MediGRID Grid Computing for Medicine and Life Sciences
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1 MediGRID Grid Computing for Medicine and Life Sciences Anette Weisbecker, Fraunhofer IAO, Stuttgart Otto Rienhoff, Georg-August-Universität, Göttingen International Symposium on Grid Computing Taipei, 28 th March 2007
2 Overview MediGRID Structure and Partners Architecture and Middleware Data Access Portal Application Classes and Applications Further Steps Seite 2
3 Structure of MediGRID Data Data... Data Metadata Metadata Metadata Coordination Classic Bioinformatics Access Control Ontology Resource Fusion Different applications in application classes Biomedical Informatics Medical Image Processing Middleware Clinical Research Others, e.g. forestry or humanities escience, Security, Interationalisation D-GRID Integration Project Seite 3
4 MediGRID - Partners Prof. Dr. Otto Rienhoff (Spokesman of Consortium) Universität Göttingen, Abteilung Medizinische Informatik Telematikplattform für Medizinische Forschungsnetze e.v., Berlin, Sebastian C. Semler Universität Göttingen, Abteilung Medizinische Informatik, Prof. Ulrich Sax Charité, Universitätsmedizin Berlin, Institut für Medizinische Informatik, Biometrie und Epidemiologie, Prof. Thomas Tolxdorff, Dr. Dagmar Krefting Universitätsklinikum Schleswig-Holstein, Institut für Klinische Molekularbiologie, Dr. Jochen Hampe Universität Marburg, Klinik für Innere Medizin mit Schwerpunkt Pneumologie, Prof. Thomas Penzel Universität Leipzig, Institut für Medizinische Informatik, Statistik und Epidemiologie; Institut für Informatik, Prof. Markus Löffler, Prof. Erhard Rahm Fraunhofer-Gesellschaft; Fraunhofer IAO, Fraunhofer FIRST, Priv.-Doz. Dr.-Ing. Anette Weisbecker Konrad-Zuse-Zentrum für Informationstechnik, Dr. Thomas Steinke Seite 4
5 Software Architecture User/ Application Developer Portal CLI Unicore Client Grid-API (GAT) VOMRS VOMRS MediGrid Applications Bioinformatics Medical Image Processing Biomedical Ontologies Clinical Research MediGrid Spezific Services Workflow Management (GWES) Resource Management (D-GRDL) Data Management SRB OGSA-DAI Security Grid Services Integration Layer GLOBUS 4 Resource Monitoring Resource Accounting UNICORE Job Management Data Access Metadata Mgmt. Dataflow Monitoring Resources & local Services open Database CPU Storage + Archives protected Database CPU Storage+Archives MediGRID Middleware MediGRID Applications optional Seite 5
6 MediGRID Resources and Grid Services MediGRID User MediGRID Developer Databases via OGSA-DAI MediGRID Administrator Grid Certificate MediGRID Applications Disk Storage MediGRID Portal Storage via SRB User and VO Management via VOMRS Archive Storage Firewall Management Grid Workflow Execution Service central MediGRID Services Sensors and technical Devices Computing Nodes Metadata- Generation via GRDBD Monitoring Daemons Fluoroscope Tomographs Computers via Globus and Unicore (glite) Seite 6
7 Portal based Access to MediGRID MediGRID User MediGRID Developer Genome Sequence Analysis MediGRID Administrator Grid Certificate Statistical Analysis of Functional Brain Images SNP Selection Bioinformatics MediGRID Certificate Medical Image Processing 3D Prostate Biopsy Ontology Access Ontologies Virtual Vascular Surgery Standard Grid Portlets Developer Support Administration Credential Management Resource Monitoring File Browser Workflow Management D-GRDL Metadata Creation D-GRDL Metadata Management Resource Management Seite 7
8 Grid Workflows and Virtualisation Result Requirements: D-GRDL Resource Metadata Management (D-Grid) D-GRDL Management (D-Grid) GRDB Daemon (InstantGrid) Monitoring Data (Globus MDS + Ganglia) Input Parameter for Applications MediGRID Job-Initialisation Portal MediGRID Resources Automatic Resource Selection Workflow Initialisation Job Submission GWES GWES Grid Workflow Execution Service Seite 8
9 Data Virtualisation with Storage Resource Broker (SRB) Data Management and Data Virtualisation with in the Grid Abstraction Layer in Grid Filemanager move file logical no changes on logical view Physical Layer on Storage Resources Storage Resource A Storage Resource. B Storage Resource C Storage Resource D move file physical no changes of physical storing Requirements: Global IDs for Data in the Grid, Metadata Management, Solution: Storage Resource Broker Seite 9
10 Database Access via OGSA-DAI Database Connection and Database Access with in the Grid OGSA-DAI Service(s) WSRF Physical Layer: Database Query for a Term Gene Ontology DB Location A Distributed Database Query Human Disease DB Location C NCI Thesaurus DB Location B Database Queries independent from Storage Location Solution: OGSA-DAI Service Seite 10
11 Certificate based Usage via MediGRID Portal User PC MediGRID D-Grid D-Grid Grid CA CA CA Zertifikate Zertifikate Certificate 1. Portal 4. Grid Application Portlets Grid Certificate MyProxy Upload Tool Portal Credential Lifetime: 2 years Lifetime : 2 hours Advantage: Grid User do not need a Grid Comupter / no Middleware Installation Proxy Certificate MyProxy Server Lifetime : 7 days 1. Login at the portal and download the MPU tools via java webstart 2. Creation of a proxy certificate and Upload on the MyProxy Server 3. Creation of Credentials via the MediGRID portal 4. Usage of portal applictions, which need credentials Grid Resources and Applications Seite 11
12 MediGRID Portal MediGRID Portal is the central access to the applications for the user GridSphere GridPortlets Certificates for secure access Integration of medical applications Applications are callable as web services (Wrapper) Global identifier for transparent data access OGSA-DAI for connection of distributed databases Petri net based workflows for application processes Seite 12
13 MediGRID Application Classes with their Applications o Bioinformatics Genome Sequence Analysis SNPSelection: Single nucleotide polymorphisms selection RNAi: ribonucleic acid interference screening Sequorr: Sequence correlation o Medical Image Processing 3D Prostate Biopsy Statistical Analysis of Functional Brain Images Virtual Vascular Surgery o Clinical Research Analysis of clinical studies in neurology o Ontologies Integration of different ontologies with heterogeneous formats Seite 13
14 Further Steps Additional Applications and Application classes Enhanced and very enhanced security Auditabiltiy, Trackability, Access rights and Access control, Trust and Trust Delegation, Safety Anonymized Data, pseudonymized Data, identifying Data ehealth Services Service Engineering for identification and definition of services Accounting and Billing Business Models International cooperations Seite 14
15 Contact Thank you for your attention! Questions? Priv.-Doz. Dr.-Ing. habil. Anette Weisbecker Fraunhofer Institute for Industrial Engineering Nobelstraße Stuttgart, Germany Phone: Professor Dr. Otto Rienhoff Abteilung Medizinische Informatik, Georg-August-Universität Göttingen Robert-Koch-Strasse Göttingen, Germany Phone: Seite 15
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