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Dr. Can Türker (Functional Genomics Center Zurich) B-Fabric for Switzerland Generalizing B-Fabric...
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Transcript of Dr. Can Türker (Functional Genomics Center Zurich) B-Fabric for Switzerland Generalizing B-Fabric...
Dr. Can Türker (Functional Genomics Center Zurich)
B-Fabric for Switzerland Generalizing B-Fabric towards an Infrastructure for Collaborative Research in Switzerland
· · · · [email protected]
· · · · Bern, January 2010
·
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
B-Fabric Architecture
· · · 4
RegisteredApplications
B-FabricRepositories
B-Fabric
Workhorses• Messaging• Copier• Indexer• Searcher• Grid Engine Worker
Frontend• Web Portal
• Workflow• Messaging
• Logging
B-FabricDatabase
External Data Stores
User PCs• Data Evaluation
Instrument PCs• Affymetrix GeneChip• ABI MALDI TOF/TOF
• LTQ-Orbitrap
Scientific Data Marts• Rosetta Resolver
• Mascot Integra
ComputingClusters
• Sun Grid Engine
LogicalImportLogicalImport
SGEExecutableSGEExecutable
AffymetrixImportAffymetrixImport
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 2007FGCZ B-FabricDeploymentJanuary 2010
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
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
• 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
EAWAG FGCZ
Collaborators
· · · 7
B-Fabric
IMSB
B-Fabric
Project Milestones/Deliveries
· · · 9
Mile-
stone
Title Date Due Comment
Project Start 01.06.09 Official Project Start
1 Organization of Project Kick-off Meeting June 09 Kick-off Meeting bringing together all project participants/collaborators
2 Setting up a web page for project documentation June 09 Deliverable: Project Web Page
3 Concept for ad-hoc integration of external data sources 31.07.09 Deliverable: Specification for ad-hoc coupling of external data sources
4 Implementing & Testing ad-hoc coupling of data sources 30.09.09 Deliverable: B-Fabric with support for ad-hoc data source coupling
5 Quarterly Progress Report Sep 09 Deliverable: Progress Report
6 Coupling selected external data sources from EAWAG 30.11.09 Deliverable: Selected EAWAG data resources are coupled with B-Fabric
7 B-Fabric Demonstration Dec 09 Public B-Fabric Demo
8 Quarterly Progress Report Dec 09 Deliverable: Progress Report
9 Conception of a role-based access model 31.01.10 Deliverable: Specification of a role-based access model for B-Fabric
10 Quarterly Progress Report Mar 10 Deliverable: Progress Report
11 Implementing & Testing the role-based access model 31.05.10 Deliverable: B-Fabric supporting a role-based access model
12 Concept for Authentication via SwitchAAI Shibboleth 30.06.10 Deliverable: Specification of the Integration of SwitchAAI Shibboleth into B-Fabric
13 Annual Progress Report & Project Meeting Jun 10 Meeting Goal: evaluating project state and achievements and defining actions if
needed
14 Implementing & Testing SwitchAAI Shibboleth-based Authentication 31.07.10 Deliverable: B-Fabric with support for SwitchAAI Shibboleth-based authentication
15 Deployment and Evaluation of B-Fabric at IMSB 31.08.10 Deliverable: B-Fabric running and evaluated at IMSB
16 Quarterly Progress Report Sep 10 Deliverable: Progress Report
17 Revision & Generalization of the annotation management 31.10.10 Deliverable: Specification of the generalized annotation management
18 Quarterly Progress Report Dec 10 Deliverable: Progress Report
19 Implementing & Testing of the annotation management 28.02.11 Deliverable: B-Fabric with generalized annotation management feature
20 Evaluation of Generalized Annotation management 31.03.11 Deliverable: Evaluation report on B-Fabric running at FGCZ/IMSB
21 Quarterly Progress Report Mar 11 Deliverable: Progress Report
22 B-Fabric Demonstration May 11 Public B-Fabric Demo
23 B-Fabric Publication May 11 Paper(s) on B-Fabric accepted for presentation at conferences and workshops, resp.
24 Final Revisions & Bugfixing 31.05.11 Deliverable: Final B-Fabric Version
25 B-Fabric User Manual & FAQ 31.05.11 Deliverable: B-Fabric User Manual and FAQ
26 Final Project Report & Project Meeting June 11 Summary and presentation of the results of this project
Project Finish 31.05.11 Official Project Finish
People Behind B-Fabric
· · · 10
Prof. Ralph SchlapbachFGCZ Scientific Director B-Fabric Initiator & Sponsor
Dr. Can TürkerB-Fabric
Project Leader
Dieter JohoB-Fabric
Design & Development
Marco SchmidtFGCZ IT Coordinator (Admin/Support)
FGCZ Bio-Informatics Experts Dr. Christian Panse, Simon Barkow Oesterreicher, Dr. Hubert RehrauerFeeding and Coupling B-Fabric with External Applications
Dr. Fuat AkalB-Fabric
Design & Development
Further B-Fabric
Developers:
Christian DeckerMichael Fetzer
Benedikt Thelen
Felix KnechtGiacomo Pati
(Otego AG Zurich)