This paper describes the evolution of the main services of the ProGenGrid (Proteomics & Genomics Grid) system, a distributed and ubiquitous grid environment ("virtual laboratory"), based on Workflow and supporting the design, execution and monitoring of "in silico" experiments in bioinformatics.ProGenGrid is a Grid-based Problem Solving Environment that allows the composition of data sources and bioinformatics programs wrapped as Web Services (WS). The use of WS provides ease of use and fosters re-use. The resulting workflow of WS is then scheduled on the Grid, leveraging Grid-middleware services. In particular, ProGenGrid offers a modular bag of services and currently is focused on the biological simulation of two important bioinformatics problems: prediction of the secondary structure of proteins, and sequence alignment of proteins. Both services are based on an enhanced data access service.
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Stud Health Technol Inform
October 2008
SPACI Consortium, University of Salento, Lecce & NNL/CNR-INFM, Lecce, Italy.
This paper describes a protein tertiary structure prediction service implemented in a Grid Environment. The service has been used for predicting the dicarboxylate carrier (DIC) of Saccharomyces cerevisiae by using the homology modelling approach. The visualization of the predicted model is made possible by using an interactive virtual reality environment based on X3D and Ajax3d technologies.
View Article and Find Full Text PDFStud Health Technol Inform
September 2007
CACT-NNL/CNR-INFM, CMCC, University of Salento, Lecce, Italy.
This paper describes the evolution of the main services of the ProGenGrid (Proteomics & Genomics Grid) system, a distributed and ubiquitous grid environment ("virtual laboratory"), based on Workflow and supporting the design, execution and monitoring of "in silico" experiments in bioinformatics.ProGenGrid is a Grid-based Problem Solving Environment that allows the composition of data sources and bioinformatics programs wrapped as Web Services (WS). The use of WS provides ease of use and fosters re-use.
View Article and Find Full Text PDFStud Health Technol Inform
July 2005
CACT/ISUFI and SPACI Consortium, University of Lecce, 73100 Lecce, Italy.
In this paper we describe the ProGenGrid (Proteomics and Genomics Grid) system, developed at the CACT/ISUFI of the University of Lecce which aims at providing a virtual laboratory where e-scientists can simulate biological experiments, composing existing analysis and visualization tools, monitoring their execution, storing the intermediate and final output and finally, if needed, saving the model of the experiment for updating or reproducing it. The tools that we are considering are software components wrapped as Web Services and composed through a workflow. Since bioinformatics applications need to use high performance machines or a high number of workstations to reduce the computational time, we are exploiting a Grid infrastructure for interconnecting wide-spread tools and hardware resources.
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