1. Dr. Can Türker (Functional Genomics Center Zurich) B-Fabric for Switzerland Generalizing B-Fabric towards an Infrastructure for Collaborative Research in Switzerland · · · · tuerker@fgcz.ethz.ch · · · · Bern, January 2010 ·

2. · · · 2 B-Fabric: The FGCZ Approach to Data Management and Integration

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 · · · 3

4. B-Fabric Architecture · · · 4 Registered Applications B-Fabric Repositories B-Fabric Workhorses Messaging Copier Indexer Searcher Grid Engine Worker Frontend Web Portal Workflow Messaging Logging B-Fabric Database B-Fabric Database External Data Stores User PCs Data Evaluation Instrument PCs Affymetrix GeneChip ABI MALDI TOF/TOF LTQ-Orbitrap Scientific Data Marts Rosetta Resolver Mascot Integra Computing Clusters Sun Grid Engine LogicalImport SGEExecutable AffymetrixImport  Completely based on open source technologies  Implementation started in 2005  Running in daily business at FGCZ since 2007  Completely based on open source technologies  Implementation started in 2005  Running in daily business at FGCZ since 2007 Users1559 Institutes225 Organizations59 Projects756 Extracts3699 Workunits (experiments)24108 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 · · · 5

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 · · · 6

7. 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 EAWAGFGCZ Collaborators · · · 7 B-Fabric IMSB B-Fabric

8. Task: Ad-hoc coupling of data sources · · · 8

9. Project Milestones/Deliveries · · · 9 Mile- stone TitleDate DueComment Project Start01.06.09Official Project Start 1Organization of Project Kick-off MeetingJune 09Kick-off Meeting bringing together all project participants/collaborators 2Setting up a web page for project documentationJune 09Deliverable: Project Web Page 3Concept for ad-hoc integration of external data sources31.07.09Deliverable: Specification for ad-hoc coupling of external data sources 4Implementing & Testing ad-hoc coupling of data sources30.09.09Deliverable: B-Fabric with support for ad-hoc data source coupling 5Quarterly Progress ReportSep 09Deliverable: Progress Report 6Coupling selected external data sources from EAWAG30.11.09Deliverable: Selected EAWAG data resources are coupled with B-Fabric 7B-Fabric DemonstrationDec 09Public B-Fabric Demo 8Quarterly Progress ReportDec 09Deliverable: Progress Report 9Conception of a role-based access model31.01.10Deliverable: Specification of a role-based access model for B-Fabric 10Quarterly Progress ReportMar 10Deliverable: Progress Report 11Implementing & Testing the role-based access model31.05.10Deliverable: B-Fabric supporting a role-based access model 12Concept for Authentication via SwitchAAI Shibboleth30.06.10Deliverable: Specification of the Integration of SwitchAAI Shibboleth into B-Fabric 13Annual Progress Report & Project MeetingJun 10Meeting Goal: evaluating project state and achievements and defining actions if needed 14Implementing & Testing SwitchAAI Shibboleth-based Authentication31.07.10Deliverable: B-Fabric with support for SwitchAAI Shibboleth-based authentication 15Deployment and Evaluation of B-Fabric at IMSB31.08.10Deliverable: B-Fabric running and evaluated at IMSB 16Quarterly Progress ReportSep 10Deliverable: Progress Report 17Revision & Generalization of the annotation management31.10.10Deliverable: Specification of the generalized annotation management 18Quarterly Progress ReportDec 10Deliverable: Progress Report 19Implementing & Testing of the annotation management28.02.11Deliverable: B-Fabric with generalized annotation management feature 20Evaluation of Generalized Annotation management31.03.11Deliverable: Evaluation report on B-Fabric running at FGCZ/IMSB 21Quarterly Progress ReportMar 11Deliverable: Progress Report 22B-Fabric DemonstrationMay 11Public B-Fabric Demo 23B-Fabric PublicationMay 11Paper(s) on B-Fabric accepted for presentation at conferences and workshops, resp. 24Final Revisions & Bugfixing31.05.11Deliverable: Final B-Fabric Version 25B-Fabric User Manual & FAQ31.05.11Deliverable: B-Fabric User Manual and FAQ 26Final Project Report & Project MeetingJune 11Summary and presentation of the results of this project Project Finish31.05.11Official Project Finish

10. People Behind B-Fabric · · · 10 Prof. Ralph Schlapbach FGCZ Scientific Director B-Fabric Initiator & Sponsor Dr. Can Türker B-Fabric Project Leader Dieter Joho B-Fabric Design & Development 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 Dr. Fuat Akal B-Fabric Design & Development Further B-Fabric Developers: Christian Decker Michael Fetzer Benedikt Thelen Felix Knecht Giacomo Pati (Otego AG Zurich)