[Joelib-devel] Re: [QSAR-devel] Molecular Open Web Services

[Stefan K. <ste...@un...>]

Hi everybody,
I just wanted to mention that NMRShiftDB offers certain web services, lik=
e=20
searches etc. These are mainly used by the stand-alone client, similar to=
=20
RPC, but can be used by every client. They are actually restricted to acc=
ess=20
from Java programs, since some input is cdk objects, but this could be=20
changed. We do also currently not have WSDL descriptions, since I did not=
=20
find a good description/example of it. But I would try to do this, so we=20
could do something like a chemoinformatics web services directory.
Generally speaking I got the impression that the interoperability of web=20
servies has its limitions. Apart from the obvious problem with data types=
, I=20
would not bet on being able to use any service with any client indepently=
 of=20
langage, server etc. used.
Stefan Kuhn

Am Sunday 12 December 2004 17:17 schrieb Peter Murray-Rust:
> [Crossposted to several OpenSource lists - please reply thoughtfully. I
> will collate significant replies]
>
> We have been investigating Web Services as a means of distributing Open
> molecular functionality. YY has set up a range of services on our site:
> http://wwmm.ch.cam.ac.uk/gridsphere/gridsphere
> I believe that web services provide a valuable approach for some of wha=
t we
> want to do. Rather than linking a library or executable into the code, =
a
> call is made to a WS. Thus, for example, we have set up an InChI server=
:
> http://wwmm.ch.cam.ac.uk/gridsphere/gridsphere?cid=3Dgenerateinchi&Java=
Script
>=3Denabled where the input is supplied as CML or legacy ASCII and the ou=
tput
> returned as ASCII.
>
> Note that WS do not require graphical i/o or a human to click for the
> service - they can be called programmatically from a wide range of bind=
ings
> (probably not FORTRAN)
>
> WS have several advantages:
> - the user doesn't have to install the code
> - the user doesn't have to maintain the code
> - complex architectures can be hidden behind the surface
> - it leads to cleaner component design
> - the developer may not have to worry about porting
> - it avoids the "jar explosion and version" problem that we have when u=
sing
> other systems
> - assuming the WS is open it can be cloned and installed elsewhere, thu=
s
> adding redundancy
> - several generic systems (e.g. http://taverna.sf.net) are being develo=
ped
> to support component-based approaches including WS.
> - attractive when the operation is a relatively infrequent requirement
> - good for teaching
>
> There may be some disadvantages:
> - the user may not always be connected or the service is not available.
> Solution: install the service on your local machine and/or create mirro=
rs
> - there may be a performance hit - is this is actually a problem?
> - the application requires the state to be maintained (WS are easier fo=
r
> stateless protocols). All our protocols are  stateless.
>
> I think WS has a lot to offer our community. For example I'd like to us=
e
> JOELib or CDK to calculate molecular properties. It's an effort to link
> these into a single bloated app as every time some library changes the
> whole lot has to be recompiled. With WS I can calculate the properties =
I
> want independently of the implementation.
>
> Are others in this community interested? What services would people lik=
e?
> Our own list includes but is not limited to:
> - calculate 2D coords for connection table
> - calculate 3D coords for molecule
> - MM, MD, MO calculations
> - calculate descriptors for molecule
> - calculate properties for molecules
> - legacy conversions
> - search databases
> - create SVG diagrams for molecules and reactions
> - create PNGs
>
> If you have a working application it's relatively easy to create a WS. =
YY
> has created pages:
> http://wwmm.ch.cam.ac.uk/moin/WebServiceUsage
> http://wwmm.ch.cam.ac.uk/moin/WebServiceDev
>
> P.
>
>
> Peter Murray-Rust
> Unilever Centre for Molecular Informatics
> Chemistry Department, Cambridge University
> Lensfield Road, CAMBRIDGE, CB2 1EW, UK
> Tel: +44-1223-763069
>
>
>
> -------------------------------------------------------
> SF email is sponsored by - The IT Product Guide
> Read honest & candid reviews on hundreds of IT Products from real users.
> Discover which products truly live up to the hype. Start reading now.
> http://productguide.itmanagersjournal.com/
> _______________________________________________
> Qsar-devel mailing list
> Qsa...@li...
> https://lists.sourceforge.net/lists/listinfo/qsar-devel

--=20
Stefan Kuhn M. A.
Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de)
Z=FClpicher Str. 47, 50674 Cologne
Tel: +49(0)221-470-7428   Fax: +49 (0) 221-470-7786
My public PGP key is available at http://pgp.mit.edu