From: Peter Murray-R. <pm...@ca...> - 2004-12-16 00:05:01
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At 13:13 15/12/2004 +0100, Stefan Kuhn wrote: >Hi everybody, I have answered this on the QSAR list - a brief additional comment >I just wanted to mention that NMRShiftDB offers certain web services, like >searches etc. These are mainly used by the stand-alone client, similar to >RPC, but can be used by every client. They are actually restricted to= access >from Java programs, since some input is cdk objects, but this could be >changed. We do also currently not have WSDL descriptions, since I did not >find a good description/example of it. But I would try to do this, so we >could do something like a chemoinformatics web services directory. >Generally speaking I got the impression that the interoperability of web >servies has its limitions. Apart from the obvious problem with data types,= I >would not bet on being able to use any service with any client indepently= of >langage, server etc. used. This need not be a problem. Web services does not necessarily need a human-operated client emitting=20 photons. They can be called from a program. So it would be perfectly=20 possible to create a WS chain with contributions like - read journal TOC (JUMBO) - substructure search of known data (OB) - extract supplemental 3D data and spectra (JUMBO) - calculate NMR spectrum GAMESS - calculate NMR spectrum (NMRShiftDB) - calculate descriptors (CDK, JOELib) etc. - this is just an example to show that different groups contribute=20 different services If the data are agreed types and all serialized in agreed format then it's= =20 trivial to call them from programs. That is what we are all working on... If there are objects (e.g. spectra) we need agreed representations=20 (CMLSpect, JCAMP) and GUIs for humans. But we need this anyway. P. >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 what= 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&JavaScri= pt > >=3Denabled where the input is supplied as CML or legacy ASCII and the= output > > 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= bindings > > (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= using > > other systems > > - assuming the WS is open it can be cloned and installed elsewhere, thus > > adding redundancy > > - several generic systems (e.g. http://taverna.sf.net) are being= developed > > 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= mirrors > > - there may be a performance hit - is this is actually a problem? > > - the application requires the state to be maintained (WS are easier for > > stateless protocols). All our protocols are stateless. > > > > I think WS has a lot to offer our community. For example I'd like to use > > 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= like? > > 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 > >-- >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 Peter Murray-Rust Unilever Centre for Molecular Informatics Chemistry Department, Cambridge University Lensfield Road, CAMBRIDGE, CB2 1EW, UK Tel: +44-1223-763069 |