1,720,955 research outputs found
Creación de un pipeline para análisis de datos metagenómicos basado en Nextflow
Full text link[ES] La metagenómica es una disciplina que surge ante la imposibilidad de aislar y cultivar la (amplia) mayoría de los organismos microbianos que viven en los ecosistemas naturales. El término hace referencia al estudio del conjunto de genomas de los organismos que habitan una muestra natural, al fin de describir, quiénes son y cuáles son sus potencialidades genéticas. Gracias a los considerables avances en el campo de la biología molecular, las nuevas tecnologías de secuenciación masiva (Next Generation Sequencing, NGS) y la bioinformática, la metagenómica se postula como una de las disciplinas con mayor progreso, en la actualidad, en el campo de la ecología microbiana.
Una parte fundamental del análisis metagenómico son las herramientas bioinformáticas empleadas para analizar los resultados de secuenciación; aunque esta disciplina puede considerarse bastante reciente, existen ya una gran variedad de bases de datos, pipelines (flujo de trabajo) y programas. Con respecto a los pipelines, estos se desarrollan para la integración de diversos paquetes de software complementarios y para la automatización de los procesos; no obstante, al aumentar la complejidad del análisis aparecen obstáculos que dificultan el uso de pipelines de alto rendimiento: incompatibilidad entre los diferentes paquetes de software, requisitos de actualización contradictorios, gestión de un elevado número de archivos intermedios y temporales u optimización de los recursos de computación. A fin de solventar todos estos problemas, recientemente ha surgido un lenguaje específico de dominio (DLS) llamado Nextflow. Este permite la adaptación de pipelines escritos en cualquier lenguaje de programación. La elección de Nextflow para el desarrollo de un pipeline para análisis metagenómicos se justifica por características como el uso de tecnologías de contenedores multi-escala, su integración en repositorios de software, la paralelización y la definición de canales de entrada y salida para el inicio automático de cada sub-proceso. Además, el modelo de flujo de datos mejora a otras herramientas alternativas; ya que, el procesamiento ¿top-down¿ no necesita gran espacio de almacenamiento. En definitiva, Nextflow se presenta como una solución flexible y robusta debido a la simplificación, al control del flujo de datos y a la gestión de los resultados que se recogen de los análisis metagenómicos.
En esta tesis, se presenta un pipeline de análisis basado en Nextflow que recoge los pasos principales del análisis metagenómico. El pipeline propuesto proporciona al usuario una herramienta que evita el proceso de instalación de los programas necesarios en el análisis y ejecuta los pasos más dispendiosos desde el punto de vista comunicacional en el análisis metagenómico. El pipeline recibe como entrada los datos brutos a analizar, procedentes de una o más muestras y continua con los pasos de control de calidad, ensamblado, anotación y cuantificación de cada anotación. Finalmente, proporciona, de forma clara y resumida, los resultados necesarios para los siguientes análisis estadísticos descriptivos y/o diferenciales; actuando de forma transparente, robusta y altamente reproducible, acelerando los tiempos de ejecución, ahorrando espacio de almacenamiento para el análisis y optimizando así los recursos informáticos disponibles.[EN] Metagenomics is a discipline that arose from the impossibility of isolating and cultivating most of microbial organisms that live in natural ecosystems. The term refers to the study of the genomes of the organisms that inhabit a natural sample in order to describe which microorganisms they are and what their genetic potentialities are. Because of the considerable advances in the field of molecular biology, Next Generation Sequencing technologies (NGS) and bioinformatics, metagenomics is currently one of the most advanced disciplines in the field of microbial ecology.
The analysis of sequencing results is performed by bioinformatic tools that are an essential part of metagenomic analysis; although this discipline may be considered quite recent, a wide variety of databases, pipelines (workflows) and programs have been developed. Pipelines are used for the integration of different and complementary software packages, and for the automation of processes. However, as the complexity of the analysis increases, obstacles which hinder the use of high-performance pipelines appear: incompatibility between different software packages, conflicting upgrade requirements, management of a large number of intermediate and temporary files, and optimization of computing resources. In order to overcome all these problems, a domain-specific language (DLS) called Nextflow has recently emerged. Nextflow allows the adaptation of pipelines written in any programming language. The choice of Nextflow for the development of a metagenomic analysis pipeline is justified by features such as the use of multi-scale containerization, its integration with software repositories, parallelization and the definition of input and output channels for the automatic start of each sub-process. In addition, the data flow model improves other alternative tools, because the top to bottom processing does not require large storage space. In conclusion, Nextflow stands to be a flexible and robust solution owing to the simplification, data flow control and management of the results collected from metagenomic analysis.
In this thesis, a Nextflow-based analysis pipeline, that captures the main steps of metagenomic analysis, is presented. The workflow provides the user with a tool that avoids the process of installing the necessary programs for the analysis and executes the most complex and communicatively problematic stages in metagenomic analysis. The pipeline receives as input the raw data to be analyzed from one or more samples and it continues with the steps of quality control, assembly, annotation, and quantification of each annotation. Finally, it provides, in a clear and summarized way, the necessary results for the following descriptive and/or differential statistical analysis, acting in a transparent, robust and highly reproducible way, speeding up execution times, saving storage space for the analysis, and optimizing the available informatic resources.Lomas Redondo, A. (2021). Creación de un pipeline para análisis de datos metagenómicos basado en Nextflow. Universitat Politècnica de València. https://riunet.upv.es/handle/10251/171195TFG
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
Author Under Sail The Imagination of Jack London, 1893-1902
No full textIn Author Under Sail, Jay Williams offers the first complete literary biography of Jack London as a professional writer engaged in the labor of writing. It examines the authorial imagination in London's work, the use of imagination in both his fiction and nonfiction, and the ways he defined imagination in the creative process in his business dealings with his publishers, editors, and agents. In this first volume of a two-volume biography, Williams traverses the years 1893 to 1902, from London's "Story of a Typhoon" to The People of the Abyss. The Jack London who emerges in the pages of Author Under Sail is a writer whose partnership with publishers, most notably his productive alliance with George Brett of Macmillan, was one of the most formative in American literary history. London pioneered many author models during the heyday of realism and naturalism, blurring the boundaries of these popular genres by focusing on absorption and theatricality and the representation of the seen and unseen. London created an impassioned, sincere, and extremely personal realism unlike that of other American writers of the time. Author Under Sail is a literary tour de force that reveals the full range of London as writer, creative citizen, and entrepreneur at the same time it sheds light on the maverick side of machine-age literature.Intro -- Title Page -- Copyright Page -- Dedication -- Contents -- Acknowledgments -- Introduction -- 1. Spirit Truth -- 2. From Absorption to Theatricality and Back Again -- 3. "I Will Build a New Present" -- 4. Sons as Authors -- 5. Fathers as Publishers -- 6. The Daughter as Author -- 7. Lovers as Authors -- 8. At Sea with the Family -- 9. Yellow News, Yellow Stories -- 10. The Return Home -- Notes -- Bibliography -- Index -- About Jay WilliamsIn Author Under Sail, Jay Williams offers the first complete literary biography of Jack London as a professional writer engaged in the labor of writing. It examines the authorial imagination in London's work, the use of imagination in both his fiction and nonfiction, and the ways he defined imagination in the creative process in his business dealings with his publishers, editors, and agents. In this first volume of a two-volume biography, Williams traverses the years 1893 to 1902, from London's "Story of a Typhoon" to The People of the Abyss. The Jack London who emerges in the pages of Author Under Sail is a writer whose partnership with publishers, most notably his productive alliance with George Brett of Macmillan, was one of the most formative in American literary history. London pioneered many author models during the heyday of realism and naturalism, blurring the boundaries of these popular genres by focusing on absorption and theatricality and the representation of the seen and unseen. London created an impassioned, sincere, and extremely personal realism unlike that of other American writers of the time. Author Under Sail is a literary tour de force that reveals the full range of London as writer, creative citizen, and entrepreneur at the same time it sheds light on the maverick side of machine-age literature.Description based on publisher supplied metadata and other sources.Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, YYYY. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries
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