op yr yr yr yr yr ig ig ig ig ig ht ht ht ht ht pr pr pr pr pr ot ot ot ot ot ec ec ec ec ec te te te te te ed d d d d d .F .F .F .F .F .F 10 10 10 10 10 1 00 00 00 00 00 Po Po Po Po Po st st st st st er er er er er s. s. s. s. s. C C C C C op op op op op yr yr yr yr yr yr ig ig ig ig ig ig ht ht ht ht ht ht pr pr pr pr pr ot ot ot ot ot ec ec ec ec ec te te te te te d. d. d. d. d. F1 F1 F1 F1 F1 00 00 00 00 00 0 0 0 0 0 Po Po Po Po Po Po st st st st st st er er er er er e s. s. s. s. s. C C C C C op op op op op yr yr yr yr yr ig ig ig ig ig ht ht ht ht ht pr pr pr pr pr ot ot ot ot ot 1 2 3
MM:
[email protected]; DC:
[email protected]
Motivation
Genome Browsers
Data Visualization Data Analysis
Analysis Software
Data Management
LIMS
Experimental Data
Annotation Data
op
Re q u i r e m e n t s :
None of the existing tools addresses completely to the needs of the high throughput laboratories and research centers, combining and integrating heterogeneous data. Contemporary multi-disciplinary research environment imposes a dynamic, userfriendly management system that fully supports data integration and visualization, data access and analysis. Ad2BioDB integrates present needs and adapts for future
Operating System Independent Data Type Tolerance Multiple Analysis Management Analysis & Visualization
Phenotype
Users
Methodology
Ad2BioDB is an open source project based on Adempiere ERP. We chose Adempiere ERP as starting base for our platform since it natively supports datawarehousing and business logics for enterprises. Above Adempiere ERP we integrated a plugin function for Bioinformatics and genomic data management. This feature allows having a unique software suite both for administrative needs and scientific purposes. Ad2BioDB is designed in three main components (3tierd): (1) an application server, that is devoted to process all user-system interactions, (2) a database server for all data queries that triggers data user actions, and (3) a processing server, that manages data manipulation, import/export, and jobs’ management
Application Server • MVC-paradigm C • Presentation layer (Java, ZK) V M • Web Access • Business logic • User actions (import/export/…) 4
2
1
Processing Server • Job management • Data synchronization
3
Genotyping Data Sequencing Data
Gene Expression Data
Database Server
• Data management • User tracking history • Events triggering
The Ad2BioDB implemented architecture
Results
Ad2BioDB is being developed on the Eclipse IDE with an
implemented SubVersion System (SVN) store and keep track of source code and its evolution during releases. We developed Ad2BioDB as a prototype in our laboratory and is currently plugged in to high performance server that processes all user requests through a cluster queuing system: this approach grants reliability, scalability and flexibility and balances computational loads to all available resources.
Example: Export Phenotype BP for large set of patients and extract all SNPs for high density chip
C
op
C
op
C
AB:
[email protected]; AC:
[email protected];
Dept. of Medicine, Surgery and Dentistry, Università degli Studi di Milano, Milan, Italy KOS Genetic Srl, Via Podgora 7, Milan, Italy Fondazione Filarete, Viale Ortles 22/4, 20139, Milano, Italy
C
op
C
Amitava Bhattacharyya1, Andrea Calabria1, Maurizio Mercurio2, and Daniele Cusi1, 2, 3
Ke y Fe a t u r e s :
Os independent and has web access using Java & Zk. Statistical reports generation Data browsing Data import/export and formatting Secure authentication levels, connections and data transfer Data protection by users’ authorization levels
Path Ahead:
Improve Plugin System Improve Reporting tool Analysis
Ad2BioDB Usage Scenario
www.hypergenes.eu
FP7 HEALTH - Grant Agreement 201550
HEALTH-2007-2.1.1-2 "Molecular epidemiological studies in existing well characterised European (and/or other) population cohorts"
