A Collaborative Environment Allowing Clinical Investigations on Integrated Biomedical Databases Matthias Assel HealthGrid 2009.

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Presentation transcript:

A Collaborative Environment Allowing Clinical Investigations on Integrated Biomedical Databases Matthias Assel HealthGrid 2009

Outline Motivation About ViroLab ViroLab Virtual Laboratory Data Integration and Access User Interfaces Example: A large-scale epidemiological Study Conclusion HealthGrid 2009

Motivation What we had… Distributed teams/groups/researchers Distributed resources providing heterogeneous data/information and capabilities Distributed applications and workflows What we wanted… Integration of users, data, workflows, applications, resources into one “virtual environment” Interdisciplinary collaboration and research Dynamic, on-demand and secure accessibility of resources and data HealthGrid 2009

About ViroLab Funded by EC within the 6th Framework Programme in the area of integrated biomedical information for better health 11 partners from 8 different European countries 3.5 year project (2006-2009) Experts from multiple disciplines (Physicians, virologists, epidemiologists, computer scientists) Develop a “Virtual Laboratory” for medical experts that allows clinical studies, medical knowledge discovery, and decision support for HIV drug resistance HealthGrid 2009

Virtual Laboratory Stack HealthGrid 2009

Data Integration and Access Usage of established HIV database management system: RegaDB Data conversion and anonymization occur within each hospital (customized scripts) Overall dataset size: ≈ 25.000 patients and 28.000 nt sequences Set of virtualisation services - Data Access Services - that allows users to perform several activities on dispersed data resources Single/central entry point for all data requests representing the only “visible” and accessible system Secure data exchange and proper access control for available resources Integrated with existing frameworks (Shibboleth, OGSA-DAI) to ease development and improve functionality HealthGrid 2009

Virtual Laboratory Stack HealthGrid 2009

User Interfaces – Experiment Creation HealthGrid 2009

User Interfaces – Experiment Execution HealthGrid 2009

User Interfaces – Experiment Execution HealthGrid 2009

User Interfaces – Drug Resistance Interpretation HealthGrid 2009

User Interfaces – Drug Resistance Interpretation HealthGrid 2009

User Interfaces – Data Access and Retrieval HealthGrid 2009

A large-scale epidemiological Study Data Access Tools DRS DA Tools Analysis Tools HealthGrid 2009

Conclusion Development of an advanced “virtual environment” for e-Science Integration of several heterogeneous hospital databases Design of advanced tools to support clinical research and practice Tools and framework are not limited to HIV field but applicable for other infectious diseases as well Prototype for future projects Collaborative interdisciplinary research is crucial but challenging HealthGrid 2009

Acknowledgements University of Amsterdam Peter Sloot, Breanndán Ó Nualláin Erasmus Medical Center Rotterdam: David van de Vijver, Dineke Frentz Catholic University Leuven: Anne-Mieke Vandamme, Pieter Libin, Kristof Theys, Stijn Imbrechts, Raphael Sangeda ACC Cyfronet AGH: Marian Bubak, Daniel Harezlak, Piotr Nowakowski HealthGrid 2009

Thank you for your attention. Any questions? http://www.virolab.org HealthGrid 2009