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Bioclipse and Webservices
Bioclipse and Webservices
Bioclipse and Webservices
Bioclipse and Webservices
Bioclipse and Webservices
Bioclipse and Webservices
Bioclipse and Webservices
Bioclipse and Webservices
Bioclipse and Webservices
Bioclipse and Webservices
Bioclipse and Webservices
Bioclipse and Webservices
Bioclipse and Webservices
Bioclipse and Webservices
Bioclipse and Webservices
Bioclipse and Webservices
Bioclipse and Webservices
Bioclipse and Webservices
Bioclipse and Webservices
Bioclipse and Webservices
Bioclipse and Webservices
Bioclipse and Webservices
Bioclipse and Webservices
Bioclipse and Webservices
Bioclipse and Webservices
Bioclipse and Webservices
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Bioclipse and Webservices

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  • 1. Bioclipse and Webservices Embrace Workshop / 2008-11-03 Egon Willighagen Uppsala University http://chem­bla­ics.blogspot.com/
  • 2. My Background • Chemist / Cheminformatician / Chemometrician – data analysis ! – small molecules • crystallography / metabolomics / QSAR • Open Data / Open Source / Open Standards – Jmol http://www.jmol.org/ – Chemistry Development Kit http://cdk.sf.net/ – Bioclipse http://www.bioclipse.net/ http://citeulike.org/user/egonw/tag/papers
  • 3. Metabolomics MetWare, http://www.metware.org/
  • 4. Drug Discovery T. Kuhn, CDK-Taverna, http://cdk-taverna.de/
  • 5. Web Service? quot;a software system designed to support interoperable machine-to- machine interaction over a networkquot;
  • 6. Web Service? • W3C quot;a software system – SOAP designed to support – WSDL interoperable machine-to- machine interaction over a networkquot; Web Services Glossary, http://www.w3.org/TR/ws-gloss/
  • 7. Web Service? • W3C quot;a software system – SOAP designed to support – WSDL interoperable machine-to- machine interaction • EMBRACE over a networkquot; – + REST
  • 8. Web Service? • W3C – SOAP – WSDL • EMBRACE – + REST
  • 9. Web Service? • W3C • Transport Layer – SOAP – HTTP – WSDL – SMTP –… • EMBRACE – + REST • Application Layer – SOAP / BioMoby – REST – ...
  • 10. Do we care? ... • As scientist we are interested in solving our questions, not in technical solutions... • But ... – commitment – open standards
  • 11. What about Databases? • If database retrieval is a service too... • Retrieval services have different requirements than computation services...
  • 12. What about Databases? • Big Downloads – BioMart – FTP sites • Exploration ... – Browser • Userscripts • Ubiquity – Semantics • Link to Workflows ! Userscripts for the Life Sciences, doi:10.1186/1471-2105-8-487
  • 13. What do we use them for? • Massive computation – workflows (Taverna, ...) – integrate and mine databases But what then? – visualization – feed to R – convert to PDF – ...
  • 14. Human Validation: Bioclipse
  • 15. Bioclipse and Webservices • Strong integrated services: MyNMRShiftDB Kuhn and Steinbeck, http://www.nmrshiftdb.org/
  • 16. Bioclipse' Service Integration • Webservices – SOAP – BioMoby – Local – Taverna workflows – REST – ... • Categorization – ...
  • 17. Workflow as Service
  • 18. Bioclipse' Wishlist • Strong Data Types – Semantics – Like BioMoby • Service Discovery and Annotation – http://biocatalogue.org/ … but than Open – SAWSDL, Semantic Annotation for WSDL … but then independent, possibly social – BioMoby … but then decentralized – OWL-S ?
  • 19. OWL-S: Semantic Markup for Web Services http://www.w3.org/Submission/OWL-S/ Copyright 2004, Various
  • 20. SOAP over HTTP: Limitations • Synchronous – polling required • HTTP time-outs – caused by routers • Alternatives – Other transport layers: SMTP, XMPP • Relatively complex – lead to library incompatibilities – requires additional specs (WS-I)
  • 21. XMPP/IO-DATA Services • XMPP Extensible Messaging and Presence Protocol • IO-DATA “This specification defines an XMPP protocol extension for handling the input to and output from a remote entity.” – Asynchronous !
  • 22. Services == Component
  • 23. XMPP/IO-DATA envelope <iq from=quot;egonw@ws1.bmc.uu.se/homequot; id=quot;JSO-0.12.5-6quot; to=quot;cdk.ws1.bmc.uu.sequot; type=quot;setquot;> <command xmlns=quot;http://jabber.org/protocol/commandsquot; action=quot;executequot; node=quot;calculateMassquot;> <iodata xmlns=quot;urn:xmpp:tmp:io-dataquot; type=quot;inputquot;> <in> <smiles xmlns=quot;urn:xws:cdk:inputquot;>CCC</smiles> </in> </iodata> </command> </iq>
  • 24. XMPP/IO-DATA: Advantages • Asynchronous – Long running jobs • Strong Data Typing – via XML Schema provided by service itself • XML Library: xws4j – deserialization into XMLDOM • or into domain specific classes – hides XMPP layer – LGPL J. Wagener, http://sf.net/projects/xws4j/
  • 25. Conclusions • SOAP / WSDL is a solution of many • Bioclipse – SOAP, BioMoby, XMPP/IO-DATA, REST, … – Offer Interactivity • Components Missing – semantic, data type thesaurus – service annotation
  • 26. Thanx • Bioclipse Team – Uppsala University (Prof. Wikberg) – EBI/Hinxton (dr. Steinbeck) • MetWare Team – PRI/Wageningen (dr. van Ham) – IPB/Halle (dr. Neumann) • Johannes Wagener (XMPP) • Thomas Kuhn (CDK-Taverna)

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