scholarly journals Next Generation Distributed Computing for Cancer Research

2014 ◽  
Vol 13s7 ◽  
pp. CIN.S16344 ◽  
Author(s):  
Pankaj Agarwal ◽  
Kouros Owzar
Keyword(s):  
Cancer Research ◽  
Distributed Computing ◽  
Data Storage ◽  
Large Scale ◽  
Next Generation ◽  
Scalable Computing ◽  
Performance Benchmarking ◽  
Hadoop Cluster ◽  
Set Up ◽  
Next Generation Sequencing Ngs

Advances in next generation sequencing (NGS) and mass spectrometry (MS) technologies have provided many new opportunities and angles for extending the scope of translational cancer research while creating tremendous challenges in data management and analysis. The resulting informatics challenge is invariably not amenable to the use of traditional computing models. Recent advances in scalable computing and associated infrastructure, particularly distributed computing for Big Data, can provide solutions for addressing these challenges. In this review, the next generation of distributed computing technologies that can address these informatics problems is described from the perspective of three key components of a computational platform, namely computing, data storage and management, and networking. A broad overview of scalable computing is provided to set the context for a detailed description of Hadoop, a technology that is being rapidly adopted for large-scale distributed computing. A proof-of-concept Hadoop cluster, set up for performance benchmarking of NGS read alignment, is described as an example of how to work with Hadoop. Finally, Hadoop is compared with a number of other current technologies for distributed computing.

Research and Design of the Distributed Mass Small File Storage System Based on WCF

2013 ◽  
Vol 765-767 ◽  
pp. 1087-1091
Author(s):  
Hong Lin ◽  
Shou Gang Chen ◽  
Bao Hui Wang
Keyword(s):  
Fault Tolerance ◽  
Distributed Computing ◽  
Data Storage ◽  
Large Scale ◽  
Storage System ◽  
Hardware Platform ◽  
File Storage ◽  
Computing Framework ◽  
Research And Design ◽  
Small File

Recently, with the development of Internet and the coming of new application modes, data storage has some new characters and new requirements. In this paper, a Distributed Computing Framework Mass Small File storage System (For short:Dnet FS) based on Windows Communication Foundation in .Net platform is presented, which is lightweight, good-expansibility, running in cheap hardware platform, supporting Large-scale concurrent access, and having certain fault-tolerance. The framework of this system is analyzed and the performance of this system is tested and compared. All of these prove this system meet requirements.

scholarly journals New Algorithms for Secure Outsourcing of Large-Scale Systems of Linear Equations

2020 ◽  
Vol 9 (5) ◽  
pp. 545-550
Keyword(s):  
Cloud Computing ◽  
Distributed Computing ◽  
Data Storage ◽  
Large Scale ◽  
Homomorphic Encryption ◽  
Linear Equations ◽  
Force Transmission ◽  
Large Scale Systems ◽  
Secure Outsourcing ◽  
Systems Of Linear Equations

Cloud computing is the on-request accessibility of computer system resources, specially data storage and computing power, without direct dynamic management by the client. In the simplest terms, cloud computing means storing and accessing data and programs over the Internet instead of your computer’s hard drive. Along the improvement of cloud computing, more and more applications are migrated into the cloud. A significant element of distributed computing is pay-more only as costs arise. Distributed computing gives strong computational capacity to the general public at diminished cost that empowers clients with least computational assets to redistribute their huge calculation outstanding burdens to the cloud, and monetarily appreciate the monstrous computational force, transmission capacity, stockpiling, and even reasonable programming that can be partaken in a compensation for each utilization way Tremendous bit of leeway is the essential objective that forestalls the wide scope of registering model for clients when their secret information are expended during the figuring procedure. Critical thinking is a system to arrive at the pragmatic objective of specific instruments that tackles the issues as well as shield from pernicious practices.. In this paper, we examine secure outsourcing for large-scale systems of linear equations, which are the most popular problems in various engineering disciplines. Linear programming is an operation research technique formulates private data by the customer for LP problem as a set of matrices and vectors, to develop a set of efficient privacypreserving problem transformation techniques, which allow customers to transform original LP problem into some arbitrary one while protecting sensitive input/output information. Identify that LP problem solving in Cloud component is efficient extra cost on cloud server. In this paper we are utilizing Homomorphic encryption system to increase the performance and time efficiency

A Review: Map Reduce Framework for Cloud Computing

2018 ◽  
Vol 7 (4.6) ◽  
pp. 13
Author(s):  
Mekala Sandhya ◽  
Ashish Ladda ◽  
Dr. Uma N Dulhare ◽  
. . ◽  
. .
Keyword(s):  
Data Mining ◽  
Cloud Computing ◽  
Distributed Computing ◽  
Data Storage ◽  
High Performance ◽  
Large Scale ◽  
Distributed Storage ◽  
Large Data ◽  
Mass Data ◽  
Internet Information

In this generation of Internet, information and data are growing continuously. Even though various Internet services and applications. The amount of information is increasing rapidly. Hundred billions even trillions of web indexes exist. Such large data brings people a mass of information and more difficulty discovering useful knowledge in these huge amounts of data at the same time. Cloud computing can provide infrastructure for large data. Cloud computing has two significant characteristics of distributed computing i.e. scalability, high availability. The scalability can seamlessly extend to large-scale clusters. Availability says that cloud computing can bear node errors. Node failures will not affect the program to run correctly. Cloud computing with data mining does significant data processing through high-performance machine. Mass data storage and distributed computing provide a new method for mass data mining and become an effective solution to the distributed storage and efficient computing in data mining. 

scholarly journals Computing in High Energy Physics

2005 ◽  
Vol 20 (14) ◽  
pp. 3021-3032
Author(s):  
Ian M. Fisk
Keyword(s):  
Distributed Computing ◽  
Large Scale ◽  
High Energy Physics ◽  
High Energy ◽  
Next Generation ◽  
Physical Infrastructure ◽  
Commodity Computing ◽  
Physics Experiments ◽  
Insight Into ◽  
Energy Physics

In this review, the computing challenges facing the current and next generation of high energy physics experiments will be discussed. High energy physics computing represents an interesting infrastructure challenge as the use of large-scale commodity computing clusters has increased. The causes and ramifications of these infrastructure challenges will be outlined. Increasing requirements, limited physical infrastructure at computing facilities, and limited budgets have driven many experiments to deploy distributed computing solutions to meet the growing computing needs for analysis reconstruction, and simulation. The current generation of experiments have developed and integrated a number of solutions to facilitate distributed computing. The current work of the running experiments gives an insight into the challenges that will be faced by the next generation of experiments and the infrastructure that will be needed.

scholarly journals Next-generation sequencing in neuropathological diagnosis of infections of the nervous system

2016 ◽  
Author(s):  
Steven L. Salzberg ◽  
Florian Breitwieser ◽  
Anupama Kumar ◽  
Haiping Hao ◽  
Peter Burger ◽  
...  
Keyword(s):  
Spinal Cord ◽  
Nervous System ◽  
Next Generation Sequencing ◽  
Large Scale ◽  
Infectious Agent ◽  
Next Generation ◽  
Dna And Rna ◽  
Wide Range ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Objective: To determine the feasibility of next-generation sequencing (NGS) microbiome approaches in the diagnosis of infectious disorders in brain or spinal cord biopsies in patients with suspected central nervous system (CNS) infections. Methods: In a prospective-pilot study, we applied NGS in combination with a new computational analysis pipeline to detect the presence of pathogenic microbes in brain or spinal cord biopsies from ten patients with neurological problems indicating possible infection but for whom conventional clinical and microbiology studies yielded negative or inconclusive results. Results: Direct DNA and RNA sequencing of brain tissue biopsies generated 8.3 million to 29.1 million sequence reads per sample, which successfully identified with high confidence the infectious agent in three patients, identified possible pathogens in two more, and helped to understand neuropathological processes in three others, demonstrating the power of large-scale unbiased sequencing as a novel diagnostic tool. Validation techniques confirmed the pathogens identified by NGS in each of the three positive cases. Clinical outcomes were consistent with the findings yielded by NGS on the presence or absence of an infectious pathogenic process in eight of ten cases, and were non-contributory in the remaining two. Conclusions: NGS-guided metagenomic studies of brain, spinal cord or meningeal biopsies offer the possibility for dramatic improvements in our ability to detect (or rule out) a wide range of CNS pathogens, with potential benefits in speed, sensitivity, and cost. NGS-based microbiome approaches present a major new opportunity to investigate the potential role of infectious pathogens in the pathogenesis of neuroinflammatory disorders.

scholarly journals The Impact of Next Generation Sequencing in Cancer Research

Cancers ◽  
2020 ◽  
Vol 12 (10) ◽  
pp. 2928
Author(s):  
Katia Nones ◽  
Ann-Marie Patch
Keyword(s):  
Cancer Research ◽  
Next Generation Sequencing ◽  
Massively Parallel Sequencing ◽  
Massively Parallel ◽  
Next Generation ◽  
Parallel Sequencing ◽  
Next Generation Sequencing Ngs ◽  
The Impact ◽  
Generation Sequencing ◽  
Technical Revolution

Next generation sequencing (NGS) describes the technical revolution that enabled massively parallel sequencing of fragmented nucleic acids, thus making possible our current genomic understanding of cancers [...]

scholarly journals NEXT GENERATION SEQUENCING TECHNOLOGIES TOWARDS EXPLORATION OF MEDICINAL PLANTS

2021 ◽  
Vol 9 (4) ◽  
pp. 507-516
Author(s):  
Sunanya Das ◽  
◽  
Rukmini Mishra ◽  
Keyword(s):  
Next Generation Sequencing ◽  
Medicinal Plants ◽  
Large Scale ◽  
Plant Cover ◽  
Next Generation ◽  
Sequencing Technologies ◽  
Medicinal Value ◽  
Modern Biotechnology ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

With the ever-increasing population, the plant cover is decreasing at an alarming rate. The medicinal plants are most affected by this because they are present in the last tier of cultivation. Let it be pharmaceutical companies or people using it for herbalism, medicinal plants have been exploited without getting a chance to flourish in their natural environment. Modern biotechnology acts as a bridge between the cultivation and utilization of medicinal plants. Next Generation Sequencing (NGS) technology which is a decade old but emerging field helps to unveil the importance of medicinal plants. Thus, it paves the way for sustenance of medicinal plants by molecular breeding, micropropagation, large-scale tissue culture, and other methods to conserve the plants with great medicinal value. Various NGS technologies can be found in the market like Ilumina, PacBio, Ion Torrent, and others. The present review will summarize the NGS technologies and their potential use to study the genomes, transcriptome, epigenome, and interactome of medicinal plants towards the identification of bioactive compounds.

scholarly journals Moving Next-Generation Sequencing into the Clinic

2021 ◽  
Vol 42 (03) ◽  
pp. 221-228
Author(s):  
Omshree Shetty ◽  
Mamta Gurav ◽  
Prachi Bapat ◽  
Nupur Karnik ◽  
Gauri Wagh ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Molecular Diagnostics ◽  
Single Gene ◽  
Tertiary Care ◽  
Genetic Alterations ◽  
Next Generation ◽  
Pathology Laboratory ◽  
Set Up ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

AbstractWith an advancement in the field of molecular diagnostics, there has been a profound evolution in the testing modalities, especially in the field of oncology. In the past decade, sequencing technology has evolved drastically with the advent of high-throughput next-generation sequencing (NGS). Subsequently, the single-gene tests have been replaced by multigene panel-based assays, deep sequencing, massively parallel whole genome, whole-exome sequencing, and so on. NGS has provided molecular diagnostics professionals a wonderful tool to explore and unearth the genetic alterations, underpinning the pathophysiology of the disease. However, this development has posed new challenges which consist of the following; understanding the technology, types of platforms available, various sequencing strategies, bioinformatics and data analysis algorithm, reporting of various variants, and validation of assays and overall for developing NGS assay for clinical utility. The challenges involved sometimes impede development of these high-end assays in laboratories. The present article provides a broad overview of our journey in setting up the NGS assay in a molecular pathology laboratory at a tertiary care oncology center. We hereby describe various important points and steps to be followed while working on the NGS setup, right from its inception to final drafting of the reports, with inclusion of various validation steps. We aim at providing a beginner’s guide to set up NGS assays in the laboratory using recommended best practices and various international guidelines.

scholarly journals Exotic airborne bacteria identified in urban resuspended dust by next generation sequencing

2019 ◽  
Vol 99 ◽  
pp. 04009
Author(s):  
Nora Kováts ◽  
Eszter Horváth ◽  
Katalin Hubai ◽  
András Hoffer ◽  
Beatrix Jancsek-Turóczi ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Large Scale ◽  
Rrna Gene ◽  
Pathogenic Microorganisms ◽  
Next Generation ◽  
Culture Independent ◽  
Next Generation Sequencing Ngs ◽  
Siberian Permafrost ◽  
Generation Sequencing ◽  
Airborne Transport

The airborne transport of bacteria is a well-known phenomenon, making it possible to exchange species between ecosystems, but it also provides a tool for spreading of pathogenic microorganisms. As part of a large-scale study, microbial community of inhalable and respirable fractions (PM1-10) of resuspended dust collected in Budapest (Hungary) has been characterised by culture-independent next generation sequencing (NGS) of variable 16S rRNA gene regions. Apart from common, mostly ubiqituos soil and organic material-dwelling bacteria, exotic airborne species have been identified, such as Variovorax ginsengisoli, previously isolated from Korean ginseng fields or Exiguobacterium sibiricum, isolated from the Siberian permafrost.

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