From: Peter Murray-R. <pm...@ca...> - 2004-12-16 16:39:25
|
At 15:11 16/12/2004 +0100, E.L. Willighagen wrote: >-----BEGIN PGP SIGNED MESSAGE----- >Hash: SHA1 > > > What I am suggesting here is that we look at systems like Taverna (or > > Kepler). We have built a very successful workflow with Taverna that works > > well. > >Screenshot? http://taverna.sf.net/docs.html Assume every purple box is a CDK/JUMBO/JOElib method arranged to have no side effects and to choose inputs and outputs from a set of agreed types. If these types are ASCII then any types of code can be used (InChI, OpenBabel, bkchem) If they are Java objects it works nicely but we have to agree on the objects and make sure their structures is very well documented. I think ASCII/XML is safest. P. > > There is quite a large development team and they are very responsive. > > They already have Jmol as a viewer. They have a model where (say) other > > renderers such as JCP could be integrated. The system can run as > > standalone, web services grid-enabled, etc. > > > > The first task is for us to agree on the object we pass. These are safest > > if they are serialized (e.g. in CML) > >JOELib has QSAR output in CML1, and CDK since yesterday in CML2... >For the last see: http://wwmm.ch.cam.ac.uk/moin/ChemistryDevelopmentKit An obvious component is therefore CMLConverter to read one type and output the other. This components should be based on JUMBO or OpenBabel for example > > but it appears that for non-persistent > > objects Java will work (works fine for me). It could be that octet has a > > role here. > >Yes, on the object level it should be Octet indeed. Good. > > YY is currently setting up pages where you can develop your own simple WS > > aggregation. A typical example is > > "find the molecular mass for a SMILES".* > > > > We can do this in two steps: > > - convert SMILES to CML (OB) > > - calculate MWt (JUMBO: MoleculeTool.getMolecularMass()); > > > > The idea will be to create (very simple) workflow on-the-fly. It is likely > > that we shall be able to save these as Taverna XML objects > >I'll look at it. I think it will take a day or so. P. >Egon > >- -- >e.w...@sc... >PhD-student on Molecular Representation in Chemometrics >Radboud University Nijmegen >http://www.cac.science.ru.nl/people/egonw/ >GPG: 1024D/D6336BA6 >-----BEGIN PGP SIGNATURE----- >Version: GnuPG v1.0.7 (SunOS) > >iD8DBQFBwZd+d9R8I9Yza6YRAq/WAJ4/W/qLG3xV669GcYDY8eFb5nwWJQCePG1h >hE4IgPaQ4KEvlf+aZCVU8Sk= >=wJWi >-----END PGP SIGNATURE----- Peter Murray-Rust Unilever Centre for Molecular Informatics Chemistry Department, Cambridge University Lensfield Road, CAMBRIDGE, CB2 1EW, UK Tel: +44-1223-763069 |