Applications with Rich User Interface Powered by the GridSpace Virtual Laboratory

Polish InfrastructurePolish Infrastructurefor Supporting Computational Sciencefor Supporting Computational Science

in the European Research Spacein the European Research Space

Applications with Rich User Interface Powered by Applications with Rich User Interface Powered by the GridSpace Virtual Laboratorythe GridSpace Virtual Laboratory

Maciej Malawski (1, 2), Tomasz Gubała (2), Tomasz Jadczyk (2), Maciej Malawski (1, 2), Tomasz Gubała (2), Tomasz Jadczyk (2), Katarzyna Prymula (3, 4), Irena Roterman (3), Marian Bubak (1, 2)Katarzyna Prymula (3, 4), Irena Roterman (3), Marian Bubak (1, 2)

(1) Institute of Computer Science AGH, Mickiewicza 30, 30-059 Kraków, (1) Institute of Computer Science AGH, Mickiewicza 30, 30-059 Kraków, PolandPoland

(2) ACC Cyfronet AGH, ul. Nawojki 11, 30-950 Kraków, Poland(2) ACC Cyfronet AGH, ul. Nawojki 11, 30-950 Kraków, Poland

(3) Department of Bioinformatics & Telemedicine, Collegium Medicum UJ, ul. (3) Department of Bioinformatics & Telemedicine, Collegium Medicum UJ, ul. Św. Łazarza 16 31-530 Kraków, PolandŚw. Łazarza 16 31-530 Kraków, Poland

(4) Faculty of Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 (4) Faculty of Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 Kraków, PolandKraków, Poland

e-mail: [email protected]: [email protected]

KU KDM

Zakopane, Poland, March 2010

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OutlineOutline

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 integrates computational resources and relevant data to provide users with convenient, high-level

tools for collaborative experiment planning and execution

Experimentdeveloper

Scientist End User

ExperimentPlanningEnvironment

Experiment scenario Portal

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

Users

Interfaces

Runtime

Services

Infrastructure

Application Specific Portlet

GridSpace Virtual LaboratoryGridSpace Virtual Laboratory

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Application LifecycleApplication Lifecycle

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User Interfaces of Virtual LaboratoryUser Interfaces of Virtual Laboratory

Experiment Management Interface Portal GWT, AJAX

Experiment Planning Environment Eclipse RPC

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Patient History Display ExperimentPatient History Display Experiment

GridSpace EngineExecutes in-silico

experiments

Result StoreContains payloads

and metadata aboutexperiment results

Experiment ManagementInterface (EMI)

Main experimentation GUI

Data AccessSecure, uniform

access to multipledata sources

Rich interface: Dynamically generated HTML/JavaScript page stored in Result Store Dynamically created PDF file

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PredictiPrediction ofon of Ligand Binding Site Ligand Binding Sites in ViroLabs 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 time-

consuming 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 moviesDemo movies

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ConclusionsConclusions

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 2.0Towards 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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ReferencesReferences

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