Dr. Can Türker (Functional Genomics Center Zurich)

1. B-Fabric for SwitzerlandGeneralizing B-Fabric towards an Infrastructure for Collaborative Research in Switzerland Dr. Can Türker (Functional Genomics Center Zurich)

2. B-Fabric: The FGCZ Approach to Data Management and Integration Data Capture and Annotation Unified Web-based Data Access/Provision Secure Transparent Data Storage Run/Feed External Applications Ad-hoc Transparent Information Retrieval Data Curation

3. B-Fabric from the User’s Perspective Functionality • Register samples/extracts • Import and annotate data files • One-click access to all “my” data • Browse data network • Quick/Advanced search • Export and download data • Direct link to open tasks • Run external applications • Manage annotations Benefits • Secure, long-term data storage • Easy web-based data access • Fast access to relevant data • Data reuse • Reduced annotation work through automatic export to external marts • Access-controlled data sharing • Increased data quality • Generation of reports etc. • Reproducibility of research results

4. B-Fabric Architecture External Data Stores • Instrument PCs • Affymetrix GeneChip • ABI MALDI TOF/TOF • LTQ-Orbitrap • Scientific Data Marts • Rosetta Resolver • Mascot Integra • Computing • Clusters • Sun Grid Engine • User PCs • Data Evaluation • Workhorses • Messaging • Copier • Indexer • Searcher • Grid Engine Worker • Frontend • Web Portal • Workflow • Messaging • Logging B-Fabric Database LogicalImport B-Fabric SGEExecutable B-Fabric Repositories Registered Applications AffymetrixImport • Completely based on open source technologies • Implementation started in 2005 • Running in daily business at FGCZ since 2007 FGCZ B-Fabric Deployment January 2010

5. Switch Project: “B-Fabric for Switzerland” • Project Number: UZH.5 • Start/End: June 2009/May 2011 • Goal: open and generalize B-Fabric such that a broader research community in Switzerland can profit from it • Two essential application scenarios: • Local deployment and administration of B-Fabric in research groups with the required technical/human resources • Ad-hoc coupling of external data resources with an FGCZ B-Fabric instance for others

6. Project Tasks: B-Fabric Generalization w.r.t. • Ad-hoc coupling of data sources • Declarative, dynamic coupling of external data resources with B-Fabric • Fine-grained, dynamically adaptable access management • Role-based access model • Fine-grained access rights • Ad-hoc granting/revoking access rights • Switch AAI Shibboleth-based authorization and authentication • Switch AAI/Shibboleth-based access to B-Fabric • Advanced annotation management: • Support optional links to external annotation vocabularies • Synchronization with external annotation vocabularies • Extend annotation review/release process

7. Collaborators • Demonstrate usefulness of B-Fabric outside FGCZ • Institute of Molecular Systems Biology (IMSB), ETH Zurich: Dr. Lars Malmström • Evaluating a locally deployed instance of B-Fabric • Couple representative IMSB data sources with this IMSB B-Fabric instance • EAWAG Swiss Federal Institute of Aquatic Science and Technology: Dr. Marc Suter • Evaluating ad-hoc coupling of external data sources • Couple selected EAWAG data sources with an FGCZ B-Fabric instance IMSB FGCZ EAWAG B-Fabric B-Fabric

8. Task: Ad-hoc coupling of data sources

9. Project Milestones/Deliveries

10. People Behind B-Fabric Prof. Ralph Schlapbach FGCZ Scientific Director B-Fabric Initiator & Sponsor Dr. Can Türker B-Fabric Project Leader Dieter Joho B-Fabric Design & Development Dr. Fuat Akal B-Fabric Design & Development Further B-Fabric Developers: Christian Decker Michael Fetzer Benedikt Thelen Felix Knecht Giacomo Pati (Otego AG Zurich) Marco Schmidt FGCZ IT Coordinator (Admin/Support) FGCZ Bio-Informatics Experts Dr. Christian Panse, Simon Barkow Oesterreicher, Dr. Hubert Rehrauer Feeding and Coupling B-Fabric with External Applications