Polish Infrastructure
for Supporting Computational Science
in the European Research Space
Applications with Rich User Interface Powered by
the GridSpace Virtual Laboratory
Maciej Malawski (1, 2), Tomasz Gubała (2), Tomasz Jadczyk (2),
Katarzyna Prymula (3, 4), Irena Roterman (3), Marian Bubak (1, 2)
(1) Institute of Computer Science AGH, Mickiewicza 30, 30-059 Kraków,
Poland
(2) ACC Cyfronet AGH, ul. Nawojki 11, 30-950 Kraków, Poland
(3) Department of Bioinformatics & Telemedicine, Collegium Medicum UJ, ul.
Św. Łazarza 16 31-530 Kraków, Poland
(4) Faculty of Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060
Kraków, Poland
e-mail: malawski@agh.edu.pl
KU KDM
Zakopane, Poland, March 2010
Outline
 Overview of GridSpace Virtual Laboratory
 Flexibility of GridSpace platform
 Example Experiments:
 Patient History Display (ViroLab domain)
 Prediction of Ligand Binding Sites in Proteins
 Towards GridSpace 2.0
 Demonstration
 References
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GridSpace Virtual Laboratory
GridSpace virtual laboratory integrates computational resources
and relevant data to provide users with convenient, high-level
tools for collaborative experiment planning and execution
Users
Interfaces
Runtime
Services
Infrastructure
Experiment
developer
Experiment
Planning
Environment
Experiment
scenario
Scientist
Portal
End User
Application Specific
Portlet
Virtual Laboratory runtime components
(Required to select resources and execute experiment scenarios)
Computational services
(services (WS, WTS, WS-RF), components
(MOCCA), jobs (EGEE, AHE))
Data services
(DAS data sources, standalone databases)
Grids, Clusters, Computers, Network
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Application Lifecycle
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User Interfaces of Virtual Laboratory
 Experiment Management Interface
 Portal
 GWT, AJAX
 Experiment Planning Environment
 Eclipse RPC
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Patient History Display Experiment
Experiment Management
Interface (EMI)
Main experimentation GUI
Result Store
Contains payloads
and metadata about
experiment results
Data Access
Secure, uniform
access to multiple
data sources
GridSpace Engine
Executes in-silico
experiments
 Rich interface:
 Dynamically generated HTML/JavaScript page stored in Result Store
 Dynamically created PDF file
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Prediction of Ligand Binding Sites in ViroLab
 Many services are publicly available,
but only via WWW or email interface
 Automated in Virtual Laboratory using:
 HTTP communications wrapping
 Task queuing system for handling timeconsuming service invocations
 Conversion to a common format
 Generating Jmol visualization scripts
 Services available as gems in the Virtual
Laboratory
 Rich interface:
 Dynamically uploaded JMol-based
viewer
 Automatic update of application
using Experiment Repository
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Demo movies
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Conclusions
 Flexibility and the features of the GridSpace platform:
 to rapidly develop scientific applications
 rich Web and graphical user interfaces
 Experiment developers have full access to rich capabilities of Ruby and its libraries
 Possible to develop applications in flexible and creative way:
 application repository – application versioning and updates
 result management – sharing and publishing results on the Web
 Extensibility allowed us to deliver applications despite changing and undefined
requirements
 Scientific community (ViroLab)
 Business applications (GREDIA)
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Towards GridSpace 2.0
 Support for more scripting languages:
 Python
 Perl
 Web console for collaborative and interactive access to PL-Grid resources
 gLite and local PBS middleware support
 Simple access to remote files
 Sharing of gems, experiments and code snippets
 Semantic Integration framework as extension of Result Management facility
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References
 P.M.A Sloot, Peter V. Coveney, G. Ertayalan, V. Mueller, C.A. Boucher, and M. Bubak: HIV
decision Support: from Molecule to Man. Philosophical Transactions of the Royal Society A, vol
367, pp 2691 - 2703, 2009, doi:10.1098/rsta.2009.0043.
 M. Bubak, M. Malawski, T. Gubala, M. Kasztelnik, P. Nowakowski, D. Harezlak, T. Bartynski, J.
Kocot, E. Ciepiela, W. Funika, D. Krol, B. Balis, M. Assel, and A. Tirado Ramos. Virtual laboratory
for collaborative applications. In M. Cannataro, editor, Handbook of Research on Computational
GridTechnologies for Life Sciences, Biomedicine and Healthcare, chapter XXVII, pages 531-551.
IGI Global, 2009
 M. Malawski, T. Bartyński, and M. Bubak. Invocation of operations from script-based grid
applications. Future Gener. Comput. Syst., 26(1):138-146, 2010.
 T. Gubala, M. Bubak, P.M.A. Sloot; Semantic Integration of Collaborative Research Environments,
In: M. Cannataro (Ed.) Handbook of Research on Computational Grid Technologies for Life
Sciences, Biomedicine and Healthcare, Information Science Reference, 2009, IGI Global.
 Bryliński M, Prymula K, Jurkowski W, Kochańczyk M, Stawowczyk E, et al. 2007 Prediction of
Functional Sites Based on the Fuzzy Oil Drop Model. PLoS Comput Biol 3(5): e94.
doi:10.1371/journal.pcbi.0030094
 Grid Space webpage http://gs.cyfronet.pl/
 PL-Grid Project, http://www.plgrid.pl/en
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