Ad2BioDB - Open Source Bioinformatics Platform for High ... · Adempiere as Bioinformatics Platform...
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Open Source Bioinformatics Platform for High-Throughput Data Management Amitava Bhattacharyya 1, § , Andrea Calabria 1, § , Maurizio Mercurio 2 , and Daniele Cusi 1, 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]
Transcript of Ad2BioDB - Open Source Bioinformatics Platform for High ... · Adempiere as Bioinformatics Platform...
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
• Introduction
• Bioinformatics platform development
• Requirements
• Architecture
• Results
• Usage Case
• Conclusion
• Future Prospects
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Introduction
• High Throughput Experimental data
Data Visualization
Data Analysis GALAXY
Genome Browsers
Data Management
Experimental Data Annotation Data Phenotype
Analysis Software
LIMS
Available solutions
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Bioinformatics platform development Requirements
Adempiere as Bioinformatics Platform
Adempiere, suitable backbone for biological data management software, Ad2Biodb
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• Multiple Data integration Experimental, Phenotype & Annotation Data
• Multi-Platform Operating System independent
• Reporting System Data summary and charts.
• Os independence and web access using Java & Zk.
• Open Source
• Administrative & business functionalities.
Bioinformatics platform development Architecture
Users Application Server
M V
C • MVC-paradigm • Presentation layer (Java, ZK) • Web Access • Business logic • User actions (import/export/…)
Database Server
• Data management • Data Integration • User tracking history • Events triggering
Processing Server
• Job management • Data synchronization
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Bioinformatics platform development Results
Export Import 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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