The ViroLab Virtual Laboratory for Viral Diseases

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Presentation transcript:

The ViroLab Virtual Laboratory for Viral Diseases http://www.virolab.org/ http://virolab.cyfronet.pl/

ViroLab Virtual Laboratory A collaborative space for science, Supports virologists, epidemiologists and clinicians in investigating the HIV virus and treating HIV-positive patients, The solutions and technology could be reused in other domains.

What is a Virtual Experiment? It mirrors a physical experiment carried out in a „real” scientific laboratory Typical lifecycle of a virtual experiment is shown on the diagram

Layered Structure of VLvl Experiment developer Clinical Virologist Users Scientist Experiment Planning Environment Experiment scenario Patient Treatment Support Interfaces ViroLab Portal Virtual Laboratory runtime components (Required to select resources and execute experiment scenarios)‏ Runtime Computational services (services (WS, WTS, WS-RF), components (MOCCA), jobs (EGEE, AHE))‏ Data services (DAS data sources, standalone databases)‏ Services Grids, Clusters, Computers, Network Infrastructure

Experiment Planning Environment Objective: to facilitate the experiment development process by providing an integrated and collaborative environment Assist in the development of experiment plans powerful GScript editor Execute experiments by integrating with the GSEngine runtime system Support collaboration between VL users groups by: Sharing experiment within groups of experiment developers Releasing experiments for scientific users Collecting feedback from experiment users Enable extendability with new features (e.g. GRR and Onto Browser plugins)

Experiment Management Interface Objective: to provide ViroLab users with an easily accessible and convenient facility for experiment and result management Browse experiment repositories in search for a suitable experiment plan Interactively run any number of experiment plans and monitor their execution status Retrieve, analyze and store scientific results Extensible support for different security models with full Shibboleth integration 6

Protein Folding Objective: demonstrate the usage of Virtual Laboratory for proteomics applications Input: protein and chain ID Output: 3D structure of protein Gems used: Protein Data Bank (PDB) Web Service Early-stage protein folding Bryliński M, Jurkowski W, Konieczny L, Roterman I. Limited conformational space for early-stage protein folding simulation Bioinformatics 20(2), 199-205 (2004)‏ DAC and WebDAV for result storage http://virolab.cyfronet.pl/trac/exampleExperiments/wiki/exex/Folding

Protein Folding Demo

Patient Treatment Support Tool (PTS) Goal: a graphical, user-friendly tool for medical users to access the ViroLab ranking services collaborative interaction via experiments run in the Virtual Laboratory

Patient Treatment Support Tool (PTS) Description: distributed system accessible to medical users via standard technologies * implementation based on the Java RPC model for interaction with web services * A. Tirado-Ramos; P.M.A. Sloot and M.T. Bubak: Grid-based Interactive Decision Support in BioMedicine, in T. El-Ghazali and Zomaya, editors, Grids for Bioinformatics and Computational Biology, pp. 225-246. John Wiley and Sons, USA, January 2008.