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Building a flexible infrastructure with Bioclipse, open source, and federated cloud services

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Presentation held at Bio-IT World Expo Europe 2009. …

Presentation held at Bio-IT World Expo Europe 2009.

Presenters:
* Ola Spjuth, Dept. Pharmaceutical Biosciences, Uppsala University, Sweden
* Lars Carlsson, Global Safety Assessment, AstraZeneca R&D, Sweden

Published in: Technology

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  • Briefly discuss what a rich client is. This is an opportunity to talk about all the pretty pictures, how making a selection in one view can change the appearance of others, drag and drop, yadda, yadda, yadda… Desktop app (not in web browser) Responsive UI, native look and feel Portability, run on multiple platforms Supports disconnected operation, servers on demand
  • A platform for building platforms The Maestro team develops mission operations software at the NASA Jet Propulsion Laboratory, including the science operations tool for the Spirit and Opportunity Mars rovers and the upcoming Phoenix and Mars Science Laboratory missions. More than a year ago, the team adopted the Eclipse Rich Client Platform as the foundation for the next version of their software and the Eclipse Java Development Tools as their development environment. Challenges: User community is everything from technophiles to technophobes. New set of tools (i.e., application) for every mission Complex applications Geographically dispersed
  • Web servers, web pages Web services: do both
  • Web servers, web pages Web services: do both
  • Web servers, web pages Web services: do both
  • Web servers, web pages Web services: do both
  • Supports: Control access to services Long-running jobs Look up available services
  • Exact database lookup InChI Nearest Neighbors CDK Fingerprints Signature Significance QSAR Toxicophores SMARTS matching
  • Data sets can be exchanged QSAR analyses can be validated and reproduced QSAR analyses can be merged and extended Establish public repositories
  • Transcript

    • 1. Building a flexible infrastructure with Bioclipse, open source, and federated cloud services 1 Dept. Pharmaceutical Biosciences, Uppsala University, Sweden 2 Global Safety Assessment, AstraZeneca R&D, Sweden Ola Spjuth 1 and Lars Carlsson 2
    • 2. Contents
        • The Bioclipse Workbench
        • Federated cloud services (XMPP)
        • Global Safety Assessment at AstraZeneca
          • Decision support for drug safety assessment
          • Site-of-metabolism prediction
          • Interpretable QSAR models
          • Molecular optimization
    • 3. Bioclipse
      •  
        • A versatile workbench for the life sciences
        • Open source, Java, builds on Eclipse (www.eclipse.org)
        • Extensible architecture - everything is a plugin
        • Use open standards if available
      Spjuth O, Helmus T, Willighagen EL, Kuhn S, Eklund M, Wagener J, Murray-Rust P, Steinbeck C, Wikberg JES. Bioclipse: an open source workbench for chemo- and bioinformatics . BMC Bioinformatics 2007, 8:59. O. Spjuth, J. Alvarsson, A. Berg, M. Eklund, S. Kuhn, C. Mäsak, G. Torrance, J. Wagener, E. L. Willighagen, C. Steinbeck, and J. E. S. Wikberg. Bioclipse 2: A scriptable integration platform for the life sciences . Submitted, 2009.
    • 4. What is a Rich Client?
        • An application that uses the windowing and GUI features of the operating system
          • Responsive UI
          • Portable
          • Offline operations
          • Servers on demand
          • Drag & drop
          • Integration with platform (files, printer etc)
          • Provisioning system
          • Much, much, more…
    • 5. Bioclipse features
        • Many plugins for the life sciences
          • e.g. 2D editor, 3D interactive visualization, sequence editors...
      •  
        •   Bioclipse 2.0: All functionality available from Bioclipse Scripting Language
      •  
        • Cheminformatics framework: The Chemistry Development Kit (CDK) - http://cdk.sourceforge.net
        •   Can utilize existing Eclipse plugins
          • Reporting tools
          • Workflows (Knime)
          • Customize for user needs
    • 6. Component-based architecture Bioclipse Proteochemometrics 2D 3D Data analysis Spectra Molecular dynamics
    • 7. Bioclipse
      • Use the well-established, mature Eclipse architecture in the life sciences
    • 8. Other Eclipse-applications: Maestro – NASA Space Mission Management
    • 9. Other Eclipse-applications: Dutch railways
    • 10. XMPP services: Background
      • A Web service is a way to provide interoperable online functionality
      • The problem:
        • Current Web service technologies (e.g. SOAP and REST)
          • are synchronous
          • do not have service discovery built-in
          • require documents describing the services
    • 11. XMPP architecture Wagener J, Spjuth O, Willighagen EL, Wikberg JES. XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous Web services . BMC Bioinformatics 2009, 10:2799
    • 12. Some mid-pres conclusions
        • Rich clients are useful
          • High-end visualizations, work offline, networked resources on demand
        • Bioclipse
          • An extensible workbench (Rich Client) for the life sciences
        • XMPP + IO-Data
          • Provides federated, asynchronous, discoverable cloud services
          • Ideal for long-running jobs
    • 13. Bioclipse and Drug Discovery Meets computational and reporting demands at various stages in the drug-discovery process DISCOVERY DEVELOPMENT LI FTIM LO CD Batch/scripting Tailored plugins Rich content
    • 14. Global Safety Assessment, AstraZeneca R&D   The objective of the group at AZ is to provide state-of-the-art tools to facilitate decision making in the drug-discovery process   The main focus is on predictive toxicology
    • 15. Ames Risk Assessment System
        • Fully Automated QSAR
        • Full Read-Across
        • QSAR Interpretation
        • Structural Warnings
    • 16. Bioclipse Software Demonstration
      •  
        • Batch/scripting (Virtual Screening)
        • Decision Support (paper submitted to JCIM, co-authors Ernst Ahlberg Helgee and Dr. Scott Boyer)
        • Molecular Optimization (paper submitted to JCIM, co-authors Ernst Ahlberg Helgee and Dr. Scott Boyer)
        • MetaPrint2D (paper to be submitted, co-authors Sam Adams, Prof. Robert C. Glen and Dr. Scott Boyer)
      Live Demo
    • 17. Bioclipse Achievements
      • In 2 years:
      • > 29.000 downloads
      • >30 contributors - Uppsala, Cambridge, Cologne, Scripps, EBI, Munich, NIH ...
      • Bioclipse 2.0 released!
      Jury’s Special Prize
    • 18. Genetta Soft AB
      • Professional consultancy services for Bioclipse
        • Custom-tailored releases
        • Develop and integrate custom functionality
        • Support, documentation, education
      www.genettasoft.com
    • 19. Acknowledgements Dept. Pharmaceutical Biosciences, Uppsala University, Sweden Prof. Jarl E. S. Wikberg Dr. Egon Willighagen Martin Eklund Jonathan Alvarsson Carl Mäsak Eskil Anderssen Annsofi Andersson Arvid Berg Bjarni Juliusson Unilever Centre for Molecular Informatics, Univ. Cambridge, UK Prof. Peter Murray-Rust Prof. Robert Glen Samuel Adams Linnaeus Centre for Bioinformatics, Uppsala, Sweden Dr. Erik Bongcam-Rudloff Sofia Burvall European Bioinformatics Institute, Hinxton, UK Dr. Christoph Steinbeck Stefan Kuhn Dr. Gilleain Torrence Cologne University Bioinformatics Centre (CUBIC), Germany Dr. Tobias Helmus Miguel Rojas Thomas Kuhn Dept Clinical Pharmacology, Uppsala University, Sweden Prof. Rolf Larsson Dr. Claes Andersson Hanna Göransson Ludwig-Maximilians-Universität, Munich, Germany Dr. Johannes Wagener
      • Dept. Pharmaceutical Biosciences, Uppsala University, Sweden
      • Prof. Johan Åqvist
      • Dr. Martin Nervall
      • Göran Wallin
      • Global Safety Assessment, AstraZeneca, Mölndal Sweden
      • Dr. Scott Boyer
      • Ernst Ahlberg Helgee
      • Van Drie Research LLC, MA, US
      • Dr. John Van Drie
      • Indiana University, IN, USA
      • Dr. Rajarshi Guha
      • Others
      • Dr. Jerome Pansanel
      • … and all others for contributing code, feature requests, bug reports, proposals, and comments!
    • 20. Thank you!
    • 21. Supporting slides
    • 22. Bioclipse Decision Support: Safety assessment Near-real time predictions
    • 23. Bioclipse Decision Support: Interpretation of models Interpret results graphically
    • 24. Bioclipse Decision Support: Optimize problematic regions Optimization invokes an XMPP service (long-running job)
    • 25. Bioclipse Decision Support: Inspect optimized structures Upon completion, results are opened for inspection
    • 26. Bioclipse Decision Support: Multiple Molecules Batch processing with overview
    • 27. Bioclipse Decision Support: Report generation Integrated report generation (export to Excel, Word, ppt, pdf, etc)
    • 28. MetaPrint2D: Site-of-metabolism prediction L. Carlsson, O. Spjuth, S. Adams, R. C. Glen, and S. Boyer.   Use of historic metabolic biotransformation data as a means of anticipating metabolic sites using metaprint2d and bioclipse . Manuscript in preparation.
    • 29. MetaPrint2D: Site-of-metabolism prediction Predict multiple structures L. Carlsson, O. Spjuth, S. Adams, R. C. Glen, and S. Boyer.   Use of historic metabolic biotransformation data as a means of anticipating metabolic sites using metaprint2d and bioclipse . Manuscript in preparation.
    • 30. Standardized QSAR in Bioclipse O. Spjuth, E. L. Willighagen, R. Guha, and J. E. S. Wikberg. Towards interoperable and reproducible QSAR analyses: Exchange of data sets. Manuscript in preparation.