1. The ViroLab Virtual Laboratory for Viral Diseases

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
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

5. 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)

6. 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

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 folding Bryliński M, Jurkowski W, Konieczny L, Roterman I. Limited conformational space for early-stage protein folding simulation Bioinformatics 20(2), (2004)‏
DAC and WebDAV for result storage

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 John Wiley and Sons, USA, January 2008.