1. Attività grid di Biomedicina in Italia e in Europa
Livia Torterolo BIO-Lab, DIST University of Genoa

2. Grid Open Day, 13 marzo 2007, Catania
About Bio-Lab …
BIO-Lab: Laboratory for Bioimages and Bioengineering
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

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

4. Grid Open Day, 13 marzo 2007, Catania
Italian GRID projects
GRID.IT: An Italian National Research Council Project on Grid Computing
LITBIO: Laboratory of Interdisciplinary Technologies in Bioinformatics
BMPortal: BioMedical Portal
(portal development in progress…)
Grid Open Day, 13 marzo 2007, Catania

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

6. 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

7. 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

8. Grid Open Day, 13 marzo 2007, Catania
SPM working on Web
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

9. 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

10. 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

11. 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

12. 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

13. 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

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

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

16. 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

17. 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

18. 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

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

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