[Joelib-devel] Molecular Open Web Services

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

[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=generateinchi&JavaScript=enabled
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