Parameter Sweep Workflows for Modelling Carbohydrate Recognition

Authors:
Tamas Kiss;Pamela Greenwell;Hans Heindl;Gabor Terstyanszky;Noam Weingarten
Affiliations:
School of Electronics and Computer Science, University of Westminster, London, UK W1W 6UW;School of Life Sciences, University of Westminster, London, UK W1W 6UW;School of Life Sciences, University of Westminster, London, UK W1W 6UW;School of Electronics and Computer Science, University of Westminster, London, UK W1W 6UW;School of Electronics and Computer Science, University of Westminster, London, UK W1W 6UW
Venue:
Journal of Grid Computing
Year:
2010

Citing 12
Cited 4

SMILES, a chemical language and information system. 1. introduction to methodology and encoding rules

Journal of Chemical Information & Computer Sciences
The SDSC storage resource broker

CASCON '98 Proceedings of the 1998 conference of the Centre for Advanced Studies on Collaborative research
Short note: molecular docking: An example of grid enabled applications

New Generation Computing - Grid systems for life sciences
GridSphere: An Advanced Portal Framework

EUROMICRO '04 Proceedings of the 30th EUROMICRO Conference
BOINC: A System for Public-Resource Computing and Storage

GRID '04 Proceedings of the 5th IEEE/ACM International Workshop on Grid Computing
myExperiment: social networking for workflow-using e-scientists

Proceedings of the 2nd workshop on Workflows in support of large-scale science
A grid-based genetic algorithm combined with an adaptive simulated annealing for protein structure prediction

Soft Computing - A Fusion of Foundations, Methodologies and Applications - Special issue (1143 - 1198) " Distributed Bioinspired Algorithms"; Guest editors: F. Fernández de Vega, E. Cantú-Paz
GPU acceleration of a production molecular docking code

Proceedings of 2nd Workshop on General Purpose Processing on Graphics Processing Units
A molecular docking system using CUDA

Proceedings of the 2009 International Conference on Hybrid Information Technology
Supporting NAMD application on the grid using GPE

PPAM'07 Proceedings of the 7th international conference on Parallel processing and applied mathematics
Chemomentum - UNICORE 6 based infrastructure for complex applications in science and technology

Euro-Par'07 Proceedings of the 2007 conference on Parallel processing
Globus toolkit version 4: software for service-oriented systems

NPC'05 Proceedings of the 2005 IFIP international conference on Network and Parallel Computing

WS-PGRADE/gUSE Generic DCI Gateway Framework for a Large Variety of User Communities

Journal of Grid Computing
A Grid-Enabled Gateway for Biomedical Data Analysis

Journal of Grid Computing
Scheduling parameter sweep workflow in the Grid based on resource competition

Future Generation Computer Systems
On specifying and sharing scientific workflow optimization results using research objects

WORKS '13 Proceedings of the 8th Workshop on Workflows in Support of Large-Scale Science

Quantified Score

Hi-index	0.01

Visualization

Abstract

Carbohydrate recognition is a phenomenon critical to a number of biological functions in humans. Understanding the dynamic behaviour of oligosaccharides should help in the discovery of the mechanisms which lead to specific and selective recognition of carbohydrates by proteins. Computer programs which can provide insight into such biological recognition processes have significant potential to contribute to biomedical research if the results of the simulation can prove consistent with the outcome of conventional wet laboratory experiments. In order to validate these simulation tools and support their wider uptake by the bio-scientist research community, high-level easy to use integrated environments are required to run massively parallel simulation workflows. This paper describes how the ProSim Science Gateway, based on the WS-PGRADE Grid portal, has been created to execute and visualise the results of complex parameter sweep workflows for modelling carbohydrate recognition.