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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
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Building a flexible infrastructure with Bioclipse, open source, and federated
cloud services
1 Dept. Pharmaceutical Biosciences, Uppsala University, Sweden2 Global Safety Assessment, AstraZeneca R&D, Sweden
Ola Spjuth1 and Lars Carlsson2
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
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.
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…
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
Component-based architecture
Bioclipse
Proteochemometrics
2D
3DData analysis
Spectra
Molecular dynamics
Bioclipse
• Use the well-established, mature Eclipse architecture in the life sciences
Other Eclipse-applications: Maestro – NASA Space Mission Management
Other Eclipse-applications:
Dutch railways
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
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
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
Bioclipse and Drug Discovery
Meets computational and reporting demands at various stages in the drug-discovery process
DISCOVERY DEVELOPMENT
LI FTIMLO CD
Batch/scripting Tailored plugins
Rich content
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
Ames Risk AssessmentSystem
• Fully Automated QSAR
• Full Read-Across
• QSAR Interpretation
• Structural Warnings
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
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
Genetta Soft AB
Professional consultancy services for Bioclipse• Custom-tailored releases• Develop and integrate custom functionality• Support, documentation, education
www.genettasoft.com
AcknowledgementsDept. 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!
Thank you!
Supporting slides
Bioclipse Decision Support:
Safety assessment
Near-real time predictions
Bioclipse Decision Support:
Interpretation of models
Interpret results graphically
Bioclipse Decision Support:
Optimize problematic regions
Optimization invokes an XMPP service (long-running job)
Bioclipse Decision Support:
Inspect optimized structures
Upon completion, results are opened for inspection
Bioclipse Decision Support:
Multiple Molecules
Batch processing with overview
Bioclipse Decision Support:
Report generation
Integrated report generation (export to Excel, Word, ppt, pdf, etc)
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.
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.
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.