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

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

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

Task: Ad-hoc coupling of data sources

· · · 8

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)