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Author: Francisco M Couto
Publisher:
ISBN: 9781013274459
Category : Computers
Languages : en
Pages : 106
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Book Description
This open access book is a step-by-step introduction on how shell scripting can help solve many of the data processing tasks that Health and Life specialists face everyday with minimal software dependencies. The examples presented in the book show how simple command line tools can be used and combined to retrieve data and text from web resources, to filter and mine literature, and to explore the semantics encoded in biomedical ontologies. To store data this book relies on open standard text file formats, such as TSV, CSV, XML, and OWL, that can be open by any text editor or spreadsheet application. The first two chapters, Introduction and Resources, provide a brief introduction to the shell scripting and describe popular data resources in Health and Life Sciences. The third chapter, Data Retrieval, starts by introducing a common data processing task that involves multiple data resources. Then, this chapter explains how to automate each step of that task by introducing the required commands line tools one by one. The fourth chapter, Text Processing, shows how to filter and analyze text by using simple string matching techniques and regular expressions. The last chapter, Semantic Processing, shows how XPath queries and shell scripting is able to process complex data, such as the graphs used to specify ontologies. Besides being almost immutable for more than four decades and being available in most of our personal computers, shell scripting is relatively easy to learn by Health and Life specialists as a sequence of independent commands. Comprehending them is like conducting a new laboratory protocol by testing and understanding its procedural steps and variables, and combining their intermediate results. Thus, this book is particularly relevant to Health and Life specialists or students that want to easily learn how to process data and text, and which in return may facilitate and inspire them to acquire deeper bioinformatics skills in the future. This work was published by Saint Philip Street Press pursuant to a Creative Commons license permitting commercial use. All rights not granted by the work's license are retained by the author or authors.
Author: Francisco M Couto
Publisher:
ISBN: 9781013274459
Category : Computers
Languages : en
Pages : 106
Get Book
Book Description
This open access book is a step-by-step introduction on how shell scripting can help solve many of the data processing tasks that Health and Life specialists face everyday with minimal software dependencies. The examples presented in the book show how simple command line tools can be used and combined to retrieve data and text from web resources, to filter and mine literature, and to explore the semantics encoded in biomedical ontologies. To store data this book relies on open standard text file formats, such as TSV, CSV, XML, and OWL, that can be open by any text editor or spreadsheet application. The first two chapters, Introduction and Resources, provide a brief introduction to the shell scripting and describe popular data resources in Health and Life Sciences. The third chapter, Data Retrieval, starts by introducing a common data processing task that involves multiple data resources. Then, this chapter explains how to automate each step of that task by introducing the required commands line tools one by one. The fourth chapter, Text Processing, shows how to filter and analyze text by using simple string matching techniques and regular expressions. The last chapter, Semantic Processing, shows how XPath queries and shell scripting is able to process complex data, such as the graphs used to specify ontologies. Besides being almost immutable for more than four decades and being available in most of our personal computers, shell scripting is relatively easy to learn by Health and Life specialists as a sequence of independent commands. Comprehending them is like conducting a new laboratory protocol by testing and understanding its procedural steps and variables, and combining their intermediate results. Thus, this book is particularly relevant to Health and Life specialists or students that want to easily learn how to process data and text, and which in return may facilitate and inspire them to acquire deeper bioinformatics skills in the future. This work was published by Saint Philip Street Press pursuant to a Creative Commons license permitting commercial use. All rights not granted by the work's license are retained by the author or authors.
Author: Francisco M. Couto
Publisher: Springer
ISBN: 3030138453
Category : Medical
Languages : en
Pages : 98
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Book Description
This open access book is a step-by-step introduction on how shell scripting can help solve many of the data processing tasks that Health and Life specialists face everyday with minimal software dependencies. The examples presented in the book show how simple command line tools can be used and combined to retrieve data and text from web resources, to filter and mine literature, and to explore the semantics encoded in biomedical ontologies. To store data this book relies on open standard text file formats, such as TSV, CSV, XML, and OWL, that can be open by any text editor or spreadsheet application. The first two chapters, Introduction and Resources, provide a brief introduction to the shell scripting and describe popular data resources in Health and Life Sciences. The third chapter, Data Retrieval, starts by introducing a common data processing task that involves multiple data resources. Then, this chapter explains how to automate each step of that task by introducing the required commands line tools one by one. The fourth chapter, Text Processing, shows how to filter and analyze text by using simple string matching techniques and regular expressions. The last chapter, Semantic Processing, shows how XPath queries and shell scripting is able to process complex data, such as the graphs used to specify ontologies. Besides being almost immutable for more than four decades and being available in most of our personal computers, shell scripting is relatively easy to learn by Health and Life specialists as a sequence of independent commands. Comprehending them is like conducting a new laboratory protocol by testing and understanding its procedural steps and variables, and combining their intermediate results. Thus, this book is particularly relevant to Health and Life specialists or students that want to easily learn how to process data and text, and which in return may facilitate and inspire them to acquire deeper bioinformatics skills in the future.
Author: Jyotika Singh
Publisher: CRC Press
ISBN: 1000902269
Category : Computers
Languages : en
Pages : 393
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Book Description
Natural Language Processing in the Real World is a practical guide for applying data science and machine learning to build Natural Language Processing (NLP) solutions. Where traditional, academic-taught NLP is often accompanied by a data source or dataset to aid solution building, this book is situated in the real world where there may not be an existing rich dataset. This book covers the basic concepts behind NLP and text processing and discusses the applications across 15 industry verticals. From data sources and extraction to transformation and modelling, and classic Machine Learning to Deep Learning and Transformers, several popular applications of NLP are discussed and implemented. This book provides a hands-on and holistic guide for anyone looking to build NLP solutions, from students of Computer Science to those involved in large-scale industrial projects.
Author: Joemon M. Jose
Publisher: Springer Nature
ISBN: 3030454428
Category : Computers
Languages : en
Pages : 709
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Book Description
This two-volume set LNCS 12035 and 12036 constitutes the refereed proceedings of the 42nd European Conference on IR Research, ECIR 2020, held in Lisbon, Portugal, in April 2020.* The 55 full papers presented together with 8 reproducibility papers, 46 short papers, 10 demonstration papers, 12 invited CLEF papers, 7 doctoral consortium papers, 4 workshop papers, and 3 tutorials were carefully reviewed and selected from 457 submissions. They were organized in topical sections named: Part I: deep learning I; entities; evaluation; recommendation; information extraction; deep learning II; retrieval; multimedia; deep learning III; queries; IR – general; question answering, prediction, and bias; and deep learning IV. Part II: reproducibility papers; short papers; demonstration papers; CLEF organizers lab track; doctoral consortium papers; workshops; and tutorials. *Due to the COVID-19 pandemic, this conference was held virtually.
Author: David R. Anderson
Publisher: Springer Science & Business Media
ISBN: 0387740759
Category : Science
Languages : en
Pages : 203
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Book Description
This textbook introduces a science philosophy called "information theoretic" based on Kullback-Leibler information theory. It focuses on a science philosophy based on "multiple working hypotheses" and statistical models to represent them. The text is written for people new to the information-theoretic approaches to statistical inference, whether graduate students, post-docs, or professionals. Readers are however expected to have a background in general statistical principles, regression analysis, and some exposure to likelihood methods. This is not an elementary text as it assumes reasonable competence in modeling and parameter estimation.
Author: Vishal Goar
Publisher: Springer Nature
ISBN: 9811554218
Category : Technology & Engineering
Languages : en
Pages : 556
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Book Description
This book features selected research papers presented at the International Conference on Advances in Information Communication Technology and Computing (AICTC 2019), held at the Government Engineering College Bikaner, Bikaner, India, on 8–9 November 2019. It covers ICT-based approaches in the areas ICT for energy efficiency, life cycle assessment of ICT, green IT, green information systems, environmental informatics, energy informatics, sustainable HCI and computational sustainability.
Author: Lee Harland
Publisher: Elsevier
ISBN: 1908818247
Category : Computers
Languages : en
Pages : 583
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Book Description
The free/open source approach has grown from a minor activity to become a significant producer of robust, task-orientated software for a wide variety of situations and applications. To life science informatics groups, these systems present an appealing proposition - high quality software at a very attractive price. Open source software in life science research considers how industry and applied research groups have embraced these resources, discussing practical implementations that address real-world business problems. The book is divided into four parts. Part one looks at laboratory data management and chemical informatics, covering software such as Bioclipse, OpenTox, ImageJ and KNIME. In part two, the focus turns to genomics and bioinformatics tools, with chapters examining GenomicsTools and EBI Atlas software, as well as the practicalities of setting up an ‘omics’ platform and managing large volumes of data. Chapters in part three examine information and knowledge management, covering a range of topics including software for web-based collaboration, open source search and visualisation technologies for scientific business applications, and specific software such as DesignTracker and Utopia Documents. Part four looks at semantic technologies such as Semantic MediaWiki, TripleMap and Chem2Bio2RDF, before part five examines clinical analytics, and validation and regulatory compliance of free/open source software. Finally, the book concludes by looking at future perspectives and the economics and free/open source software in industry. Discusses a broad range of applications from a variety of sectors Provides a unique perspective on work normally performed behind closed doors Highlights the criteria used to compare and assess different approaches to solving problems
Author: Kerstin Denecke
Publisher: Springer
ISBN: 331920582X
Category : Medical
Languages : en
Pages : 168
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Book Description
This book introduces the field of Health Web Science and presents methods for information gathering from written social media data. It explores the availability and utility of the personal medical information shared on social media platforms and determines ways to apply this largely untapped information source to healthcare systems and public health monitoring. Introducing an innovative concept for integrating social media data with clinical data, it addresses the crucial aspect of combining experiential data from social media with clinical evidence, and explores how the variety of available social media content can be analyzed and implemented. The book tackles a range of topics including social media’s role in healthcare, the gathering of shared information, and the integration of clinical and social media data. Application examples of social media for health monitoring, along with its usage in patient treatment are also provided. The book also considers the ethical and legal issues of gathering and utilizing social media data, along with the risks and challenges that must be considered when integrating social media data into healthcare choices. With an increased interest internationally in E-Health, Health 2.0, Medicine 2.0 and the recent birth of the discipline of Web Science, this book will be a valuable resource for researchers and practitioners investigating this emerging topic.
Author: Sören Auer
Publisher: Springer
ISBN: 3030060160
Category : Computers
Languages : en
Pages : 218
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Book Description
This book constitutes revised selected papers from the 13th International Conference on Data Integration in the Life Sciences, DILS 2018, held in Hannover, Germany, in November 2018. The 5 full, 8 short, 3 poster and 4 demo papers presented in this volume were carefully reviewed and selected from 22 submissions. The papers are organized in topical sections named: big biomedical data integration and management; data exploration in the life sciences; biomedical data analytics; and big biomedical applications.
Author: Dino Quintero
Publisher: IBM Redbooks
ISBN: 073845690X
Category : Computers
Languages : en
Pages : 88
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Book Description
This IBM® Redpaper publication provides an update to the original description of IBM Reference Architecture for Genomics. This paper expands the reference architecture to cover all of the major vertical areas of healthcare and life sciences industries, such as genomics, imaging, and clinical and translational research. The architecture was renamed IBM Reference Architecture for High Performance Data and AI in Healthcare and Life Sciences to reflect the fact that it incorporates key building blocks for high-performance computing (HPC) and software-defined storage, and that it supports an expanding infrastructure of leading industry partners, platforms, and frameworks. The reference architecture defines a highly flexible, scalable, and cost-effective platform for accessing, managing, storing, sharing, integrating, and analyzing big data, which can be deployed on-premises, in the cloud, or as a hybrid of the two. IT organizations can use the reference architecture as a high-level guide for overcoming data management challenges and processing bottlenecks that are frequently encountered in personalized healthcare initiatives, and in compute-intensive and data-intensive biomedical workloads. This reference architecture also provides a framework and context for modern healthcare and life sciences institutions to adopt cutting-edge technologies, such as cognitive life sciences solutions, machine learning and deep learning, Spark for analytics, and cloud computing. To illustrate these points, this paper includes case studies describing how clients and IBM Business Partners alike used the reference architecture in the deployments of demanding infrastructures for precision medicine. This publication targets technical professionals (consultants, technical support staff, IT Architects, and IT Specialists) who are responsible for providing life sciences solutions and support.
