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BITS2007 Meeting
BITS2007 Meeting



26-28 April 2007 Napoli, Italy

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Microarray data infrastructure using Gebbalab based on Alfresco technology
 
Motivation
Great progress has been made in recent years in integrating technologies and
innovations in computer science with those of the life sciences. However, many
activities in biological and especially clinical research still do not have access to
the necessary computer technology. Hospitals, for example, often perform outstanding
research but lack the bioinformatics tools which could fully exploit the activities
carried out. The GeBBALab project is addressing these problems by creating a "virtual
laboratory" with contributions from both scientific and technological/industrial
partners. 
The project has identified two key areas:
1.	Microarray data infrastructure and analysis
2.	Integration of patient and clinical data with genomics information
Although the latter objective is of critical importance in health care this is still
under discussion. This abstract will therefore concentrate on the GebbaLab (Genetics,
Biotecnologie and Bioinformatica Applicata) infrastructure for microarray storage and
analysis, also because one of the consortium members already provides a microarray
analysis service and so can guide and test its design. We emphasise, however, that
the system has been designed to allow the addition of clinical data


Methods
The efficient storage and analysis of microarray data is of considerable interest and
there is much activity worldwide. In general most researchers adopt a "single
workstation approach" for data management and analysing expression data. However this
method is rapidly becoming inconvenient for many reasons:
- There is no provision for the systematic recording of experimental
information 
- Current PCs are not sufficiently powerful for analysing data
- Comparison with data from other researchers or public repositories is
difficult
Careful consideration of these points has suggested the following criteria for the
design of the microarray infrastructure. 
- Users must be given the opportunity to use a wide range of common and
user-friendly tools for data entry and for the different platforms available, e.g.
Affymetrix, Agilent, Illumina etc.
- Data should be distributed
- Data must be recorded in a format which allows interoperability of all the
data sources
- User-friendly portals or clients are required to access resources and
powerful computational facilities to process datasets
To satisfy these criteria the infrastructure was structured into two distinct
levels:
1.	The data entry and storage level.
2.	The application level for running analysis applications.
The system consists of a "central" node and many "satellite" nodes, each of which
with its own data store, potentially virtualized. The system has been designed in a
modular way in order to work even in case of unavailability of the central node. In
fact in our schema "central" merely indicates a central registry for distributed
indexing and querying. Data is stored, analyzed and exchanged through a complex
architecture build upon Alfresco, an advanced Open Source Enterprise Content
Management that provides a common interface and access to distributed data sources.
Alfresco also includes user authentication and various levels of access privileges,
thus allowing many degrees of data security and privacy. Our effort have been lead to
build upon the Alfresco structure many software modules in order to manipulate MAGE-ML
files, extract metadata from MAGE-MLs, to store and index metadata into the repository
for querying microarray data according to different search criteria. All the modules
are provided through a SOA (Service Oriented Architecture) layer among different web
applications that allow users to choose, through a web portal, the appropriate
software from those available that transparently invokes algorithms to fetch the data
for analysis. High performance servers are available for CPU or memory intensive
calculations


Results
We have demonstrated a user-oriented, powerful infrastructure for microarray data
management and analysis. It allows the user to enter data and being distributed
avoids the limitations of a centralised server. A prototype using Alfresco is already
available and microarray researchers are invited to contact the authors if they wish
to experiment with the system. Future enhancements to Gebbalab will include analysis
applications and, crucially, the possibility of integrating patient data.
 
Id: 133
Place: Napoli, Italy
Centro Congressi "Federico II"
Via Partenope 36
Napoli
Starting date:
27-Apr-2007   15:20
Duration: 20'
Contribution type: Oral
Primary Authors: GIULIANI, silvia (High Performance Systems Division, CINECA, Casalecchio di Reno (Bologna))
Co-Authors: ROSSI, simona (DAMA, University of Ferrara, Ferrara)
D`ASCIA, sergio (NSI - Nier Soluzioni Informatiche, Castel Maggiore (Bologna))
ROSSI, elda (High Performance Systems Division, CINECA, Casalecchio di Reno (Bologna))
EMERSON, andrew (High Performance Systems Division, CINECA, Casalecchio di Reno (Bologna))
FIAMENI, giuseppe (High Performance Systems Division, CINECA, Casalecchio di Reno (Bologna))
TAGLIAVINI, luca (DAMA, University of Ferrara, Ferrara)
FRANGIAMONE, giuseppe (NSI - Nier Soluzioni Informatiche, Castel Maggiore (Bologna))
VOLINIA, stefano (DAMA, University of Ferrara, Ferrara)
Presenters: GIULIANI, silvia
Material: slide Slides
 
Included in session: Session 4: Biomedical Informatics
Included in track: Biomedical informatics
 




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