[Joelib-help] CMLRSS and WWMM and OpenMolecules

[Peter Murray-R. <pm...@ca...>]

[crossposted, so please be considerate in replies]

Greetings to the OpenSource chemistry community,

We have recently developed a method for publishing molecules on an RSS 
feed, CMLRSS and hope this may be of interest.  CMLRSS consists of a 
standard RSS news feed with CML embedded in those items which contain 
chemistry. When viewed with a CML-aware client such as Jmol or JChempaint 
with the rssviewer plugin the molecule appears in appropriate form (2D or 
3D). This is a simple method to provide an Open feed of molecules of all 
types. Details are at http://wwmm.ch.cam.ac.uk/moin/CmlRss

We would first like to thank the OpenSource chemistry community for 
contributing much to this. The viewers (Jmol/JChempaint) are in Java, and 
many of the molecules have been converted using OpenBabel and/or CDK. The 
WorldWideMolecularMatrix and CMLRSS are being presented at the ACS meeting 
in Anaheim http://oasys2.confex.com/acs/227nm/techprogram/P725453.HTM. We 
append details below.

We invite members of the OpenSource chemistry community and others to 
contribute feeds of Open molecules. Tools to create feeds are available on 
our site and we intend to add CMLRSS output to CDK, OpenBabel, etc. (If you 
can write CML then it's easy to add the <item> information for CMLRSS). If 
you have molecules, with or without ancillary information, you wish to make 
available see http://wwmm.ch.cam.ac.uk/moin/CmlRss.
We already have proof of concept for molecules, properties, spectra (no 
viewer yet) and crystallography. The feeds do not have to be large - but 
the entries should be interesting or useful in some way. Note that 2D, 3D, 
5D (2D+3D) and 8D (2D, 3D +fractional) coordinate systems are all allowable.

The system is designed to allow aggregation of molecules (e.g. in a Xindice 
database) and to be re-used. For example the output of one feed could be 
input to another service such as JOELib which computes properties and 
descriptors. This is still under construction (V0.2)

PeterMR

Announcement
===========

As part of a session on "Research Collaboratories, Virtual laboratories and 
Grid Computing" at the
forthcoming ACS meeting (http://oasys2.confex.com/acs/227nm/techprogram/ )
we are presenting on "Semantic Grid computing - the WorldWideMolecularMatrix"
Part of this will focus on the theme of RSS which I posted about last year. We
have now developed a chemical component to this, now christened CMLRSS, and 
it is
the purpose of this email to invite people if they wish, to join in to this 
"virtual laboratory",
and hence "participate" in the ACS session.
The procedure is as follows
a) For an introduction to the concept, see eg 
http://www.ch.ic.ac.uk/rzepa/cmlrss_distrib/
or http://wwmm.ch.cam.ac.uk/moin/CmlRss
b)We have prepared a distribution kit available either from 
http://www.ch.ic.ac.uk/rzepa/cmlrss_distrib/
or from http://wwmm.ch.cam.ac.uk/moin/RssClient We emphasize that whilst we 
believe this to
function correctly, it has not yet been comprehensively tested on all 
platforms, and some
components are still at the "late alpha", or "early beta" stage. Needless 
to say, we welcome
comments and reports of bugs!
c) You can view the existing CMLRSS grid by installing either Jmol (a 3D 
molecule viewer)
or JChempaint (a 2D editor) as provided, along with the CMLRSS plugin in 
the kit
(these are Java programs so you will have to have Java installed). By
running this, you will open around 8 existing RSS "Channels" and hence 
subscribe to chemical
feeds from these sites. You can if you wish aggregate these feeds into one, 
then filter them
down by (e.g. element). You will notice several themes in the existing 
channels,
including an aggregation of the long running "Molecules of the Month" 
sites, several
database sites (NMR, X-Ray, ChemStock) and the World-Wide Molecular Matrix.
d) You are also welcome to follow the instructions in the above 
distribution to
create your own CMLRSS channel (I might add that several of the sites 
mentioned above
were our beta testers for this kit; it took only one or two days to get up 
and running).
If you do so, please let us know so that we can add you to the list (one of 
the many
"todo" items is to organise the addition of further channels in a better way).
I should end with the observation that as far as we know, this is the 
furthest that the
RSS concept has been pushed into a science field, and another step towards the
"semantic web" espoused by Sir Tim Berners-Lee. We would of course love to 
hear
about your experiences with this system.
-- 
Henry Rzepa.
+44 (020) 7594 5774 (Voice); +44 (0870) 132 3747 (eFax)
http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 
2AZ, UK.


Peter Murray-Rust
Unilever Centre for Molecular Informatics
Chemistry Department, Cambridge University
Lensfield Road, CAMBRIDGE, CB2 1EW, UK
Tel: +44-1223-763069