to download COD and
to contribute to its development if you wish.
Another project which we have started recently, and which I would like
to discuss and coordinate with you, is the Theoretical Crystallography
Open Database (TCOD, http://www.crystallography.net/tcod/). After our
successful development of COD (which contains experimental crystal
structures), and after several requests from a community, we have
started TCOD to collect published structures, computed using DFT and
other methods.
Peter has told me that the NWChem group, who is present on this mailing
list :), has done a large work in developing ontologies to describe
various computational methods and encode (meta)data in CML. It seems to
me like a good idea to join our efforts, to make a set of descriptions
and quality criteria endorsed by computational community, and to have a
comprehensive representation of computation results in TCOD.
I'm looking forward to hear from you!
Sincerely,
Saulius
P.S. In a short while, I'll post another message regarding presentation
of TCOD at the IUCr 2014 Congress in Montreal.
--
Dr. Saulius GraÅŸulis
Vilnius University Institute of Biotechnology, Graiciuno 8
LT-02241 Vilnius, Lietuva (Lithuania)
fax: [phone] / phone (office): ([phone]
mobile: [phone]
------------------------------------------------------------------------------
Managing the Performance of Cloud-Based Applications
Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
Read the Whitepaper.
http://pubads.g.doubleclick.net/gampad/clk?id=121051231&iu=/4140/ostg.clktrk
_______________________________________________
Blueobelisk-discuss mailing list
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

[Saulius Gražulis]

Post by Robert Hanson
Do you know about all the cool crystallographic capabilities of Jmol?

Yes, we do use Jmol extensively! Thanks for great software!

Post by Robert Hanson
Latest is incommensurately modulated structures.

These I have not used yet. Very interesting!