Open Source Bioinformatics Platform
for High-Throughput Data Management
Amitava Bhattacharyya1, §, Andrea Calabria1, §,
Maurizio Mercurio2, and Daniele Cusi1, 2, 3
1
Dept. of Medicine, Surgery and Dentistry, Università degli Studi di
Milano, Milan, Italy 2 KOS Genetic Srl, Via Podgora 7, Milan, Italy
3 Fondazione Filarete, Viale Ortles 22/4, 20139, Milano, Italy
§ Corresponding Authors
AB: [email protected]; AC: [email protected];
MM: [email protected]; DC: [email protected]
Content
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Introduction
Bioinformatics platform development
• Requirements
• Architecture
• Results
• Usage Case
Conclusion
Future Prospects
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Introduction
• High Throughput Experimental data
Available solutions
Genome
Browsers
Analysis Software
Data Visualization
Data Analysis
GALAXY
Data Management
LIMS
Experimental Data
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Annotation Data
Phenotype
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Bioinformatics platform development
Requirements
Adempiere as Bioinformatics Platform
• Multiple Data integration
Experimental, Phenotype &
Annotation Data
• Multi-Platform Operating
System independent
• Os independence and web
access using Java & Zk.
• Open Source
• Administrative & business
functionalities.
• Reporting System Data
summary and charts.
Adempiere, suitable backbone for biological data management software, Ad2Biodb
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Bioinformatics platform development
Architecture
Application Server
C
Users
V
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M
MVC-paradigm
Presentation layer (Java, ZK)
Web Access
Business logic
User actions (import/export/…)
Database Server
Processing Server
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Data management
Data Integration
User tracking history
Events triggering
• Job management
• Data synchronization
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Bioinformatics platform development
Results
Import
Export
Report
•Process
•Workflow
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Bioinformatics platform development
Usage Case
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Bioinformatics platform development
Usage Case
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Bioinformatics platform development
Usage Case
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Conclusion
• Ad2BioDB integrates many heterogeneous biological
data for complex knowledge extraction
• Beneficial features to biological data management.
Future Directions
• Improve Plugin System
• Improve Reporting tool
• Analysis
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