Scientific Data Spaces - Experiences from the EGI-ACE project.

This paper presents the approach adopted by the EGI-ACE project for the setup and delivery of Data Spaces for various scientific domains. The work was implemented by members of the EGI e-infrastructure and of several European Research Infrastructures in the context of the European Open Science Cloud programme. Our results are several Data Space services that enable the reuse and exploitation of open, scientific big data for compute intensive use cases.

A protein structure prediction service in the ProGenGrid system.

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.

A grid-enabled protein secondary structure predictor.

We present an integrated Grid system for the prediction of protein secondary structures, based on the frequent automatic update of proteins in the training set. The predictor model is based on a feed-forward multilayer perceptron (MLP) neural network which is trained with the back-propagation algorithm; the design reuses existing legacy software and exploits novel grid components. The predictor takes into account the evolutionary information found in multiple sequence alignment (MSA); the information is obtained running an optimized parallel version of the PSI-BLAST tool, based on the MPI Master-Worker paradigm.

A services oriented system for bioinformatics applications on the grid.

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.

ProGenGrid: a grid-enabled platform for bioinformatics.

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.