ad2biodb - open source bioinformatics platform for high ... · adempiere as bioinformatics platform...
TRANSCRIPT
![Page 1: Ad2BioDB - Open Source Bioinformatics Platform for High ... · Adempiere as Bioinformatics Platform Adempiere, suitable backbone for biological data management software, Ad2Biodb](https://reader030.vdocuments.mx/reader030/viewer/2022040405/5e9983a9e95cbb17e545a3ca/html5/thumbnails/1.jpg)
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]
![Page 2: Ad2BioDB - Open Source Bioinformatics Platform for High ... · Adempiere as Bioinformatics Platform Adempiere, suitable backbone for biological data management software, Ad2Biodb](https://reader030.vdocuments.mx/reader030/viewer/2022040405/5e9983a9e95cbb17e545a3ca/html5/thumbnails/2.jpg)
Content
• Introduction
• Bioinformatics platform development
• Requirements
• Architecture
• Results
• Usage Case
• Conclusion
• Future Prospects
14/10/2011 2
![Page 3: Ad2BioDB - Open Source Bioinformatics Platform for High ... · Adempiere as Bioinformatics Platform Adempiere, suitable backbone for biological data management software, Ad2Biodb](https://reader030.vdocuments.mx/reader030/viewer/2022040405/5e9983a9e95cbb17e545a3ca/html5/thumbnails/3.jpg)
Introduction
• High Throughput Experimental data
Data Visualization
Data Analysis GALAXY
Genome Browsers
Data Management
Experimental Data Annotation Data Phenotype
Analysis Software
LIMS
Available solutions
14/10/2011 3
![Page 4: Ad2BioDB - Open Source Bioinformatics Platform for High ... · Adempiere as Bioinformatics Platform Adempiere, suitable backbone for biological data management software, Ad2Biodb](https://reader030.vdocuments.mx/reader030/viewer/2022040405/5e9983a9e95cbb17e545a3ca/html5/thumbnails/4.jpg)
Bioinformatics platform development Requirements
Adempiere as Bioinformatics Platform
Adempiere, suitable backbone for biological data management software, Ad2Biodb
14/10/2011 4
• 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.
![Page 5: Ad2BioDB - Open Source Bioinformatics Platform for High ... · Adempiere as Bioinformatics Platform Adempiere, suitable backbone for biological data management software, Ad2Biodb](https://reader030.vdocuments.mx/reader030/viewer/2022040405/5e9983a9e95cbb17e545a3ca/html5/thumbnails/5.jpg)
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
14/10/2011 5
![Page 6: Ad2BioDB - Open Source Bioinformatics Platform for High ... · Adempiere as Bioinformatics Platform Adempiere, suitable backbone for biological data management software, Ad2Biodb](https://reader030.vdocuments.mx/reader030/viewer/2022040405/5e9983a9e95cbb17e545a3ca/html5/thumbnails/6.jpg)
Bioinformatics platform development Results
Export Import Report
•Process •Workflow
14/10/2011 6
![Page 7: Ad2BioDB - Open Source Bioinformatics Platform for High ... · Adempiere as Bioinformatics Platform Adempiere, suitable backbone for biological data management software, Ad2Biodb](https://reader030.vdocuments.mx/reader030/viewer/2022040405/5e9983a9e95cbb17e545a3ca/html5/thumbnails/7.jpg)
Bioinformatics platform development Usage Case
14/10/2011 7
![Page 8: Ad2BioDB - Open Source Bioinformatics Platform for High ... · Adempiere as Bioinformatics Platform Adempiere, suitable backbone for biological data management software, Ad2Biodb](https://reader030.vdocuments.mx/reader030/viewer/2022040405/5e9983a9e95cbb17e545a3ca/html5/thumbnails/8.jpg)
Bioinformatics platform development Usage Case
14/10/2011 8
![Page 9: Ad2BioDB - Open Source Bioinformatics Platform for High ... · Adempiere as Bioinformatics Platform Adempiere, suitable backbone for biological data management software, Ad2Biodb](https://reader030.vdocuments.mx/reader030/viewer/2022040405/5e9983a9e95cbb17e545a3ca/html5/thumbnails/9.jpg)
Bioinformatics platform development Usage Case
14/10/2011 9
![Page 10: Ad2BioDB - Open Source Bioinformatics Platform for High ... · Adempiere as Bioinformatics Platform Adempiere, suitable backbone for biological data management software, Ad2Biodb](https://reader030.vdocuments.mx/reader030/viewer/2022040405/5e9983a9e95cbb17e545a3ca/html5/thumbnails/10.jpg)
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
14/10/2011 10
![Page 11: Ad2BioDB - Open Source Bioinformatics Platform for High ... · Adempiere as Bioinformatics Platform Adempiere, suitable backbone for biological data management software, Ad2Biodb](https://reader030.vdocuments.mx/reader030/viewer/2022040405/5e9983a9e95cbb17e545a3ca/html5/thumbnails/11.jpg)
14/10/2011 11