High Performance Reductive Strategies For Big Data From Lc Ms Ms Proteomics

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High-Performance Algorithms for Mass Spectrometry-Based Omics

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Author : Fahad Saeed
Publisher : Springer Nature
ISBN 13 : 3031019601
Total Pages : 146 pages
Book Rating : 4.0/5 (31 download)

Book Synopsis High-Performance Algorithms for Mass Spectrometry-Based Omics by : Fahad Saeed

Download or read book High-Performance Algorithms for Mass Spectrometry-Based Omics written by Fahad Saeed and published by Springer Nature. This book was released on 2022-09-02 with total page 146 pages. Available in PDF, EPUB and Kindle. Book excerpt: To date, processing of high-throughput Mass Spectrometry (MS) data is accomplished using serial algorithms. Developing new methods to process MS data is an active area of research but there is no single strategy that focuses on scalability of MS based methods. Mass spectrometry is a diverse and versatile technology for high-throughput functional characterization of proteins, small molecules and metabolites in complex biological mixtures. In the recent years the technology has rapidly evolved and is now capable of generating increasingly large (multiple tera-bytes per experiment) and complex (multiple species/microbiome/high-dimensional) data sets. This rapid advance in MS instrumentation must be matched by equally fast and rapid evolution of scalable methods developed for analysis of these complex data sets. Ideally, the new methods should leverage the rich heterogeneous computational resources available in a ubiquitous fashion in the form of multicore, manycore, CPU-GPU, CPU-FPGA, and IntelPhi architectures. The absence of these high-performance computing algorithms now hinders scientific advancements for mass spectrometry research. In this book we illustrate the need for high-performance computing algorithms for MS based proteomics, and proteogenomics and showcase our progress in developing these high-performance algorithms.

Proteomics Data Analysis

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Author : Daniela Cecconi
Publisher :
ISBN 13 : 9781071616413
Total Pages : 326 pages
Book Rating : 4.6/5 (164 download)

Book Synopsis Proteomics Data Analysis by : Daniela Cecconi

Download or read book Proteomics Data Analysis written by Daniela Cecconi and published by . This book was released on 2021 with total page 326 pages. Available in PDF, EPUB and Kindle. Book excerpt: This thorough book collects methods and strategies to analyze proteomics data. It is intended to describe how data obtained by gel-based or gel-free proteomics approaches can be inspected, organized, and interpreted to extrapolate biological information. Organized into four sections, the volume explores strategies to analyze proteomics data obtained by gel-based approaches, different data analysis approaches for gel-free proteomics experiments, bioinformatic tools for the interpretation of proteomics data to obtain biological significant information, as well as methods to integrate proteomics data with other omics datasets including genomics, transcriptomics, metabolomics, and other types of data. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detailed implementation advice that will ensure high quality results in the lab. Authoritative and practical, Proteomics Data Analysis serves as an ideal guide to introduce researchers, both experienced and novice, to new tools and approaches for data analysis to encourage the further study of proteomics.

Handbook of Bioanalytics

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Author : Bogusław Buszewski
Publisher : Springer Nature
ISBN 13 : 3030956601
Total Pages : 1091 pages
Book Rating : 4.0/5 (39 download)

Book Synopsis Handbook of Bioanalytics by : Bogusław Buszewski

Download or read book Handbook of Bioanalytics written by Bogusław Buszewski and published by Springer Nature. This book was released on 2022-06-30 with total page 1091 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents an authoritative review of analytical methods used for diagnostics, medical therapy and for forensic purposes. Divided into 4 parts, the book discusses new challenges in bioanalytics, covers bioanalysis as a source of clinical, pharmaceutical and forensic information, explores natural resources as a source of biologically active compounds, and offers new analytical strategies and equipment solutions. Written by interdisciplinary expert academics, this work will appeal to a wide readership of students, researchers and professionals interested in the fields of medicine, chemistry, pharmaceutical, life and health sciences, engineering and environmental protection. Clinicians and employees of forensic laboratories will also find this work instructive and informative.

Water Security: Big Data-Driven Risk Identification, Assessment and Control of Emerging Contaminants

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Author : Bin Liang
Publisher : Elsevier
ISBN 13 : 0443141711
Total Pages : 671 pages
Book Rating : 4.4/5 (431 download)

Book Synopsis Water Security: Big Data-Driven Risk Identification, Assessment and Control of Emerging Contaminants by : Bin Liang

Download or read book Water Security: Big Data-Driven Risk Identification, Assessment and Control of Emerging Contaminants written by Bin Liang and published by Elsevier. This book was released on 2024-06-12 with total page 671 pages. Available in PDF, EPUB and Kindle. Book excerpt: Water Security: Big Data-Driven Risk Identification, Assessment and Control of Emerging Contaminants contains the latest information on big data-driven risk detection and analysis, risk assessment and environmental health effect, intelligent risk control technologies, and global control strategy of emerging contaminants. First, this book highlights advances and challenges throughout the detection of emerging chemical contaminants (e.g., antimicrobials, microplastics) by sensors or mass spectrometry, as well as emerging biological contaminant (e.g., ARGs, pathogens) by a combination of next- and third-generation sequencing technologies in aquatic environment. Second, it discusses in depth the ecological risk assessment and environmental health effects of emerging contaminants. Lastly, it presents the most up-to-date intelligent risk management technologies. This book shares instrumental global strategy and policy analysis on how to control emerging contaminants. Offering interdisciplinary and global perspectives from experts in environmental sciences and engineering, environmental microbiology and microbiome, environmental informatics and bioinformatics, intelligent systems, and knowledge engineering, this book provides an accessible and flexible resource for researchers and upper level students working in these fields. - Covers the detection, high-throughput analyses, and environmental behavior of the typical emerging chemical and biological contaminants - Focuses on chemical and biological big data driven aquatic ecological risk assessment models and techniques - Highlights the intelligent management and control technologies and policies for emerging contaminants in water environments

Introduction to Modern Liquid Chromatography

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Author : Lloyd R. Snyder
Publisher : John Wiley & Sons
ISBN 13 : 1118210395
Total Pages : 831 pages
Book Rating : 4.1/5 (182 download)

Book Synopsis Introduction to Modern Liquid Chromatography by : Lloyd R. Snyder

Download or read book Introduction to Modern Liquid Chromatography written by Lloyd R. Snyder and published by John Wiley & Sons. This book was released on 2011-09-20 with total page 831 pages. Available in PDF, EPUB and Kindle. Book excerpt: The latest edition of the authoritative reference to HPLC High-performance liquid chromatography (HPLC) is today the leading technique for chemical analysis and related applications, with an ability to separate, analyze, and/or purify virtually any sample. Snyder and Kirkland's Introduction to Modern Liquid Chromatography has long represented the premier reference to HPLC. This Third Edition, with John Dolan as added coauthor, addresses important improvements in columns and equipment, as well as major advances in our understanding of HPLC separation, our ability to solve problems that were troublesome in the past, and the application of HPLC for new kinds of samples. This carefully considered Third Edition maintains the strengths of the previous edition while significantly modifying its organization in light of recent research and experience. The text begins by introducing the reader to HPLC, its use in relation to other modern separation techniques, and its history, then leads into such specific topics as: The basis of HPLC separation and the general effects of different experimental conditions Equipment and detection The column—the "heart" of the HPLC system Reversed-phase separation, normal-phase chromatography, gradient elution, two-dimensional separation, and other techniques Computer simulation, qualitative and quantitative analysis, and method validation and quality control The separation of large molecules, including both biological and synthetic polymers Chiral separations, preparative separations, and sample preparation Systematic development of HPLC separations—new to this edition Troubleshooting tricks, techniques, and case studies for both equipment and chromatograms Designed to fulfill the needs of the full range of HPLC users, from novices to experts, Introduction to Modern Liquid Chromatography, Third Edition offers the most up-to-date, comprehensive, and accessible survey of HPLC methods and applications available.

LC-MS/MS in Proteomics

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Author : Pedro R. Cutillas
Publisher : Humana Press
ISBN 13 : 9781607617815
Total Pages : 330 pages
Book Rating : 4.6/5 (178 download)

Book Synopsis LC-MS/MS in Proteomics by : Pedro R. Cutillas

Download or read book LC-MS/MS in Proteomics written by Pedro R. Cutillas and published by Humana Press. This book was released on 2011-04-06 with total page 330 pages. Available in PDF, EPUB and Kindle. Book excerpt: With the development of new quantitative strategies and powerful bioinformatics tools to cope with the analysis of the large amounts of data generated in proteomics experiments, liquid chromatography with tandem mass spectrometry (LC-MS/MS) is making possible the analysis of proteins on a global scale, meaning that proteomics can now start competing with cDNA microarrays for the analysis of whole genomes. In LC-MS/MS in Proteomics: Methods and Applications, experts in the field provide protocols and up-to-date reviews of the applications of LC-MS/MS, with a particular focus on MS-based methods of protein and peptide quantification and the analysis of post-translational modifications. Beginning with overviews of the use of LC-M/MS in protein analysis, the book continues with topics such as protocols for the analysis of post-translational modifications, with particular focus on phosphorylation and glycosylation, popular techniques for quantitative proteomics, such as multiple reaction monitoring, metabolic labelling, and chemical tagging, biomarker discovery in biological fluids, as well as novel applications of LC-MS/MS. Written in the highly successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective subjects, lists of necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Comprehensive and cutting-edge, LC-MS/MS in Proteomics: Methods and Applications presents the techniques and concepts necessary in order to aid proteomic practitioners in the application of LC-MS/MS to essentially any biological problem.

Sample Preparation in Biological Mass Spectrometry

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Author : Alexander R. Ivanov
Publisher : Springer Science & Business Media
ISBN 13 : 9400708289
Total Pages : 1081 pages
Book Rating : 4.4/5 (7 download)

Book Synopsis Sample Preparation in Biological Mass Spectrometry by : Alexander R. Ivanov

Download or read book Sample Preparation in Biological Mass Spectrometry written by Alexander R. Ivanov and published by Springer Science & Business Media. This book was released on 2011-06-15 with total page 1081 pages. Available in PDF, EPUB and Kindle. Book excerpt: The aim of this book is to provide the researcher with important sample preparation strategies in a wide variety of analyte molecules, specimens, methods, and biological applications requiring mass spectrometric analysis as a detection end-point. In this volume we have compiled the contributions from several laboratories which are employing mass spectrometry for biological analysis. With the latest inventions and introduction of highly sophisticated mass spectrometry equipment sample preparation becomes an extremely important bottleneck of biomedical analysis. We have a goal of giving the reader several successful examples of sample preparation, development and optimization, leading to the success in analytical steps and proper conclusions made at the end of the day. This book is structured as a compilation of contributed chapters ranging from protocols to research articles and reviews. The main philosophy of this volume is that sample preparation methods have to be optimized and validated for every project, for every sample type and for every downstream analytical technique.

Hayes' Principles and Methods of Toxicology

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Author : A. Wallace Hayes
Publisher : CRC Press
ISBN 13 : 1000875776
Total Pages : 2143 pages
Book Rating : 4.0/5 (8 download)

Book Synopsis Hayes' Principles and Methods of Toxicology by : A. Wallace Hayes

Download or read book Hayes' Principles and Methods of Toxicology written by A. Wallace Hayes and published by CRC Press. This book was released on 2023-07-03 with total page 2143 pages. Available in PDF, EPUB and Kindle. Book excerpt: Hayes’ Principles and Methods of Toxicology has long been established as a reliable and informative reference for the concepts, methodologies, and assessments integral to toxicology. The new edition contains updated and new chapters with the addition of new authors while maintaining the same high standards that have made this book a benchmark resource in the field. Key Features: The comprehensive yet concise coverage of various aspects of fundamental and applied toxicology makes this book a valuable resource for educators, students, and professionals. Questions provided at the end of each chapter allow readers to test their knowledge and understanding of the material covered. All chapters have been updated and over 60 new authors have been added to reflect the dynamic nature of toxicological sciences New topics in this edition include Safety Assessment of Cosmetics and Personal Care Products, The Importance of the Dose/Rate Response, Novel Approaches and Alternative Models, Epigenetic Toxicology, and an Expanded Glossary. The volume is divided into 4 major sections, addressing fundamental principles of toxicology (Section I. "Principles of Toxicology"), major classes of established chemical hazards (Section II. "Agents"), current methods used for the assessment of various endpoints indicative of chemical toxicity (Section III. "Methods"), as well as toxicology of specific target systems and organs (Section IV. "Organ- and System-Specific Toxicology"). This volume will be a valuable tool for the audience that wishes to broaden their understanding of hazards and mechanisms of toxicity and to stay on top of the emerging methods and concepts of the rapidly advancing field of toxicology and risk assessment.

Trace Quantitative Analysis by Mass Spectrometry

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Author : Robert K. Boyd
Publisher : John Wiley & Sons
ISBN 13 : 1119964393
Total Pages : 1179 pages
Book Rating : 4.1/5 (199 download)

Book Synopsis Trace Quantitative Analysis by Mass Spectrometry by : Robert K. Boyd

Download or read book Trace Quantitative Analysis by Mass Spectrometry written by Robert K. Boyd and published by John Wiley & Sons. This book was released on 2011-08-24 with total page 1179 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a serious introduction to the subject of mass spectrometry, providing the reader with the tools and information to be well prepared to perform such demanding work in a real-life laboratory. This essential tool bridges several subjects and many disciplines including pharmaceutical, environmental and biomedical analysis that are utilizing mass spectrometry: Covers all aspects of the use of mass spectrometry for quantitation purposes Written in textbook style to facilitate understanding of this topic Presents fundamentals and real-world examples in a ‘learning-though-doing’ style

Processing Metabolomics and Proteomics Data with Open Software

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Author : Robert Winkler
Publisher : Royal Society of Chemistry
ISBN 13 : 1788017218
Total Pages : 460 pages
Book Rating : 4.7/5 (88 download)

Book Synopsis Processing Metabolomics and Proteomics Data with Open Software by : Robert Winkler

Download or read book Processing Metabolomics and Proteomics Data with Open Software written by Robert Winkler and published by Royal Society of Chemistry. This book was released on 2020-03-19 with total page 460 pages. Available in PDF, EPUB and Kindle. Book excerpt: Metabolomics and proteomics allow deep insights into the chemistry and physiology of biological systems. This book expounds open-source programs, platforms and programming tools for analysing metabolomics and proteomics mass spectrometry data. In contrast to commercial software, open-source software is created by the academic community, which facilitates the direct interaction between users and developers and accelerates the implementation of new concepts and ideas. The first section of the book covers the basics of mass spectrometry, experimental strategies, data operations, the open-source philosophy, metabolomics, proteomics and statistics/ data mining. In the second section, active programmers and users describe available software packages. Included tutorials, datasets and code examples can be used for training and for building custom workflows. Finally, every reader is invited to participate in the open science movement.

Proteomics Sample Preparation

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Author : Jörg von Hagen
Publisher : John Wiley & Sons
ISBN 13 : 3527644695
Total Pages : 498 pages
Book Rating : 4.5/5 (276 download)

Book Synopsis Proteomics Sample Preparation by : Jörg von Hagen

Download or read book Proteomics Sample Preparation written by Jörg von Hagen and published by John Wiley & Sons. This book was released on 2011-08-24 with total page 498 pages. Available in PDF, EPUB and Kindle. Book excerpt: This long-awaited first guide to sample preparation for proteomics studies overcomes a major bottleneck in this fast growing technique within the molecular life sciences. By addressing the topic from three different angles -- sample, method and aim of the study -- this practical reference has something for every proteomics researcher. Following an introduction to the field, the book looks at sample preparation for specific techniques and applications and finishes with a section on the preparation of sample types. For each method described, a summary of the pros and cons is given, as well as step-by-step protocols adaptable to any specific proteome analysis task.

Protein and Peptide Analysis by LC-MS

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Author : Thomas Letzel
Publisher : Royal Society of Chemistry
ISBN 13 : 1849733147
Total Pages : 195 pages
Book Rating : 4.8/5 (497 download)

Book Synopsis Protein and Peptide Analysis by LC-MS by : Thomas Letzel

Download or read book Protein and Peptide Analysis by LC-MS written by Thomas Letzel and published by Royal Society of Chemistry. This book was released on 2011-07-22 with total page 195 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is the first example in presenting LC-MS strategies for the analysis of peptides and proteins with detailed information and hints about the needs and problems described from experts on-the-job. The best advantage is -for sure- the practical insight of experienced analysts into their novel protein analysis techniques. Readers starting in 'Proteomics' should be able to repeat each experiment with own equipment and own protein samples, like clean-up, direct protein analysis, after (online) digest, with modifications and others. Furthermore, the reader will learn more about strategies in protein analysis, like quantitative analysis, industrial standards, functional analysis and more.

The Encyclopedia of Mass Spectrometry

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Author : Michael L. Gross
Publisher :
ISBN 13 : 9780080438474
Total Pages : 1098 pages
Book Rating : 4.4/5 (384 download)

Book Synopsis The Encyclopedia of Mass Spectrometry by : Michael L. Gross

Download or read book The Encyclopedia of Mass Spectrometry written by Michael L. Gross and published by . This book was released on 2006-10-30 with total page 1098 pages. Available in PDF, EPUB and Kindle. Book excerpt: Presents information on the biographies of recognized pioneers and innovators in the field of mass spectrometry. - Highlights over 120 innovators in mass spectrometry, including several Nobel Prize winners. Discusses instrumentation and their uses, also providing interesting information on the careers, characters, and life stories of the people who did the work. Offers unique insight into the careers and personalities of luminaries in the field.

HPLC of Peptides and Proteins

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Author : Marie-Isabel Aguilar
Publisher : Springer Science & Business Media
ISBN 13 : 1592597424
Total Pages : 411 pages
Book Rating : 4.5/5 (925 download)

Book Synopsis HPLC of Peptides and Proteins by : Marie-Isabel Aguilar

Download or read book HPLC of Peptides and Proteins written by Marie-Isabel Aguilar and published by Springer Science & Business Media. This book was released on 2008-02-03 with total page 411 pages. Available in PDF, EPUB and Kindle. Book excerpt: The introduction of high-performance liquid chromatography (HPLC) to the analysis of peptides and proteins some 25 years ago revolutionized the biological sciences by enabling the rapid and sensitive analysis of peptide and protein structure through the exquisite speed, sensitivity, and resolution that can be easily obtained. Today, HPLC in its various modes has become the pivotal technique in the characterization of peptides and proteins and currently plays a critical role in both our understanding of biological processes and in the development of peptide- and protein-based pharmaceuticals. The number of applications of HPLC in peptide and protein purification continues to expand at an extremely rapid rate. Solid-phase peptide synthesis and recombinant DNA techniques have allowed the production of large quantities of peptides and proteins that need to be highly purified. HPLC techniques are also used extensively in the isolation and characterization of novel proteins that will become increasingly important in the postgenomic age. The design of multidimensional purification schemes to achieve high levels of product purity further demonstrates the power of HPLC techniques not only in the characterization of cellular events, but also in the production of pepti- and protein-based therapeutics. HPLC continues to be at the heart of the analytical techniques with which scientists in both academia and in industry must arm themselves to be able to fully characterize the identity, purity, and potency of peptides and proteins.

Proteomic and Metabolomic Approaches to Biomarker Discovery

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Author : Haleem J. Issaq
Publisher : Academic Press
ISBN 13 : 0123947952
Total Pages : 489 pages
Book Rating : 4.1/5 (239 download)

Book Synopsis Proteomic and Metabolomic Approaches to Biomarker Discovery by : Haleem J. Issaq

Download or read book Proteomic and Metabolomic Approaches to Biomarker Discovery written by Haleem J. Issaq and published by Academic Press. This book was released on 2013-05-20 with total page 489 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteomic and Metabolomic Approaches to Biomarker Discovery demonstrates how to leverage biomarkers to improve accuracy and reduce errors in research. Disease biomarker discovery is one of the most vibrant and important areas of research today, as the identification of reliable biomarkers has an enormous impact on disease diagnosis, selection of treatment regimens, and therapeutic monitoring. Various techniques are used in the biomarker discovery process, including techniques used in proteomics, the study of the proteins that make up an organism, and metabolomics, the study of chemical fingerprints created from cellular processes. Proteomic and Metabolomic Approaches to Biomarker Discovery is the only publication that covers techniques from both proteomics and metabolomics and includes all steps involved in biomarker discovery, from study design to study execution. The book describes methods, and presents a standard operating procedure for sample selection, preparation, and storage, as well as data analysis and modeling. This new standard effectively eliminates the differing methodologies used in studies and creates a unified approach. Readers will learn the advantages and disadvantages of the various techniques discussed, as well as potential difficulties inherent to all steps in the biomarker discovery process. A vital resource for biochemists, biologists, analytical chemists, bioanalytical chemists, clinical and medical technicians, researchers in pharmaceuticals, and graduate students, Proteomic and Metabolomic Approaches to Biomarker Discovery provides the information needed to reduce clinical error in the execution of research. - Describes the use of biomarkers to reduce clinical errors in research - Includes techniques from a range of biomarker discoveries - Covers all steps involved in biomarker discovery, from study design to study execution

Chemical Proteomics

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Author : Gerard Drewes
Publisher : Humana Press
ISBN 13 : 9781617793639
Total Pages : 0 pages
Book Rating : 4.7/5 (936 download)

Book Synopsis Chemical Proteomics by : Gerard Drewes

Download or read book Chemical Proteomics written by Gerard Drewes and published by Humana Press. This book was released on 2011-11-08 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The multidisciplinary science of chemical proteomics studies how small molecules of synthetic or natural origin bind to proteins and modulate their function. In Chemical Proteomics: Methods and Protocols, expert researchers in the field provide key techniques to investigate chemical proteomics focusing on analytical strategies, how probes are generated, techniques for the discovery of small molecule targets and the probing of target function, and small molecule ligand and drug discovery. Written in the highly successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Chemical Proteomics : Methods and Protocols seeks to provide methodologies that will contribute to a wider application of chemical proteomics methods in biochemical and cell biological laboratories.

Fish Structural Proteins and its Derivatives: Functionality and Applications

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Author : Maya Raman
Publisher : Springer Nature
ISBN 13 : 9819725623
Total Pages : 202 pages
Book Rating : 4.8/5 (197 download)

Book Synopsis Fish Structural Proteins and its Derivatives: Functionality and Applications by : Maya Raman

Download or read book Fish Structural Proteins and its Derivatives: Functionality and Applications written by Maya Raman and published by Springer Nature. This book was released on with total page 202 pages. Available in PDF, EPUB and Kindle. Book excerpt: