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 Infrastructure Overview Component Architecture, Features, and Demonstrations Reporting Conclusions and Future Directions

Cell Therapeutics, Inc 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

Informatics Background Traditional MDL/ISIS shop Drawbacks: ­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

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

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

JChem Import Automated Replication ISIS/Host DbJChem Db Legacy Registration System

Import Process

Data Model

DAO-layer(Structure Search Component)

Persistent Query Definition

Structure Search Navigation

Simple Java code

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

Compound Search – Italian localization

Marvin Sketcher Applet

Compound Profile – Italian localization

UI Examples – HTS Browser Query Page Hyperlink Documentation Result Pages

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

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

Image Services

Image Services in UI

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

Report Example

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.

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

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