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NeuroLOG ANR-06-TLOG-024
Software technologies for integration of process and data in medical imaging
http://neurolog.polytech.unice.fr
A transitional middleware to support neurosciences on the EGEE grid
Alban Gaignard, Javier Rojas Balderrama,
Franck Michel, David Godard,
Diane Lingrand, Johan Montagnat
CNRS – I3S Laboratory
Sophia-Antipolis, France
4th EGEE User Forum
Catania – Sicily - Italy
NeuroLOG, 4th EGEE User Forum, A. Gaignard, J. Montagnat 2
Software technologies for integration of process, data and knowledge in medical imaging
NeuroLOG ANR-06-TLOG-024
Motivations
• Target neuroscientist community– Neuroscience has a major societal impact
• Understanding and improving healthcare of brain diseases• Discovering brain functions
– “Good candidate” for grid technologies• Huge consumer of computational resources (neuroimaging)• Collaborative work, multidisciplinarity → transdisciplinarity
• Ease multi-centric studies– Large population datasets, growing size and heterogeneity– Complex analysis pipeline, inter-operability – Distribution in a wide scale environment
• Consider existing environments !– Processing tools, databases, practices
NeuroLOG, 4th EGEE User Forum, A. Gaignard, J. Montagnat 3
Software technologies for integration of process, data and knowledge in medical imaging
NeuroLOG ANR-06-TLOG-024
Approach 1/2
• Leverage grid technologies:– Bridge between EGEE and neuroscience research centers– Federating existing data– Repository of processing tools– Virtual Organizations concepts
• Knowledge representation– Design of a domain ontology (rich queries and
representation)
• Software integration– Data integration (raw files, metadata, semantic data)
– Application workflows• Perspectives of Interaction between WFs and data
– Usability of tools by non computer experts … and even less grid technologies experts
NeuroLOG, 4th EGEE User Forum, A. Gaignard, J. Montagnat 4
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NeuroLOG ANR-06-TLOG-024
Approach 2/2
• Collaborative Neuroscience – Focus on 3 clinical applications
• Multiple sclerosis• Brain stroke• Brain tumours
– Commonalities• Neuroimages (MR)• Descriptive information• Processing tools: Registration, Skull stripping,
Normalization, Tissues classification
– Infrastructure used to • share databases• share and evaluate processing tools
NeuroLOG, 4th EGEE User Forum, A. Gaignard, J. Montagnat 5
Software technologies for integration of process, data and knowledge in medical imaging
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Design: bridging the gap
NeuroLOG, 4th EGEE User Forum, A. Gaignard, J. Montagnat 6
Software technologies for integration of process, data and knowledge in medical imaging
NeuroLOG ANR-06-TLOG-024
Design: General Architecture
NeuroLOG, 4th EGEE User Forum, A. Gaignard, J. Montagnat 7
Software technologies for integration of process, data and knowledge in medical imaging
NeuroLOG ANR-06-TLOG-024
Data Management 1/5
NeuroLOG, 4th EGEE User Forum, A. Gaignard, J. Montagnat 8
Software technologies for integration of process, data and knowledge in medical imaging
NeuroLOG ANR-06-TLOG-024
Data Management 2/5
• Data Federator tool (Business Object - SAP)
Data Federator Server
OracleDatabase
MySQL Virtual Source Table
VirtualTargetTable
Client Application
TXT
Files
Connector
JDBC (Java Database Connectivity)
Local File System, FTP,
HTTP, …
JDBCData Federator mappings
NeuroLOG, 4th EGEE User Forum, A. Gaignard, J. Montagnat 9
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NeuroLOG ANR-06-TLOG-024
Data Management 3/5
• Interoperability: variability in metadata schemas
NeuroLOG, 4th EGEE User Forum, A. Gaignard, J. Montagnat 10
Software technologies for integration of process, data and knowledge in medical imaging
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Data Management 4/5
• Domain ontologies – Medical data (e.g. image type, associated medical record,
neuro-psychological tests)– Processing tools (e.g. algorithm kinds, inputs and outputs)– Related relational database schemas
• Semi-automatic semantic data collections– Analyze DICOM headers– METAmorphose: relational DB to RDF conversion– OWL Lite representation
• Semantic queries– CORESE: conceptual graph-based query engine– SPARQL query language
NeuroLOG, 4th EGEE User Forum, A. Gaignard, J. Montagnat 11
Software technologies for integration of process, data and knowledge in medical imaging
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Data Management 5/5
Relational implementation of the ontology
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Software technologies for integration of process, data and knowledge in medical imaging
NeuroLOG ANR-06-TLOG-024
Computing Distribution 1/3
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Software technologies for integration of process, data and knowledge in medical imaging
NeuroLOG ANR-06-TLOG-024
Computing Distribution 2/3
• Workload management: gLite• Application description & enactment: MOTEUR• Application codes deployment: WS wrapper + WS
containers• Application codes packaging & publication: OSGi-like
Gridprotocol
Grid ResourcesGrid
GatewayServicewrapper
SOAP Grid API
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NeuroLOG middleware
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Deployment
Execution
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PS
2S
3
Q
S4
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Computing Distribution 3/3
Interoperability: variability in tools
NeuroLOG, 4th EGEE User Forum, A. Gaignard, J. Montagnat 15
Software technologies for integration of process, data and knowledge in medical imaging
NeuroLOG ANR-06-TLOG-024
Security and Administration
NeuroLOG, 4th EGEE User Forum, A. Gaignard, J. Montagnat 16
Software technologies for integration of process, data and knowledge in medical imaging
NeuroLOG ANR-06-TLOG-024
Secured Collaborations 1/4
• Collaboration in a Competitive/Sensitive environment• Security Requirements
– Medical data protection– Autonomous site administration (no super-admin)– Multi-centric studies → Distributed access control
• Authentication: – Multiple X509 credentials per user (EGEE / NeuroLOG)– User registration through each Site Certification Authority
• Data access control– Partly conflicting interests : Autonomy vs Collaboration– Sharing through federation-wide roles– Owners of data keep the control over its data
NeuroLOG, 4th EGEE User Forum, A. Gaignard, J. Montagnat 17
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Secured Collaborations 2/4
Network interoperability: cross-domain accessibility
NeuroLOG, 4th EGEE User Forum, A. Gaignard, J. Montagnat 18
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Secured Collaborations 3/4
Application interoperability: secured sharing use case
NeuroLOG, 4th EGEE User Forum, A. Gaignard, J. Montagnat 19
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NeuroLOG ANR-06-TLOG-024
Secured Collaborations 4/4
Application interoperability: distributed RBAC
NeuroLOG, 4th EGEE User Forum, A. Gaignard, J. Montagnat 20
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Conclusion
• Meeting neuroscientists expectations– Cope with legacy environment (interoperability issues)– Preserve sites autonomy, while enabling distributed studies– Strong data access control
• Transitional model towards HealthGrids– Foster the adoption of grid technologies– Bring grid infrastructures closer to the clinical centers– Bridging local and global resources
• Major challenge– Keep it simple... for installation, configuration and use
http://neurolog.polytech.unice.fr