B-Fabric for Switzerland Generalizing B-Fabric towards an Infrastructure for Collaborative Research in Switzerland Dr.
Download ReportTranscript B-Fabric for Switzerland Generalizing B-Fabric towards an Infrastructure for Collaborative Research in Switzerland Dr.
Slide 1
B-Fabric for Switzerland
Generalizing B-Fabric towards an Infrastructure for
Collaborative Research in Switzerland
Dr. Can Türker (Functional Genomics Center Zurich)
·
· · · [email protected]
·
· · · Bern, January 2010
·
Slide 2
B-Fabric: The FGCZ Approach to Data Management and Integration
··· 2
Slide 3
B-Fabric from the User’s Perspective
Functionality
Benefits
• Register samples/extracts
•
Secure, long-term data storage
• Import and annotate data files
•
Easy web-based data access
• One-click access to all “my” data
•
Fast access to relevant data
• Browse data network
•
Data reuse
• Quick/Advanced search
•
Reduced annotation work through
automatic export to external marts
•
Access-controlled data sharing
•
Increased data quality
•
Generation of reports etc.
•
Reproducibility of research results
• Export and download data
• Direct link to open tasks
• Run external applications
• Manage annotations
··· 3
Slide 4
B-Fabric Architecture
Scientific Data Marts
• Rosetta Resolver
• Mascot Integra
User PCs
• Data Evaluation
External Data Stores
Instrument PCs
• Affymetrix GeneChip
• ABI MALDI TOF/TOF
• LTQ-Orbitrap
Workhorses
Frontend
• Messaging
• Copier
• Indexer
• Searcher
• Grid Engine Worker
• Web Portal
• Workflow
• Messaging
• Logging
LogicalImport
B-Fabric
Database
SGEExecutable
Registered
Applications
Computing
Clusters
• Sun Grid Engine
AffymetrixImport
Completely based on open
source technologies
Implementation started in 2005
Running in daily business at FGCZ
since 2007
B-Fabric
B-Fabric
Repositories
Users
1559
Institutes
225
Organizations
59
Projects
756
Extracts
3699
Workunits (experiments)
24108
FGCZ B-Fabric
Deployment
January 2010
··· 4
Slide 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
Slide 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
Slide 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
B-Fabric
EAWAG
B-Fabric
··· 7
Slide 8
Task: Ad-hoc coupling of data sources
··· 8
Slide 9
Project Milestones/Deliveries
Mile- Title
stone
Project Start
1
Organization of Project Kick-off Meeting
2
Setting up a web page for project documentation
3
Concept for ad-hoc integration of external data sources
4
Implementing & Testing ad-hoc coupling of data sources
5
Quarterly Progress Report
6
Coupling selected external data sources from EAWAG
7
B-Fabric Demonstration
8
Quarterly Progress Report
9
Conception of a role-based access model
10
Quarterly Progress Report
11
Implementing & Testing the role-based access model
12
Concept for Authentication via SwitchAAI Shibboleth
13
Annual Progress Report & Project Meeting
14
Implementing & Testing SwitchAAI Shibboleth-based Authentication
15
Deployment and Evaluation of B-Fabric at IMSB
16
Quarterly Progress Report
17
Revision & Generalization of the annotation management
18
Quarterly Progress Report
19
Implementing & Testing of the annotation management
20
Evaluation of Generalized Annotation management
21
Quarterly Progress Report
22
B-Fabric Demonstration
23
B-Fabric Publication
24
Final Revisions & Bugfixing
25
B-Fabric User Manual & FAQ
26
Final Project Report & Project Meeting
Project Finish
Date Due Comment
01.06.09
June 09
June 09
31.07.09
30.09.09
Sep 09
30.11.09
Dec 09
Dec 09
31.01.10
Mar 10
31.05.10
30.06.10
Jun 10
31.07.10
31.08.10
Sep 10
31.10.10
Dec 10
28.02.11
31.03.11
Mar 11
May 11
May 11
31.05.11
31.05.11
June 11
31.05.11
Official Project Start
Kick-off Meeting bringing together all project participants/collaborators
Deliverable: Project Web Page
Deliverable: Specification for ad-hoc coupling of external data sources
Deliverable: B-Fabric with support for ad-hoc data source coupling
Deliverable: Progress Report
Deliverable: Selected EAWAG data resources are coupled with B-Fabric
Public B-Fabric Demo
Deliverable: Progress Report
Deliverable: Specification of a role-based access model for B-Fabric
Deliverable: Progress Report
Deliverable: B-Fabric supporting a role-based access model
Deliverable: Specification of the Integration of SwitchAAI Shibboleth into B-Fabric
Meeting Goal: evaluating project state and achievements and defining actions if needed
Deliverable: B-Fabric with support for SwitchAAI Shibboleth-based authentication
Deliverable: B-Fabric running and evaluated at IMSB
Deliverable: Progress Report
Deliverable: Specification of the generalized annotation management
Deliverable: Progress Report
Deliverable: B-Fabric with generalized annotation management feature
Deliverable: Evaluation report on B-Fabric running at FGCZ/IMSB
Deliverable: Progress Report
Public B-Fabric Demo
Paper(s) on B-Fabric accepted for presentation at conferences and workshops, resp.
Deliverable: Final B-Fabric Version
Deliverable: B-Fabric User Manual and FAQ
Summary and presentation of the results of this project
Official Project Finish
··· 9
Slide 10
People Behind B-Fabric
Prof. Ralph Schlapbach
FGCZ Scientific Director
B-Fabric Initiator & Sponsor
Dieter Joho
B-Fabric
Design & Development
Dr. Can Türker
B-Fabric
Project Leader
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
· · · 10
B-Fabric for Switzerland
Generalizing B-Fabric towards an Infrastructure for
Collaborative Research in Switzerland
Dr. Can Türker (Functional Genomics Center Zurich)
·
· · · [email protected]
·
· · · Bern, January 2010
·
Slide 2
B-Fabric: The FGCZ Approach to Data Management and Integration
··· 2
Slide 3
B-Fabric from the User’s Perspective
Functionality
Benefits
• Register samples/extracts
•
Secure, long-term data storage
• Import and annotate data files
•
Easy web-based data access
• One-click access to all “my” data
•
Fast access to relevant data
• Browse data network
•
Data reuse
• Quick/Advanced search
•
Reduced annotation work through
automatic export to external marts
•
Access-controlled data sharing
•
Increased data quality
•
Generation of reports etc.
•
Reproducibility of research results
• Export and download data
• Direct link to open tasks
• Run external applications
• Manage annotations
··· 3
Slide 4
B-Fabric Architecture
Scientific Data Marts
• Rosetta Resolver
• Mascot Integra
User PCs
• Data Evaluation
External Data Stores
Instrument PCs
• Affymetrix GeneChip
• ABI MALDI TOF/TOF
• LTQ-Orbitrap
Workhorses
Frontend
• Messaging
• Copier
• Indexer
• Searcher
• Grid Engine Worker
• Web Portal
• Workflow
• Messaging
• Logging
LogicalImport
B-Fabric
Database
SGEExecutable
Registered
Applications
Computing
Clusters
• Sun Grid Engine
AffymetrixImport
Completely based on open
source technologies
Implementation started in 2005
Running in daily business at FGCZ
since 2007
B-Fabric
B-Fabric
Repositories
Users
1559
Institutes
225
Organizations
59
Projects
756
Extracts
3699
Workunits (experiments)
24108
FGCZ B-Fabric
Deployment
January 2010
··· 4
Slide 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
Slide 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
Slide 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
B-Fabric
EAWAG
B-Fabric
··· 7
Slide 8
Task: Ad-hoc coupling of data sources
··· 8
Slide 9
Project Milestones/Deliveries
Mile- Title
stone
Project Start
1
Organization of Project Kick-off Meeting
2
Setting up a web page for project documentation
3
Concept for ad-hoc integration of external data sources
4
Implementing & Testing ad-hoc coupling of data sources
5
Quarterly Progress Report
6
Coupling selected external data sources from EAWAG
7
B-Fabric Demonstration
8
Quarterly Progress Report
9
Conception of a role-based access model
10
Quarterly Progress Report
11
Implementing & Testing the role-based access model
12
Concept for Authentication via SwitchAAI Shibboleth
13
Annual Progress Report & Project Meeting
14
Implementing & Testing SwitchAAI Shibboleth-based Authentication
15
Deployment and Evaluation of B-Fabric at IMSB
16
Quarterly Progress Report
17
Revision & Generalization of the annotation management
18
Quarterly Progress Report
19
Implementing & Testing of the annotation management
20
Evaluation of Generalized Annotation management
21
Quarterly Progress Report
22
B-Fabric Demonstration
23
B-Fabric Publication
24
Final Revisions & Bugfixing
25
B-Fabric User Manual & FAQ
26
Final Project Report & Project Meeting
Project Finish
Date Due Comment
01.06.09
June 09
June 09
31.07.09
30.09.09
Sep 09
30.11.09
Dec 09
Dec 09
31.01.10
Mar 10
31.05.10
30.06.10
Jun 10
31.07.10
31.08.10
Sep 10
31.10.10
Dec 10
28.02.11
31.03.11
Mar 11
May 11
May 11
31.05.11
31.05.11
June 11
31.05.11
Official Project Start
Kick-off Meeting bringing together all project participants/collaborators
Deliverable: Project Web Page
Deliverable: Specification for ad-hoc coupling of external data sources
Deliverable: B-Fabric with support for ad-hoc data source coupling
Deliverable: Progress Report
Deliverable: Selected EAWAG data resources are coupled with B-Fabric
Public B-Fabric Demo
Deliverable: Progress Report
Deliverable: Specification of a role-based access model for B-Fabric
Deliverable: Progress Report
Deliverable: B-Fabric supporting a role-based access model
Deliverable: Specification of the Integration of SwitchAAI Shibboleth into B-Fabric
Meeting Goal: evaluating project state and achievements and defining actions if needed
Deliverable: B-Fabric with support for SwitchAAI Shibboleth-based authentication
Deliverable: B-Fabric running and evaluated at IMSB
Deliverable: Progress Report
Deliverable: Specification of the generalized annotation management
Deliverable: Progress Report
Deliverable: B-Fabric with generalized annotation management feature
Deliverable: Evaluation report on B-Fabric running at FGCZ/IMSB
Deliverable: Progress Report
Public B-Fabric Demo
Paper(s) on B-Fabric accepted for presentation at conferences and workshops, resp.
Deliverable: Final B-Fabric Version
Deliverable: B-Fabric User Manual and FAQ
Summary and presentation of the results of this project
Official Project Finish
··· 9
Slide 10
People Behind B-Fabric
Prof. Ralph Schlapbach
FGCZ Scientific Director
B-Fabric Initiator & Sponsor
Dieter Joho
B-Fabric
Design & Development
Dr. Can Türker
B-Fabric
Project Leader
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
· · · 10