Attività grid di Biomedicina in Italia e in Europa Livia Torterolo livia.torterolo@unige.it BIO-Lab, DIST University of Genoa

Grid Open Day, 13 marzo 2007, Catania About Bio-Lab … BIO-Lab: Laboratory for Bioimages and Bioengineering http://www.bio.dist.unige.it Staff: Francesco Beltrame, Prof (ICT-CNR) Marco Fato, PhD, Assoc. Prof 1 senior consultant, 2 post-doc, 6 PhD students Collaborations Research centers (CNR, INFN, IST, CBA, etc…) Companies (NICE, Aitek, La Traccia, Ansaldo Superconductors, etc…) Hospital testbeds (S. Martino and G. Gaslini, Genoa and S. Raffaele, Milan) University of Genoa Grid Open Day, 13 marzo 2007, Catania

Biolab Research Activities Health & ICT Bioimages Tissue engineering Bioinformatics Grid Computing Grid Open Day, 13 marzo 2007, Catania

Grid Open Day, 13 marzo 2007, Catania Italian GRID projects GRID.IT: An Italian National Research Council Project on Grid Computing http://www.grid.it LITBIO: Laboratory of Interdisciplinary Technologies in Bioinformatics http://www.litbio.it BMPortal: BioMedical Portal http://grid.bio.dist.unige.it (portal development in progress…) Grid Open Day, 13 marzo 2007, Catania

European GRID projects GRIDCOORD: Co-ordinating Europe-wide Initiatives in Grid Research http://www.gridcoord.org BIOINFOGRID: Bioinformatics Grid Application for life science http://www.bioinfogrid.eu EGEE: Enabling Grids for E-sciencE NA4 generic applications NA4 biomedical applications http://www.eu-egee.org Grid Open Day, 13 marzo 2007, Catania

Computing & Data Grid: gLite Workload Management Data Management and File Access tools gLite and GFAL API Logical File Names (LFN) LCG File Catalog (LFC): data registration into the catalog AMGA Metadata Catalog: metadata association to data Security Grid Open Day, 13 marzo 2007, Catania

Medical Imaging Application I Case Study: Grid Implementation of Statistical Parametric Mapping Analysis for the Early Diagnosis of Alzheimer Grid Open Day, 13 marzo 2007, Catania

Grid Open Day, 13 marzo 2007, Catania SPM working on Web www.neuroinf.it SET of CONTROLS 1 (PET, SPECT IMAGES) STATISTICAL TOOL (SPM) SET of CONTROLS 2 (PET, SPECT IMAGES) SET of CONTROLS 3 (PET, SPECT IMAGES) IMAGE of PATHOLOGICAL SUBJECT (PET or SPECT IMAGE) STATISTICAL ANALYSIS OF THE UPLOADED IMAGE SET of CONTROLS n (PET, SPECT IMAGES) Grid Open Day, 13 marzo 2007, Catania

Grid Open Day, 13 marzo 2007, Catania SPM: Why GRID? A large set of images of normal patients is required to be used for comparison PET and SPECT studies on normal subjects are very rare Images of patients are covered by privacy and security issues and for this reason they cannot be freely moved on the net or published by the centre that made the analysis. Grid Open Day, 13 marzo 2007, Catania

Grid Open Day, 13 marzo 2007, Catania SPM working on GRID ZOPE Portal Engine Upload image and select Management node gLite User Interface SPM Application Repository node gLite Computing Element Storage Element xrootd myproxy-get-delegation GFAL Job submission MyProxy Server LCG/gLite services Resource Broker AMGA LFC User node Grid Open Day, 13 marzo 2007, Catania

JOB submission & Data management ZOPE Portal Engine Upload image and select Management node gLite User Interface SPM Application Repository node gLite Computing Element Storage Element xrootd Job submission and management Remote file access Remote processing GFAL Job submission MyProxy Server LCG/gLite services Resource Broker AMGA LFC User node Grid Open Day, 13 marzo 2007, Catania

Grid Open Day, 13 marzo 2007, Catania Catalogue queries ZOPE Portal Engine Upload image and select Management node gLite User Interface SPM Application Repository node gLite Computing Element Storage Element xrootd Catalogue query Normal images selection JDL Generation Portal Engine ZOPE GFAL MyProxy Server LCG/gLite services Resource Broker AMGA LFC Job submission Upload image and select User node Grid Open Day, 13 marzo 2007, Catania

Microarray data analysis II Case Study: Linux version of dChip, one of the most complete and diffuse free software for the microarray data analysis dChip is a Windows GUI application for microarray data analysis: Linux porting Intermediate results standardization Parallelized and Gridified Composed of different modules: data set opening and normalization model based gene expression extraction of differentially expressed genes clustering Grid Open Day, 13 marzo 2007, Catania

Grid Open Day, 13 marzo 2007, Catania Available data analysis tools Microarray analysis with dChip Grid Open Day, 13 marzo 2007, Catania

Tissue microarray analysis III Case Study: TMA Analysis PARALLELIZATION Decrease of costs and time Implicit normalization Grid Open Day, 13 marzo 2007, Catania

TMA: Why GRID? 1 block Many slices => analysis Many spots Need of storage and computational resources Need of security for handling sensible data Grid Open Day, 13 marzo 2007, Catania

Grid Open Day, 13 marzo 2007, Catania The BioMedicalPortal Developing in collaboration with: NICE (Grid Portal development & support) AITEK (databases and software development and re-engineering) INFN CT + IR&T (gLite support and data and metadata management tools) Grid Open Day, 13 marzo 2007, Catania

Grid Open Day, 13 marzo 2007, Catania BMPortal services Basic user management, GRID authentication and authorization services Basic data and metadata management (LFC+AMGA or local) Job submission (GRID, local, remote cluster) and monitoring Interface to a MySQL DB Interface to biomedical applications Web services interface Workflow management system Data and text mining tools etc...... Grid Open Day, 13 marzo 2007, Catania

Grid Open Day, 13 marzo 2007, Catania Annotated experiment data upload Grid Open Day, 13 marzo 2007, Catania

Thanks for your attention! Questions …?!? Grid Open Day, 13 marzo 2007, Catania