Reproducible Bioinformatics with Python

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ISBN 10 : OCLC:1237637606
Pages : 350 pages
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Rating : 4./5 ( users download)


Download Reproducible Bioinformatics with Python by Ken Youens-Clark PDF/Ebook Free clicking on the below button will initiate the downloading process of Reproducible Bioinformatics with Python by Ken Youens-Clark. This book is available in ePub and PDF format with a single click unlimited downloads. Life scientists today urgently need training in bioinformatics skills. Too many bioinformatics programs are poorly written and barely maintained--usually by students and postdoc researchers who've never learned basic programming skills. This practical guide shows how to exploit the best parts of Python for solving problems in biology while also creating documented, tested, reproducible software. Ken Youens-Clark, author of Tiny Python Projects (Manning), demonstrates how to write effective Python code and how to use tests to write and refactor scientific programs. You'll learn the latest Python features and tools--such as linters, formatters, type checkers, and tests--to write documented and tested programs. Create command-line Python programs that document and validate parameters Write tests to verify refactor programs and confirm they're correct Address bioinformatics ideas using Python data structures (strings, lists, and sets) and modules such as Biopython Create reproducible shortcuts and workflows using makefiles Parse essential bioinformatics file formats such as FASTA, FASTQ, and SwissProt Find patterns of text using regular expressions Use higher-order functions in Python like filter() and map().


Mastering Python for Bioinformatics

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Publisher : "O'Reilly Media, Inc."
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ISBN 10 : 9781098100858
Pages : 456 pages
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Rating : 4.0/5 (1 users download)


Download Mastering Python for Bioinformatics by Ken Youens-Clark PDF/Ebook Free clicking on the below button will initiate the downloading process of Mastering Python for Bioinformatics by Ken Youens-Clark. This book is available in ePub and PDF format with a single click unlimited downloads. Life scientists today urgently need training in bioinformatics skills. Too many bioinformatics programs are poorly written and barely maintained--usually by students and researchers who've never learned basic programming skills. This practical guide shows postdoc bioinformatics professionals and students how to exploit the best parts of Python to solve problems in biology while creating documented, tested, reproducible software. Ken Youens-Clark, author of Tiny Python Projects (Manning), demonstrates not only how to write effective Python code but also how to use tests to write and refactor scientific programs. You'll learn the latest Python features and toolsâ??including linters, formatters, type checkers, and testsâ??to create documented and tested programs. You'll also tackle 14 challenges in Rosalind, a problem-solving platform for learning bioinformatics and programming. Create command-line Python programs to document and validate parameters Write tests to verify refactor programs and confirm they're correct Address bioinformatics ideas using Python data structures and modules such as Biopython Create reproducible shortcuts and workflows using makefiles Parse essential bioinformatics file formats such as FASTA and FASTQ Find patterns of text using regular expressions Use higher-order functions in Python like filter(), map(), and reduce()


Reproducible Bioinformatics with Python

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Publisher : O'Reilly Media
Release Date :
ISBN 10 : 1098100883
Pages : 350 pages
File Format : PDF, EPUB, TEXT, KINDLE or MOBI
Rating : 4.9/5 (98 users download)


Download Reproducible Bioinformatics with Python by Ken Youens-Clark PDF/Ebook Free clicking on the below button will initiate the downloading process of Reproducible Bioinformatics with Python by Ken Youens-Clark. This book is available in ePub and PDF format with a single click unlimited downloads. Life scientists today urgently need training in bioinformatics skills. Too many bioinformatics programs are poorly written and barely maintained--usually by students and postdoc researchers who've never learned basic programming skills. This practical guide shows how to exploit the best parts of Python for solving problems in biology while also creating documented, tested, reproducible software. Ken Youens-Clark, author of Tiny Python Projects (Manning), demonstrates how to write effective Python code and how to use tests to write and refactor scientific programs. You'll learn the latest Python features and tools--such as linters, formatters, type checkers, and tests--to write documented and tested programs. Create command-line Python programs that document and validate parameters Write tests to verify refactor programs and confirm they're correct Address bioinformatics ideas using Python data structures (strings, lists, and sets) and modules such as Biopython Create reproducible shortcuts and workflows using makefiles Parse essential bioinformatics file formats such as FASTA, FASTQ, and SwissProt Find patterns of text using regular expressions Use higher-order functions in Python like filter() and map()


Implementing Reproducible Research

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Publisher : CRC Press
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ISBN 10 : 9781315360393
Pages : 448 pages
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Rating : 4.6/5 (36 users download)


Download Implementing Reproducible Research by Victoria Stodden PDF/Ebook Free clicking on the below button will initiate the downloading process of Implementing Reproducible Research by Victoria Stodden. This book is available in ePub and PDF format with a single click unlimited downloads. In computational science, reproducibility requires that researchers make code and data available to others so that the data can be analyzed in a similar manner as in the original publication. Code must be available to be distributed, data must be accessible in a readable format, and a platform must be available for widely distributing the data and code. In addition, both data and code need to be licensed permissively enough so that others can reproduce the work without a substantial legal burden. Implementing Reproducible Research covers many of the elements necessary for conducting and distributing reproducible research. It explains how to accurately reproduce a scientific result. Divided into three parts, the book discusses the tools, practices, and dissemination platforms for ensuring reproducibility in computational science. It describes: Computational tools, such as Sweave, knitr, VisTrails, Sumatra, CDE, and the Declaratron system Open source practices, good programming practices, trends in open science, and the role of cloud computing in reproducible research Software and methodological platforms, including open source software packages, RunMyCode platform, and open access journals Each part presents contributions from leaders who have developed software and other products that have advanced the field. Supplementary material is available at www.ImplementingRR.org.


Bioinformatics Data Skills

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Publisher : "O'Reilly Media, Inc."
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ISBN 10 : 9781449367503
Pages : 538 pages
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Rating : 4.6/5 (367 users download)


Download Bioinformatics Data Skills by Vince Buffalo PDF/Ebook Free clicking on the below button will initiate the downloading process of Bioinformatics Data Skills by Vince Buffalo. This book is available in ePub and PDF format with a single click unlimited downloads. Learn the data skills necessary for turning large sequencing datasets into reproducible and robust biological findings. With this practical guide, you’ll learn how to use freely available open source tools to extract meaning from large complex biological data sets. At no other point in human history has our ability to understand life’s complexities been so dependent on our skills to work with and analyze data. This intermediate-level book teaches the general computational and data skills you need to analyze biological data. If you have experience with a scripting language like Python, you’re ready to get started. Go from handling small problems with messy scripts to tackling large problems with clever methods and tools Process bioinformatics data with powerful Unix pipelines and data tools Learn how to use exploratory data analysis techniques in the R language Use efficient methods to work with genomic range data and range operations Work with common genomics data file formats like FASTA, FASTQ, SAM, and BAM Manage your bioinformatics project with the Git version control system Tackle tedious data processing tasks with with Bash scripts and Makefiles


Computational Intelligence Methods for Bioinformatics and Biostatistics

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Publisher : Springer
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ISBN 10 : 9783319443324
Pages : 286 pages
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Rating : 4.4/5 (443 users download)


Download Computational Intelligence Methods for Bioinformatics and Biostatistics by Claudia Angelini PDF/Ebook Free clicking on the below button will initiate the downloading process of Computational Intelligence Methods for Bioinformatics and Biostatistics by Claudia Angelini. This book is available in ePub and PDF format with a single click unlimited downloads. This book constitutes the thoroughly refereed post-conference proceedings of the 12th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, CIBB 2015, held in Naples, Italy, in September, 2015. The 21 revised full papers presented were carefully reviewed and selected from 24 submissions. They present problems concerning computational techniques in bioinformatics, systems biology and medical informatics discussing cutting edge methodologies and accelerate life science discoveries, as well as novel challenges with an high impact on molecular biology and translational medicine.


Enhancing Scientific Reproducibility in Biomedical Research Through Transparent Reporting

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Publisher : National Academies Press
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ISBN 10 : 9780309664066
Pages : 142 pages
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Rating : 4.6/5 (664 users download)


Download Enhancing Scientific Reproducibility in Biomedical Research Through Transparent Reporting by National Academies of Sciences, Engineering, and Medicine PDF/Ebook Free clicking on the below button will initiate the downloading process of Enhancing Scientific Reproducibility in Biomedical Research Through Transparent Reporting by National Academies of Sciences, Engineering, and Medicine. This book is available in ePub and PDF format with a single click unlimited downloads. Sharing knowledge is what drives scientific progress - each new advance or innovation in biomedical research builds on previous observations. However, for experimental findings to be broadly accepted as credible by the scientific community, they must be verified by other researchers. An essential step is for researchers to report their findings in a manner that is understandable to others in the scientific community and provide sufficient information for others to validate the original results and build on them. In recent years, concern has been growing over a number of studies that have failed to replicate previous results and evidence from larger meta-analyses, which have pointed to the lack of reproducibility in biomedical research. On September 25 and 26, 2019, the National Academies of Science, Engineering, and Medicine hosted a public workshop in Washington, DC, to discuss the current state of transparency in the reporting of preclinical biomedical research and to explore opportunities for harmonizing reporting guidelines across journals and funding agencies. Convened jointly by the Forum on Drug Discovery, Development, and Translation; the Forum on Neuroscience and Nervous System Disorders; the National Cancer Policy Forum; and the Roundtable on Genomics and Precision Health, the workshop primarily focused on transparent reporting in preclinical research, but also considered lessons learned and best practices from clinical research reporting. This publication summarizes the presentation and discussion of the workshop.


Reproducibility and Rigour in Computational Neuroscience

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Publisher : Frontiers Media SA
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ISBN 10 : 9782889638383
Pages : pages
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Rating : 4.3/5 (638 users download)


Download Reproducibility and Rigour in Computational Neuroscience by Sharon Crook PDF/Ebook Free clicking on the below button will initiate the downloading process of Reproducibility and Rigour in Computational Neuroscience by Sharon Crook. This book is available in ePub and PDF format with a single click unlimited downloads.


Evolutionary Genetics

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Publisher : Oxford University Press
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ISBN 10 : 9780192566652
Pages : 352 pages
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Rating : 4.6/5 (566 users download)


Download Evolutionary Genetics by Glenn-Peter Sætre PDF/Ebook Free clicking on the below button will initiate the downloading process of Evolutionary Genetics by Glenn-Peter Sætre. This book is available in ePub and PDF format with a single click unlimited downloads. With recent technological advances, vast quantities of genetic and genomic data are being generated at an ever-increasing pace. The explosion in access to data has transformed the field of evolutionary genetics. A thorough understanding of evolutionary principles is essential for making sense of this, but new skill sets are also needed to handle and analyze big data. This contemporary textbook covers all the major components of modern evolutionary genetics, carefully explaining fundamental processes such as mutation, natural selection, genetic drift, and speciation. It also draws on a rich literature of exciting and inspiring examples to demonstrate the diversity of evolutionary research, including an emphasis on how evolution and selection has shaped our own species. Practical experience is essential for developing an understanding of how to use genetic and genomic data to analyze and interpret results in meaningful ways. In addition to the main text, a series of online tutorials using the R language serves as an introduction to programming, statistics, and analysis. Indeed the R environment stands out as an ideal all-purpose source platform to handle and analyze such data. The book and its online materials take full advantage of the authors' own experience in working in a post-genomic revolution world, and introduces readers to the plethora of molecular and analytical methods that have only recently become available. Evolutionary Genetics is an advanced but accessible textbook aimed principally at students of various levels (from undergraduate to postgraduate) but also for researchers looking for an updated introduction to modern evolutionary biology and genetics.


The Practice of Reproducible Research

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Publisher : Univ of California Press
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ISBN 10 : 9780520294752
Pages : 368 pages
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Rating : 4.9/5 (294 users download)


Download The Practice of Reproducible Research by Justin Kitzes PDF/Ebook Free clicking on the below button will initiate the downloading process of The Practice of Reproducible Research by Justin Kitzes. This book is available in ePub and PDF format with a single click unlimited downloads. The Practice of Reproducible Research presents concrete examples of how researchers in the data-intensive sciences are working to improve the reproducibility of their research projects. In each of the thirty-one case studies in this volume, the author or team describes the workflow that they used to complete a real-world research project. Authors highlight how they utilized particular tools, ideas, and practices to support reproducibility, emphasizing the very practical how, rather than the why or what, of conducting reproducible research. Part 1 provides an accessible introduction to reproducible research, a basic reproducible research project template, and a synthesis of lessons learned from across the thirty-one case studies. Parts 2 and 3 focus on the case studies themselves. The Practice of Reproducible Research is an invaluable resource for students and researchers who wish to better understand the practice of data-intensive sciences and learn how to make their own research more reproducible.


R Programming for Bioinformatics

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Publisher : CRC Press
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ISBN 10 : 1420063685
Pages : 328 pages
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Rating : 4.2/5 (42 users download)


Download R Programming for Bioinformatics by Robert Gentleman PDF/Ebook Free clicking on the below button will initiate the downloading process of R Programming for Bioinformatics by Robert Gentleman. This book is available in ePub and PDF format with a single click unlimited downloads. Due to its data handling and modeling capabilities as well as its flexibility, R is becoming the most widely used software in bioinformatics. R Programming for Bioinformatics explores the programming skills needed to use this software tool for the solution of bioinformatics and computational biology problems. Drawing on the author’s first-hand experiences as an expert in R, the book begins with coverage on the general properties of the R language, several unique programming aspects of R, and object-oriented programming in R. It presents methods for data input and output as well as database interactions. The author also examines different facets of string handling and manipulations, discusses the interfacing of R with other languages, and describes how to write software packages. He concludes with a discussion on the debugging and profiling of R code. With numerous examples and exercises, this practical guide focuses on developing R programming skills in order to tackle problems encountered in bioinformatics and computational biology.


Systems Medicine

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Publisher : Academic Press
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ISBN 10 : 9780128160787
Pages : 1589 pages
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Rating : 4.6/5 (16 users download)


Download Systems Medicine by PDF/Ebook Free clicking on the below button will initiate the downloading process of Systems Medicine by . This book is available in ePub and PDF format with a single click unlimited downloads. Technological advances in generated molecular and cell biological data are transforming biomedical research. Sequencing, multi-omics and imaging technologies are likely to have deep impact on the future of medical practice. In parallel to technological developments, methodologies to gather, integrate, visualize and analyze heterogeneous and large-scale data sets are needed to develop new approaches for diagnosis, prognosis and therapy. Systems Medicine: Integrative, Qualitative and Computational Approaches is an innovative, interdisciplinary and integrative approach that extends the concept of systems biology and the unprecedented insights that computational methods and mathematical modeling offer of the interactions and network behavior of complex biological systems, to novel clinically relevant applications for the design of more successful prognostic, diagnostic and therapeutic approaches. This 3 volume work features 132 entries from renowned experts in the fields and covers the tools, methods, algorithms and data analysis workflows used for integrating and analyzing multi-dimensional data routinely generated in clinical settings with the aim of providing medical practitioners with robust clinical decision support systems. Importantly the work delves into the applications of systems medicine in areas such as tumor systems biology, metabolic and cardiovascular diseases as well as immunology and infectious diseases amongst others. This is a fundamental resource for biomedical students and researchers as well as medical practitioners who need to need to adopt advances in computational tools and methods into the clinical practice. Encyclopedic coverage: ‘one-stop’ resource for access to information written by world-leading scholars in the field of Systems Biology and Systems Medicine, with easy cross-referencing of related articles to promote understanding and further research Authoritative: the whole work is authored and edited by recognized experts in the field, with a range of different expertise, ensuring a high quality standard Digitally innovative: Hyperlinked references and further readings, cross-references and diagrams/images will allow readers to easily navigate a wealth of information


Ontology, Epistemology, and Teleology for Modeling and Simulation

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Publisher : Springer Science & Business Media
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ISBN 10 : 9783642311406
Pages : 372 pages
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Rating : 4.1/5 (311 users download)


Download Ontology, Epistemology, and Teleology for Modeling and Simulation by Andreas Tolk PDF/Ebook Free clicking on the below button will initiate the downloading process of Ontology, Epistemology, and Teleology for Modeling and Simulation by Andreas Tolk. This book is available in ePub and PDF format with a single click unlimited downloads. In this book, internationally recognized experts in philosophy of science, computer science, and modeling and simulation are contributing to the discussion on how ontology, epistemology, and teleology will contribute to enable the next generation of intelligent modeling and simulation applications. It is well understood that a simulation can provide the technical means to display the behavior of a system over time, including following observed trends to predict future possible states, but how reliable and trustworthy are such predictions? The questions about what we can know (ontology), how we gain new knowledge (epistemology), and what we do with this knowledge (teleology) are therefore illuminated from these very different perspectives, as each experts uses a different facet to look at these challenges. The result of bringing these perspectives into one book is a challenging compendium that gives room for a spectrum of challenges: from general philosophy questions, such as can we use modeling and simulation and other computational means at all to discover new knowledge, down to computational methods to improve semantic interoperability between systems or methods addressing how to apply the recent insights of service oriented approaches to support distributed artificial intelligence. As such, this book has been compiled as an entry point to new domains for students, scholars, and practitioners and to raise the curiosity in them to learn more to fully address the topics of ontology, epistemology, and teleology from philosophical, computational, and conceptual viewpoints.


Bioinformatics and Biomedical Engineering

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Publisher : Springer Nature
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ISBN 10 : 9783031077043
Pages : 462 pages
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Rating : 4.7/5 (77 users download)


Download Bioinformatics and Biomedical Engineering by Ignacio Rojas PDF/Ebook Free clicking on the below button will initiate the downloading process of Bioinformatics and Biomedical Engineering by Ignacio Rojas. This book is available in ePub and PDF format with a single click unlimited downloads. This volume constitutes the proceedings of the 9th International Work-Conference on IWBBIO 2020, held in Maspalomas, Gran Canaria, Spain, in June 2022. The total of 75 papers presented in the proceedings, was carefully reviewed and selected from 212 submissions. The papers cover the latest ideas and realizations in the foundations, theory, models, and applications for interdisciplinary and multidisciplinary research encompassing disciplines of computer science, mathematics, statistics, biology, bioinformatics, and biomedicine.


Big Data Analysis for Bioinformatics and Biomedical Discoveries

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Publisher : CRC Press
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ISBN 10 : 9781498724548
Pages : 274 pages
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Rating : 4.2/5 (724 users download)


Download Big Data Analysis for Bioinformatics and Biomedical Discoveries by Shui Qing Ye PDF/Ebook Free clicking on the below button will initiate the downloading process of Big Data Analysis for Bioinformatics and Biomedical Discoveries by Shui Qing Ye. This book is available in ePub and PDF format with a single click unlimited downloads. Demystifies Biomedical and Biological Big Data Analyses Big Data Analysis for Bioinformatics and Biomedical Discoveries provides a practical guide to the nuts and bolts of Big Data, enabling you to quickly and effectively harness the power of Big Data to make groundbreaking biological discoveries, carry out translational medical research, and implement personalized genomic medicine. Contributing to the NIH Big Data to Knowledge (BD2K) initiative, the book enhances your computational and quantitative skills so that you can exploit the Big Data being generated in the current omics era. The book explores many significant topics of Big Data analyses in an easily understandable format. It describes popular tools and software for Big Data analyses and explains next-generation DNA sequencing data analyses. It also discusses comprehensive Big Data analyses of several major areas, including the integration of omics data, pharmacogenomics, electronic health record data, and drug discovery. Accessible to biologists, biomedical scientists, bioinformaticians, and computer data analysts, the book keeps complex mathematical deductions and jargon to a minimum. Each chapter includes a theoretical introduction, example applications, data analysis principles, step-by-step tutorials, and authoritative references.


Bioinformatics and Functional Genomics

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Publisher : John Wiley & Sons
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ISBN 10 : 9781118581780
Pages : 1168 pages
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Rating : 4.8/5 (581 users download)


Download Bioinformatics and Functional Genomics by Jonathan Pevsner PDF/Ebook Free clicking on the below button will initiate the downloading process of Bioinformatics and Functional Genomics by Jonathan Pevsner. This book is available in ePub and PDF format with a single click unlimited downloads. The bestselling introduction to bioinformatics and genomics – now in its third edition Widely received in its previous editions, Bioinformatics and Functional Genomics offers the most broad-based introduction to this explosive new discipline. Now in a thoroughly updated and expanded third edition, it continues to be the go-to source for students and professionals involved in biomedical research. This book provides up-to-the-minute coverage of the fields of bioinformatics and genomics. Features new to this edition include: Extensive revisions and a slight reorder of chapters for a more effective organization A brand new chapter on next-generation sequencing An expanded companion website, also updated as and when new information becomes available Greater emphasis on a computational approach, with clear guidance of how software tools work and introductions to the use of command-line tools such as software for next-generation sequence analysis, the R programming language, and NCBI search utilities The book is complemented by lavish illustrations and more than 500 figures and tables - many newly-created for the third edition to enhance clarity and understanding. Each chapter includes learning objectives, a problem set, pitfalls section, boxes explaining key techniques and mathematics/statistics principles, a summary, recommended reading, and a list of freely available software. Readers may visit a related Web page for supplemental information such as PowerPoints and audiovisual files of lectures, and videocasts of how to perform many basic operations: www.wiley.com/go/pevsnerbioinformatics. Bioinformatics and Functional Genomics, Third Edition serves as an excellent single-source textbook for advanced undergraduate and beginning graduate-level courses in the biological sciences and computer sciences. It is also an indispensable resource for biologists in a broad variety of disciplines who use the tools of bioinformatics and genomics to study particular research problems; bioinformaticists and computer scientists who develop computer algorithms and databases; and medical researchers and clinicians who want to understand the genomic basis of viral, bacterial, parasitic, or other diseases.


Introduction to Biomedical Data Science

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Publisher : Lulu.com
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ISBN 10 : 9781794761735
Pages : 258 pages
File Format : PDF, EPUB, TEXT, KINDLE or MOBI
Rating : 4.6/5 (761 users download)


Download Introduction to Biomedical Data Science by Robert Hoyt PDF/Ebook Free clicking on the below button will initiate the downloading process of Introduction to Biomedical Data Science by Robert Hoyt. This book is available in ePub and PDF format with a single click unlimited downloads. Introduction to Biomedical Data Science aims to fill the data science knowledge gap experienced by many clinical, administrative and technical staff. The textbook begins with an overview of what biomedical data science is and then embarks on a tour of topics beginning with spreadsheet tips and tricks and ending with artificial intelligence. In between, important topics are covered such as biostatistics, data visualization, database systems, big data, programming languages, bioinformatics, and machine learning. The textbook is available as a paperback and ebook. Visit the companion website at https: //www.informaticseducation.org for more information. Key features: Real healthcare datasets are used for examples and exercises; Knowledge of a programming language or higher math is not required; Multiple free or open source software programs are presented; YouTube videos are embedded in most chapters; Extensive resources chapter for further reading and learning; PowerPoints and an Instructor Manual


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