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ChemAxon's Java Components in a Heterogeneous, Server-Centric Application Environment

ChemAxon's Java Components in a Heterogeneous, Server-Centric Application Environment. ChemAxon 2005 User Group Meeting May 19th and 20th, Budapest, Hungary. Mark Runyan, Alex Tulinsky, Richard Sandstrom, and Julie Myhre Cell Therapeutics, Inc. Topics. CTI Background Tactical Approach

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ChemAxon's Java Components in a Heterogeneous, Server-Centric Application Environment

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  1. ChemAxon's Java Components in a Heterogeneous, Server-Centric Application Environment ChemAxon 2005 User Group Meeting May 19th and 20th, Budapest, Hungary Mark Runyan, Alex Tulinsky, Richard Sandstrom, and Julie Myhre Cell Therapeutics, Inc

  2. Topics • CTI Background • Tactical Approach • Infrastructure Overview • Component Architecture, Features, and Demonstrations • Reporting • Conclusions and Future Directions

  3. Cell Therapeutics, Inc. • http://www.ctiseattle.com/ • 389 people in the U.S. and Europe • 25 Discovery Research Scientists in Seattle • 20 Discovery Research Scientists in Bresso, Italy • 37 in Pre-Clinical Development in Bresso, Italy • 4 FTE in Scientific Systems

  4. Informatics Background • Traditional MDL/ISIS shopDrawbacks: • Cost of deployment and licensing • Lack of native integration capabilities • Demand for integrating increasingly complex biological and chemical data • Research conducted in Italy and the United States

  5. Approach • Maintain legacy registration system • Develop cost-effective, scalable web-based system for data access and mining • Loose-coupling of component based systems • JChem chosen for chemical component • Emphasis on Open Source Infrastructure

  6. Infrastructure • Oracle and ISIS/Host on Windows 2003 Server • ActivityBase • MOE • Linux platform / open source tools • Java • Apache / Tomcat • JDO / Hibernate / Proxool • Eclipse / Jasper Reports • Ant • MySql • CVS / Bugzilla / Docbook

  7. JChem Import Legacy Registration System Automated Replication ISIS/Host Db JChem Db

  8. Import Process

  9. Data Model

  10. DAO-layer (Structure Search Component)

  11. Persistent Query Definition

  12. Structure Search Navigation

  13. Simple Java code

  14. Web Client features • Localization • Thin client • no client licensing (browser based, .pdf) • no workstation maintenance required • deployment efficiency • applet integration (Marvin) • User Profiles • shared result pages (via URL) • persistent customization • Mature, Open Source-centric tools

  15. Compound Search – Italian localization

  16. Marvin Sketcher Applet

  17. Compound Profile – Italian localization

  18. UI Examples – HTS Browser • Query Page • Hyperlink Documentation • Result Pages

  19. UI Examples – HTS Browser Cont. • Pagination Control • Hyperlink to Compound Profile • Branch to SSS or Similarly Search

  20. Web Services • Image processing • Warehouse sourced graphical objects • JChem rendered structures • Chromatograms • Dose response graphs • Statistical Plots

  21. Image Services

  22. Image Services in UI

  23. Report Design (DAO and web service based) • Design time: integrated, feature-rich, open source

  24. Report Example

  25. Conclusions • Successfully implemented ChemAxon tools: • JChem structure Import API • JChem structure search API • Marvin Sketcher for structure search input • Structure rendering API for compound image services • Marvin viewer for interactive compound display • Deployed Jasper Reports for advanced reporting • Successfully deployed web applications to Bresso, Italy over wide area network, with language localization.

  26. Future Directions • Unified Warehouse Browser in Development • More query fields and features • Column Selection from full breadth of warehouse data • Inclusion of complex biological data types • Oracle Data Cartridge implementation • Increased performance • More sophisticated and automated structural searching • JChem structure warehousing from multiple sites • Replacement of legacy compound registration system

  27. Acknowledgements • ChemAxon Technical Support • CTI Research Scientists • Ray Luiggi – VP Global Information Technology • Stewart Chipman – VP Research Programs • Ambrogio Oliva – CTI Europe - Italian Localization • Jed Malitz – Oracle DBA • Jason Shrack – Linux Administration • Open Source contributors

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