Optimizing Splicing Junction Detection in Next Generation Sequencing Data on a Virtual-GRID Infrastructure

The new protocol for sequencing the messenger RNA in a cell, named RNA-seq produce millions of short sequence fragments. Next Generation Sequencing technology allows more accurate analysis but increase needs in term of computational resources. This paper describes the optimization of a RNA-seq analysis pipeline devoted to splicing variants detection, aimed at reducing computation time and providing a multi-user/multisample environment. This work brings two main contributions. First, we optimized a well-known algorithm called TopHat by parallelizing some sequential mapping steps. Second, we designed and implemented a hybrid virtual GRID infrastructure allowing to efficiently execute multiple instances of TopHat running on different samples or on behalf of different users, thus optimizing the overall execution time and enabling a flexible multi-user environmen

HPC Cloud for Scientific and Business Applications: Taxonomy, Vision, and Research Challenges

High Performance Computing (HPC) clouds are becoming an alternative to on-premise clusters for executing scientific applications and business analytics services. Most research efforts in HPC cloud aim to understand the cost-benefit of moving resource-intensive applications from on-premise environments to public cloud platforms. Industry trends show hybrid environments are the natural path to get the best of the on-premise and cloud resources---steady (and sensitive) workloads can run on on-premise resources and peak demand can leverage remote resources in a pay-as-you-go manner. Nevertheless, there are plenty of questions to be answered in HPC cloud, which range from how to extract the best performance of an unknown underlying platform to what services are essential to make its usage easier. Moreover, the discussion on the right pricing and contractual models to fit small and large users is relevant for the sustainability of HPC clouds. This paper brings a survey and taxonomy of efforts in HPC cloud and a vision on what we believe is ahead of us, including a set of research challenges that, once tackled, can help advance businesses and scientific discoveries. This becomes particularly relevant due to the fast increasing wave of new HPC applications coming from big data and artificial intelligence.Comment: 29 pages, 5 figures, Published in ACM Computing Surveys (CSUR

Mobile Computing in Digital Ecosystems: Design Issues and Challenges

In this paper we argue that the set of wireless, mobile devices (e.g., portable telephones, tablet PCs, GPS navigators, media players) commonly used by human users enables the construction of what we term a digital ecosystem, i.e., an ecosystem constructed out of so-called digital organisms (see below), that can foster the development of novel distributed services. In this context, a human user equipped with his/her own mobile devices, can be though of as a digital organism (DO), a subsystem characterized by a set of peculiar features and resources it can offer to the rest of the ecosystem for use from its peer DOs. The internal organization of the DO must address issues of management of its own resources, including power consumption. Inside the DO and among DOs, peer-to-peer interaction mechanisms can be conveniently deployed to favor resource sharing and data dissemination. Throughout this paper, we show that most of the solutions and technologies needed to construct a digital ecosystem are already available. What is still missing is a framework (i.e., mechanisms, protocols, services) that can support effectively the integration and cooperation of these technologies. In addition, in the following we show that that framework can be implemented as a middleware subsystem that enables novel and ubiquitous forms of computation and communication. Finally, in order to illustrate the effectiveness of our approach, we introduce some experimental results we have obtained from preliminary implementations of (parts of) that subsystem.Comment: Proceedings of the 7th International wireless Communications and Mobile Computing conference (IWCMC-2011), Emergency Management: Communication and Computing Platforms Worksho

Smart Grid Technologies in Europe: An Overview

The old electricity network infrastructure has proven to be inadequate, with respect to modern challenges such as alternative energy sources, electricity demand and energy saving policies. Moreover, Information and Communication Technologies (ICT) seem to have reached an adequate level of reliability and flexibility in order to support a new concept of electricity network—the smart grid. In this work, we will analyse the state-of-the-art of smart grids, in their technical, management, security, and optimization aspects. We will also provide a brief overview of the regulatory aspects involved in the development of a smart grid, mainly from the viewpoint of the European Unio