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The ViroLab Virtual Laboratory for Viral Diseases

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,

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The ViroLab Virtual Laboratory for Viral Diseases

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

  2. 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.

  3. 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

  4. Layered Structure of VLvl Clinical Virologist Experiment developer 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

  5. ExperimentPlanning 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 integratingwith the GSEngine runtime system • Support collaboration betweenVL users groups by: • Sharing experiment withingroups of experiment developers • Releasing experimentsfor scientific users • Collecting feedback fromexperiment users • Enable extendability with new features(e.g. GRR and Onto Browser plugins)

  6. Experiment Management Interface Objective: to provide ViroLab users with an easily accessible and convenient facility for experiment and result management Browse experiment repositoriesin search for a suitableexperiment plan Interactively run any numberof experiment plansand monitor their executionstatus Retrieve, analyze andstore scientific results Extensible support fordifferent securitymodels with fullShibboleth integration

  7. 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 foldingBryliński M, Jurkowski W, Konieczny L, Roterman I. Limited conformational space for early-stage protein folding simulationBioinformatics 20(2), 199-205 (2004)‏ • DAC and WebDAV for result storage http://virolab.cyfronet.pl/trac/exampleExperiments/wiki/exex/Folding

  8. Protein Folding Demo

  9. 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

  10. 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.

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