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

A Cloud Infrastructure for Optimization of a Massive Parallel Sequencing Workflow

Massive Parallel Sequencing is a term used to describe several revolutionary approaches to DNA sequencing, the so-called Next Generation Sequencing technologies. These technologies generate millions of short sequence fragments in a single run and can be used to measure levels of gene expression and to identify novel splice variants of genes allowing more accurate analysis. The proposed solution provides novelty on two fields, firstly an optimization of the read mapping algorithm has been designed, in order to parallelize processes, secondly an implementation of an architecture that consists of a Grid platform, composed of physical nodes, a Virtual platform, composed of virtual nodes set up on demand, and a scheduler that allows to integrate the two platform

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

A Tribute to Chief Justice James R. Zazzali: More than a \u27Caretaker\u27

Chief Justice Zazzali\u27s career reveals a dedication to public service and an unyielding sympathy for the disadvantaged. Accordingly, this Tribute examines his impact on New Jersey civil law and seeks to honor both the man and his jurisprudence. Although his tenure on the Supreme Court of New Jersey lasted only seven years, and his time as Chief Justice only nine months, his impact was meaningful. His clear and accessible opinions consistently protected the state\u27s children from myriad harms including negligent educators, harassing classmates, and tortfeasing businesses. In the area of tort law, Chief Justice Zazzali was willing to incrementally expand the common law to account for evolving norms and provide injured plaintiffs with avenues for redress when appropriate. In addition, when addressing worker\u27s rights, Chief Justice Zazzali, the son of a labor lawyer and a labor lawyer himself, never forgot the plight of the worker. Finally, in the corporate law context, the Chief Justice, in a practical fashion, generally sought to level the playing field for aggrieved investors, consumers, and property owners seeking redress against corporate entities and municipalities. In short, Chief Justice Zazzali\u27s civil jurisprudence reflects his sympathy for the little guy. By taking care of the Garden State\u27s underdogs, Chief Justice Zazzali was more than a caretaker

A Novel Integrated Real-time Simulation Platform for Assessing Photovoltaic Penetration Impacts in Smart Grids

© 2017 The Authors. For future planning and development of smart grids, it is important to evaluate the impacts of PV distributed generation, especially in densely populated urban areas. In this paper we present an integrated platform, constituted by two main components: a PV simulator and a real-time distribution network simulator. The first simulates real-sky solar radiation of rooftops and estimates the PV energy production; the second simulates the behaviour of the network when generation and consumption are provided at the different buses. The platform is tested on a case study based on real data for a district of the city of Turin, Italy