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. 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. 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
- 6. Component-based architecture Bioclipse Proteochemometrics 2D 3D Data analysis Spectra Molecular dynamics
- 8. Other Eclipse-applications: Maestro – NASA Space Mission Management
- 9. Other Eclipse-applications: Dutch railways
- 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
- 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
- 20. Thank you!
- 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.
Editor's Notes
- 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