Virtual Environment for Next Generation Sequencing Analysis

Next Generation Sequencing technology, on the one hand, allows a more accurate analysis, and, on the other hand, increases the amount of data to process. A new protocol for sequencing the messenger RNA in a cell, known as RNA- Seq, generates millions of short sequence fragments in a single run. These fragments, or reads, can be used to measure levels of gene expression and to identify novel splice variants of genes. The proposed solution is a distributed architecture consisting of a Grid Environment and a Virtual Grid Environment, in order to reduce processing time by making the system scalable and flexibl

Internames: a name-to-name principle for the future Internet

We propose Internames, an architectural framework in which names are used to identify all entities involved in communication: contents, users, devices, logical as well as physical points involved in the communication, and services. By not having a static binding between the name of a communication entity and its current location, we allow entities to be mobile, enable them to be reached by any of a number of basic communication primitives, enable communication to span networks with different technologies and allow for disconnected operation. Furthermore, with the ability to communicate between names, the communication path can be dynamically bound to any of a number of end-points, and the end-points themselves could change as needed. A key benefit of our architecture is its ability to accommodate gradual migration from the current IP infrastructure to a future that may be a ubiquitous Information Centric Network. Basic building blocks of Internames are: i) a name-based Application Programming Interface; ii) a separation of identifiers (names) and locators; iii) a powerful Name Resolution Service (NRS) that dynamically maps names to locators, as a function of time/location/context/service; iv) a built-in capacity of evolution, allowing a transparent migration from current networks and the ability to include as particular cases current specific architectures. To achieve this vision, shared by many other researchers, we exploit and expand on Information Centric Networking principles, extending ICN functionality beyond content retrieval, easing send-to-name and push services, and allowing to use names also to route data in the return path. A key role in this architecture is played by the NRS, which allows for the co-existence of multiple network "realms", including current IP and non-IP networks, glued together by a name-to-name overarching communication primitive.Comment: 6 page

Accelerating sequential programs using FastFlow and self-offloading

FastFlow is a programming environment specifically targeting cache-coherent shared-memory multi-cores. FastFlow is implemented as a stack of C++ template libraries built on top of lock-free (fence-free) synchronization mechanisms. In this paper we present a further evolution of FastFlow enabling programmers to offload part of their workload on a dynamically created software accelerator running on unused CPUs. The offloaded function can be easily derived from pre-existing sequential code. We emphasize in particular the effective trade-off between human productivity and execution efficiency of the approach.Comment: 17 pages + cove

Multi-path Probabilistic Available Bandwidth Estimation through Bayesian Active Learning

Knowing the largest rate at which data can be sent on an end-to-end path such that the egress rate is equal to the ingress rate with high probability can be very practical when choosing transmission rates in video streaming or selecting peers in peer-to-peer applications. We introduce probabilistic available bandwidth, which is defined in terms of ingress rates and egress rates of traffic on a path, rather than in terms of capacity and utilization of the constituent links of the path like the standard available bandwidth metric. In this paper, we describe a distributed algorithm, based on a probabilistic graphical model and Bayesian active learning, for simultaneously estimating the probabilistic available bandwidth of multiple paths through a network. Our procedure exploits the fact that each packet train provides information not only about the path it traverses, but also about any path that shares a link with the monitored path. Simulations and PlanetLab experiments indicate that this process can dramatically reduce the number of probes required to generate accurate estimates

A novel wireless mobile platform integrated with optical fibre sensors

This paper presents a novel design of wireless mobile platform which enables effective integration of a number of optical fibre sensors with an advanced mobile wireless sensor network (WSN) and allows for potential applications such as monitoring in remote and harsh environments and tracking, exploiting fully the advantages offered both by mobile WSN and by advanced optical fibre sensing technologies. The platform which was designed and implemented consists of an optical fibre sensor module and a smart mobile WSN module, which shows important advantages for mobile sensing and tracking and mesh networking. In this study, a fibre Bragg grating (FBG)-based temperature sensor was specially designed and integrated successfully into the optical fibre sensor module as an exemplar to investigate the performance of the integrated system based on the mobile WSN platform. The positive experimental results obtained have confirmed the functionality of the platform designed and demonstrated its capacity for real-time optical fibre sensor data monitoring, processing and wireless transmission. The successful creation of this type of wireless mobile platform with optical fibre sensors would be expected to make an important impact on many sectors, where either conventional optical sensor designs or WSNs alone cannot meet the systems requirements