Community Grids Lab Work

1. Community Grids Lab Work Marlon Pierce CICC Quarterly Meeting Jan 27, 2006

2. Some Notes on Our Approach • Everything is based around Web Services. • We build some. • We inherit some • UDDI, WS-Context • We take some • NIH’s COMPARE and Cambridge’s WWMM suite. • Services are fundamental units of action • Clients to services can come in different varieties. • Taverna workflow clients • Portlet-based portal clients • Other client environments and tools (like BPEL workflow engines) are compatible. • All work with our same services. Web Service Web Service Web Service Portal Taverna

3. Why Taverna? • Taverna is an open-source workflow and annotation tool developed by the UK e-Science program. • A nice client-side workbench tool for collecting services into a meta-application. • Taverna works with generic Web Services • WSIF helps you build client interfaces from WSDL. • Designed to support bio-informatics applications. • Also used extensively by our Cambridge collaborators. • We anticipate extensive, ongoing support for it through the OMII. • For example, maybe better Globus and OGSA-DAI client support.

4. Summary of Services • Execution and File Web Services (J. Kim) • Makebits, dvikm • Supporting Wild Use Cases • VOTable Services (S. Patel) • Generic XML tabular data model from Virtual Observatory community. • Potentially useful as intermediate data format for application (BCI, CDK codes) output and for screening center results. • Sima will discuss a use case. • Comes with parsers and a Java API. • Wrapped now as a Web Service • VOTables serve as data model. • Table instances on remote servers can thus be manipulated. • Inherited tools (VOPlot) can plot VOTable data.

5. Upcoming Work: Globus and TeraGrid • Globus services will greatly simplify running codes on high performance computing environments. • Secure job submission, support for PBS, secure remote file management. • Available on TeraGrid. • Dvikmeans and some CDK codes should benefit. • It has been a little problematic to develop Taverna clients. • Not currently well documented • We are working on intermediate Globus services for this. • Wrapping the Java CoG Kit for protection from Globus version changes. • And the CoG’s nice API. • But expect UK efforts in long term to replace.

6. Cambridge Tools • Downloads put together by Nick Day: • http://wwmm.ch.cam.ac.uk/download/ • A bundled Tomcat server that includes all services and also portlets (i.e. service clients for browsers). • Services listed on next slide. • Portlets are compatible with OGCE, LEAD, and other work that IU has done. • A version of Taverna that includes CDK and Jumbo51 tools. • Some workflow examples (Jake will demo) • We really would like to explore some applications using these but need help from chemists, cheminformatics folks.

7. Jumbo and Open Babel • Jumbo is Peter Murray-Rust’s suite of Java tools for manipulating the Chemistry Markup Language. • Can also form the basis for CML Web Services • Open Babel is a “cross-platform program and library designed to interconvert between many file formats used in molecular modeling, computational chemistry, and many related areas.” • Wrap with Web Services

8. CDK: the Chemistry Development Kit • CDK is a Java-based, object-oriented set of chemistry libraries and packages. • Model-view-controller design to separate structure from representation (i.e. 2d, 3d, text for same data model). • Data classes: element, isotope, atom, bond, etc. • Allows you to programmatically build your molecules, etc. • Lots of tools • Format converters, rotators, translators, surface area calculators. • CDK forms the basis for several other applications: • Jchempaint: Java editor for 2D chemical structures. • Seneca: distributed/parallel application for computer-assisted structure elucidation (CASE) • Nmrshiftdb: open, online database for organic structures and their nuclear magnetic resonance (nmr) spectra. • Can form basis of yet more services....

9. WWMM Web Services • XindiceServer • OBServer (i.e. OpenBabel) • Mopac • JumboToolServer • JumboConverter • INChiServer • INChiGoogle • Gamess • Exist • CMLRSSServer • CML2SVG • CML2Jmol • CML2Gamess • CDX2CML • Build3d

10. Some notes from Peter Murray Rust • InChI Generator - this will generate a unique identifier for a molecule. This will increasingly be the unique handle for retrieving molecules • Openbabel: will convert from any format to any other format • InChIGoogle: searches for any molecules on the web that have InChIs • “The value of any particular service will increase proportionally to the total number. A chemoinformatics app consists of tens of different functionalities. Other things in our pipeline are 2D layout, 2D image generation, etc. By the time all these add up then there is quite a lot!” --PMR

11. Web Site, Blog, and Mailing List • The web site, www.chembiogrid.org, is plain old HTML (for simplicity and long-term maintainability) backed by a WebDAV server. • You can use DAV clients (built into Windows, for example) to log into the server and upload web material. • Our DAV server runs inside of Tomcat, so it can serve up HTML, JSP, and similar stuff. • But not Perl, PHP, CGI or similar. • It’s virtually hosted through Apache, so if you really want PHP, we can work something out. • We also set up a Wiki.... • We are blogging related stuff (on VOTables, Taverna Life Lessons, etc) at http://communitygrids.blogspot.com. • I think this is a useful way to post notes. • We can create a specific blog for this project if you want. • Mailing list: cicc-dev-l@listserv.indiana.edu. • Contact me if you want to subscribe.