Egon Willighagen | 24 Mar 09:04 2014
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CML Schema maintenance

Hi all,

because there were some things I like to update with respect to the
CML Schema, I have asked Peter and Henry if I could pick up
maintenance of the XML Schema. The result is this:

https://github.com/egonw/cml-schema

I have already applied two patches to add four recent new element symbols [0].

If you have additional points, you can file those here:

https://github.com/egonw/cml-schema/issues

Egon

--

-- 
E.L. Willighagen
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
ORCID: 0000-0001-7542-0286

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Peter Murray-Rust | 2 Mar 11:09 2014
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Re: Google Summer of Code 2014 options?

Is this still possible (I was invited to a phylogenetic project but told that it wasn't funded). So has the deadline passed?


On Sat, Mar 1, 2014 at 11:41 PM, Egon Willighagen <egon.willighagen-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
Hi all,

another year, another Google Summer of Code. And again it is possible
to work on Open Source tools in the area of chemistry.

Below are a few things that I have spotted. What else is out there?

* NRNB mentoring organization [0]
 - Cytoscape has a chemical structure viz plugin based on the CDK that
needs updating
 - PathVisio has a chemical structure viz plugin based on the CDK that
needs updating
 - There is a project idea to integrate Cytoscape into Bioclipse
 - There is a project idea to integrate PathVisio into Bioclipse
* VTK mentoring organization [1]
 - various chemistry related ideas
* ScaffoldHunter (GPLv3) [2]
 - no specific ideas, but based on the CDK, and could use updating to CDK 1.5

Anything else?

Egon

0.http://nrnb.org/gsoc/index.html#ideas-tab
1.http://www.vtk.org/Wiki/VTK/GSoC
2.http://scaffoldhunter.sourceforge.net/wiki/doku.php?id=project_ideas

--
E.L. Willighagen
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
ORCID: 0000-0001-7542-0286

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Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
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Egon Willighagen | 1 Mar 13:41 2014
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Google Summer of Code 2014 options?

Hi all,

another year, another Google Summer of Code. And again it is possible
to work on Open Source tools in the area of chemistry.

Below are a few things that I have spotted. What else is out there?

* NRNB mentoring organization [0]
 - Cytoscape has a chemical structure viz plugin based on the CDK that
needs updating
 - PathVisio has a chemical structure viz plugin based on the CDK that
needs updating
 - There is a project idea to integrate Cytoscape into Bioclipse
 - There is a project idea to integrate PathVisio into Bioclipse
* VTK mentoring organization [1]
 - various chemistry related ideas
* ScaffoldHunter (GPLv3) [2]
 - no specific ideas, but based on the CDK, and could use updating to CDK 1.5

Anything else?

Egon

0.http://nrnb.org/gsoc/index.html#ideas-tab
1.http://www.vtk.org/Wiki/VTK/GSoC
2.http://scaffoldhunter.sourceforge.net/wiki/doku.php?id=project_ideas

--

-- 
E.L. Willighagen
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
ORCID: 0000-0001-7542-0286

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Robert Hanson | 23 Feb 19:08 2014

referencing of data

Can someone explain to me the general schema for referencing data in the BODR? I'm not seeing it. For example, at

https://github.com/wadejong/bodr/tree/c7917225cad829507bdd4c8c2fe7ebd3d795c021/bodr/elements

I see xml and bibxml files, but I see nothing that connects those. Just randomly named files. Is there something in, for example, elements.xml, that points one to the specific bibxml for a specific entry?

Bob


--
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

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Wibe de Jong | 20 Feb 08:07 2014

BODR covalent radii patch (all elements)

Hi,

I have updated the covalent radii for all 118 elements following the definition of one consistent set of radii published Pyykko and Atsumi in Chem. Eur. J. published in 2009. This addresses all elements for which the radii were not given (mainly heavy elements), and updates others. 

The git pull request can be found at https://github.com/egonw/bodr 

Please peer review, comment, and apply. 

Thanks,

Bert
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Saulius Gražulis | 10 Feb 16:44 2014
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Re: [TCOD] Presenting TCOD at the IUCr 23rd Congress?

Dear Stefaan,
Dear Björkman,
Dear Linas,

On 02/10/2014 03:41 PM, Stefaan Cottenier wrote:
> Yes, I agree to be on the author list. Something as TCOD deserves a 
> good try -- although I'm not fully convinced yet in which shape it 
> needs to be in order to be realistic and useful.

On 02/10/2014 04:16 PM, Björkman Torbjörn wrote:
> I'll be happy to join.

On 02/10/2014 05:09 PM, Linas Vilciauskas wrote:
> I'd like to participate! The first version of cif dictionary I wrote 
> was just a very rough sketch which I basically made in order to 
> understand the cif dictionary rules etc...

many thanks for your fast and enthusiastic responses! With you in the
team, we move forward. Peter and Armel are positive as well, I
understand. Tomorrow I will upload the TCOD poster/talk abstract to IUCr.

In your posts, you raise a lot of interesting and important issues, and
I will drop in some thoughts of mine in a while.

Regards,
Saulius

--

-- 
Dr. Saulius Gražulis
Vilnius University Institute of Biotechnology, Graiciuno 8
LT-02241 Vilnius, Lietuva (Lithuania)
fax: (+370-5)-2602116 / phone (office): (+370-5)-2602556
mobile: (+370-684)-49802, (+370-614)-36366

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Saulius Gražulis | 10 Feb 14:14 2014
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Presenting TCOD at the IUCr 23rd Congress?

Dear colleagues,

as I am going to the 23rd Congress of IUCr this year, I though that this
would be a good opportunity to present TCOD to crystallographic and
chemical community there.

Unfortunately, the deadline of abstract submission is tomorrow,
2014-02-11, so I need a short feedback from you ASAP... I apologize for
such a short notice.

At this stage, TCOD poster/talk is not to present some spectacular
results, but rather to inform community and to make sure that everyone
is invited, so that nobody is excluded. Only in this case will the TCOD
have its value.

I attach a project of an abstract and an author list. If you do not
mind, I present the abstract as a presenting author and thus put my name
first; otherwise the list is alphabetical. If the NWchem people, or
anyone else, would wish to participate and to provide their input about
computational data representation and ontologies, I'd be glad to include
them as co-authors. At the moment, I have included people on the tcod
mailing list (except that I do not know the full name of , and Peter and
Nicola with whom we discussed TCOD in detail; I hope you will
participate :).

Since we are a new team, I'll do as follows:

a) those who e-mail me till tomorrow (2014-02-11) that they participate
in the presentation I leave on the author list;

b) those people who do not agree or *do not reply* by 2014-02-11 I will
leave out as not consenting with their authorship;

c) If no one from the theoretical community replies, I'll probably
refrain from submitting the abstract.

d) If you join the team, I'll submit the abstract and the author list
tomorrow, on 2014-02-11.

Me, Andrius and Antanas will do all the technical editing of the poster
or slides; any comments on the text from you are welcome (but please
keep in mind that the abstract is limited to 2000 chars). The most
important contribution from you wold be the ideas:

-- how to describe the computation data so that it is useful and
reusable (what parameters need to be specified for different methods)?

-- what quality criteria do we want to put on structures in TCOD (and in
general on published DFT and other structures)? In other words, what
computed structures will we be happy with?

After the abstract submission we will have some time to polish TCOD
policy details, data dictionaries (initial version can be found here:
http://www.crystallography.net/tcod/cif/dictionaries/) and software
pipeline (we will take care of this last bit in Vilnius, but
participants are welcome :).

Regards,
Saulius

-- 
Dr. Saulius Gražulis
Vilnius University Institute of Biotechnology, Graiciuno 8
LT-02241 Vilnius, Lietuva (Lithuania)
fax: (+370-5)-2602116 / phone (office): (+370-5)-2602556
mobile: (+370-684)-49802, (+370-614)-36366
As computational chemistry methods enjoy unprecedented growth,
computer power increases and price/performance ratio drops, a large
number of crystal structures can today be refined and their properties
computed using modern theoretical approaches, such as DFT, HF, QM/MM,
MCMM methods. Availability of several open source codes for
computational and quantum chemistry and open-access crystallographic
databases enables large scale computations of material structures and
properties. We thus increasingly feel that an open collection of
theoretically computed chemical structures would be a valuable
resource for chemists, physicists, engineers and crystallographers. To
address this need, we have launched a Theoretical Crystallography Open
Database (TCOD, http://www.crystallography.net/). The TCOD database
sets a goal to collect a comprehensive set of computed chemical and
crystal structures that would be made available under Open Data
license and invites all computational to deposit their published
computation results or pre-publication data. Accompanied with a large
set of experimentally determined structures in the COD database, the
TCOD opens immediate possibilities for experimental and theoretical
data cross-validation, matching chemical structure with computed
chemical properties, and linking to numerous other chemical,
biological and medical databases.

To ensure high quality of deposited data, TCOD offers ontologies in a
form of CIF dictionaries that describe parameters of computed chemical
and crystal structures, and an automated pipeline that checks each
submitted structure against a set of community-specified criteria for
convergence, computation quality and reproducibility. The scope of
TCOD and validation tools make TCOD a high-quality, comprehensive
theoretical structure database, immediately usable in a broad range of
disciplines.
Saulius Gražulis and
Andrius Merkys and
Antanas Vaitkus and
Armel Le Bail and
Daniel Chateigner and
Giovanni Pizzi and
Linas Vilčiauskas and
L. Smrčok and
Marie-Bernadette Lepetit and
Nicola Marzari and
Peter Murray-Rust and
Riccardo Sabatini and
Stefaan Cottenier and
Torbjorn Bjorkman and
the Blue Obelisk + NWChem people...
Launching Theoretical Crystallography Open Database.
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Saulius Gražulis | 10 Feb 12:37 2014
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Best wishes from the COD team!

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 Gražulis
Vilnius University Institute of Biotechnology, Graiciuno 8
LT-02241 Vilnius, Lietuva (Lithuania)
fax: (+370-5)-2602116 / phone (office): (+370-5)-2602556
mobile: (+370-684)-49802, (+370-614)-36366

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Egon Willighagen | 6 Nov 11:50 2013
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vacancies in our group (for doing Open stuff in a EU setting)

Hi all,

our group has three vacancies open. Our group does a lot of open chem-
and bioinformatics, and includes the Open Source projects
WikiPathways, PathVisio, BridgeDb, the CDK, etc.

Two of the three positions (a postdoc and PhD position) are for a EU
FP7 project that I will start early next year, where we will use open
approaches to set up a database around safe-by-design nanomaterials.
We have recently made a demo based on the CDK, Bioclipse and AMBIT, so
several Blue Obelisk projects are involved:

PhD Student 'Safe-by-Design Nanomaterials', part of EU FP7 project
within the NanoSafety Cluster
https://www.academictransfer.com/20444/

Postdoc 'Safe-by-Design Nanomaterials', part of EU FP7 project
European NanoSafety Cluster
https://www.academictransfer.com/20445/

Please feel free to share these vacancies with interested candidates.

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
ORCID: 0000-0001-7542-0286

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Egon Willighagen | 25 Oct 11:22 2013
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BODR/CDK-based app in the F-Droid app store

Hi all,

with a lot of pleasure I can tell you that my very basic, one
afternoon Android hacky app has made it into the F-Droid app store:

https://f-droid.org/repository/browse/?fdid=com.github.egonw.isotopes

It uses the Blue Obelisk Data Repository and the Chemistry Development
Kit. It's GPLv3 and the source is available from GitHub, see the above
record.

F-Droid itself is a must read app store for Blue Obelisk-ers, as it
focuses only on Open Source Android apps.

Grtz,

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
ORCID: 0000-0001-7542-0286

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Suman Layek | 23 Oct 22:25 2013

SMILES and metal complex

Hi All,

Does anyone know how to represent an octahedral complex by SMILES?

Thanks,

Suman

 

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