[BlueObelisk-discuss] Request for Information about Code libraries for CML

[Peter Murray-Rust]

As a result of the "Semantic Physical Science" workshop earlier this year (
http://www-pmr.ch.cam.ac.uk/wiki/Semantic_Physical_Science) we are writing
a paper for J.Cheminformatics on "Building a code library for CML". We'd
like information from anyone who has implemented a toolset to read and/or
write CML. The paper will analyse some of these in depth and record others.
The minimal amount of information is probably the coverage (through the
usage of CML Elements) , the language and a few additional fields (this are
mainly tickboxes). At present we are covering:

- Neylon/Python
- VTK
- Avogadro
- Chem4Word
- OpenBabel
- CDK/JChemPaint
- FoX
- Jmol
- JUMBO-system

We'd very much like others to contribute - it can be closed source as well
as Open, We are generally interested in systems that use Schema2.4 or
Schema3.0 as previous versions are deprecated. Note that Schema 2.4 has
been used by the community for about 5 years with no emendations. Schema3
does not introduce new functionality but has a more modern approach using
conventions rather than content-models.

We are creating a spreadsheet and it may be simplest to share this in a
dropbox.

If you write a section on your code then this will generally mean that you
are listed as an author. We only want descriptions of the CML
interface/API/coverage - not the greater functionality of the
program/library

If you aren't on the list above, please mail either this list or me.

Hoping for contributions

[Egon Willighagen]

Post by Peter Murray-Rust
If you write a section on your code then this will generally mean that you
are listed as an author. We only want descriptions of the CML
interface/API/coverage - not the greater functionality of the program/library

I like to contribute text on the design of the CML reading used by the
CDK and thus JChemPaint, Bioclipse, and others.

Egon

[Peter Murray-Rust]

Post by Peter Murray-Rust

Post by Peter Murray-Rust
If you write a section on your code then this will generally mean that

you

Post by Peter Murray-Rust
are listed as an author. We only want descriptions of the CML
interface/API/coverage - not the greater functionality of the

program/library
I like to contribute text on the design of the CML reading used by the
CDK and thus JChemPaint, Bioclipse, and others.

Thanks Egon. I have given you access to dropbox. Suggest you write your
material and then quickly paste it into the text (to avoid clashes).

Post by Peter Murray-Rust
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

[Ola Spjuth]

Dear Peter,

CML is a central part of the Bioclipse API and toolset and ensures interoperability between plugins locally in Bioclipse and over distributed web services. While much relies on CDK for reading/writing, I can also contribute a paragraph on CML extensions I implemented for a molecular dynamics project in Bioclipse, as well as assist Egon with atom type info roundtripping. I would be happy to contribute on these topics, please let me know if you think any of this would be suitable additions to your paper.

Kind regards,

Ola


--
Ola Spjuth, PhD
Department of Pharmaceutical Biosciences
Box 541, Uppsala University
Sweden

Email: ***@farmbio.uu.se
Ph: [phone]

Bioclipse: http://www.bioclipse.net

Post by Peter Murray-Rust
Neylon/Python
VTK
Avogadro
Chem4Word
OpenBabel
CDK/JChemPaint
FoX
Jmol
JUMBO-system
We'd very much like others to contribute - it can be closed source as well as Open, We are generally interested in systems that use Schema2.4 or Schema3.0 as previous versions are deprecated. Note that Schema 2.4 has been used by the community for about 5 years with no emendations. Schema3 does not introduce new functionality but has a more modern approach using conventions rather than content-models.
We are creating a spreadsheet and it may be simplest to share this in a dropbox.
If you write a section on your code then this will generally mean that you are listed as an author. We only want descriptions of the CML interface/API/coverage - not the greater functionality of the program/library
If you aren't on the list above, please mail either this list or me.
Hoping for contributions
--
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
[phone]
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[Peter Murray-Rust]

Post by Ola Spjuth
Dear Peter,
CML is a central part of the Bioclipse API and toolset and ensures
interoperability between plugins locally in Bioclipse and over distributed
web services. While much relies on CDK for reading/writing, I can also
contribute a paragraph on CML extensions I implemented for a molecular
dynamics project in Bioclipse, as well as assist Egon with atom type info
roundtripping. I would be happy to contribute on these topics, please let
me know if you think any of this would be suitable additions to your paper.

Yes it would be great and you would be an author. The emphasis is on the
CML and any downstream functionality that uses or otherwise relies on CML.
And I am keen that we have a checklist (approximate) of the elements and
other relavent aspects of CML

Post by Ola Spjuth
Kind regards,
Ola
--
Ola Spjuth, PhD
Department of Pharmaceutical Biosciences
Box 541, Uppsala University
Sweden
Ph: [phone]
Bioclipse: http://www.bioclipse.net
As a result of the "Semantic Physical Science" workshop earlier this year (
http://www-pmr.ch.cam.ac.uk/wiki/Semantic_Physical_Science) we are
writing a paper for J.Cheminformatics on "Building a code library for
CML". We'd like information from anyone who has implemented a toolset to
read and/or write CML. The paper will analyse some of these in depth and
record others. The minimal amount of information is probably the coverage
(through the usage of CML Elements) , the language and a few additional
- Neylon/Python
- VTK
- Avogadro
- Chem4Word
- OpenBabel
- CDK/JChemPaint
- FoX
- Jmol
- JUMBO-system
We'd very much like others to contribute - it can be closed source as well
as Open, We are generally interested in systems that use Schema2.4 or
Schema3.0 as previous versions are deprecated. Note that Schema 2.4 has
been used by the community for about 5 years with no emendations. Schema3
does not introduce new functionality but has a more modern approach using
conventions rather than content-models.
We are creating a spreadsheet and it may be simplest to share this in a dropbox.
If you write a section on your code then this will generally mean that you
are listed as an author. We only want descriptions of the CML
interface/API/coverage - not the greater functionality of the
program/library
If you aren't on the list above, please mail either this list or me.
Hoping for contributions
--
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
[phone]
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