Essential Computing Skills For Biologists PDF Download
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Author | : Stefano Allesina |
Publisher | : Princeton University Press |
Total Pages | : 440 |
Release | : 2019-01-15 |
Genre | : Computers |
ISBN | : 0691182752 |
Download Computing Skills for Biologists Book in PDF, ePub and Kindle
A concise introduction to key computing skills for biologists While biological data continues to grow exponentially in size and quality, many of today’s biologists are not trained adequately in the computing skills necessary for leveraging this information deluge. In Computing Skills for Biologists, Stefano Allesina and Madlen Wilmes present a valuable toolbox for the effective analysis of biological data. Based on the authors’ experiences teaching scientific computing at the University of Chicago, this textbook emphasizes the automation of repetitive tasks and the construction of pipelines for data organization, analysis, visualization, and publication. Stressing practice rather than theory, the book’s examples and exercises are drawn from actual biological data and solve cogent problems spanning the entire breadth of biological disciplines, including ecology, genetics, microbiology, and molecular biology. Beginners will benefit from the many examples explained step-by-step, while more seasoned researchers will learn how to combine tools to make biological data analysis robust and reproducible. The book uses free software and code that can be run on any platform. Computing Skills for Biologists is ideal for scientists wanting to improve their technical skills and instructors looking to teach the main computing tools essential for biology research in the twenty-first century. Excellent resource for acquiring comprehensive computing skills Both novice and experienced scientists will increase efficiency by building automated and reproducible pipelines for biological data analysis Code examples based on published data spanning the breadth of biological disciplines Detailed solutions provided for exercises in each chapter Extensive companion website
Author | : Wang Ziling |
Publisher | : World Scientific |
Total Pages | : 304 |
Release | : 2013-10-10 |
Genre | : Computers |
ISBN | : 1848169264 |
Download Essential Computing Skills for Biologists Book in PDF, ePub and Kindle
This is a handbook of methods and protocols for biologists. It aimed at undergraduate, graduate students and researchers originally trained in biological or medical sciences who need to know how to access the data archives of genomes, proteins, metabolites, gene expression profiles and the questions these data and tools can answer. For each chapter, the conceptual and experimental background is provided, together with specific guidelines for handling raw data, including preprocessing and analysis. The content is structured into three parts. Part one introduces basic knowledge about popular bioinformatics tools, databases and web resources. Part two presents examples of omics bioinformatics applications. Part three provides basic statistical analysis skills and programming skills needed to handle and analyze omics datasets.
Author | : Stefano Allesina |
Publisher | : Princeton University Press |
Total Pages | : 440 |
Release | : 2019-01-15 |
Genre | : Science |
ISBN | : 0691183961 |
Download Computing Skills for Biologists Book in PDF, ePub and Kindle
A concise introduction to key computing skills for biologists While biological data continues to grow exponentially in size and quality, many of today’s biologists are not trained adequately in the computing skills necessary for leveraging this information deluge. In Computing Skills for Biologists, Stefano Allesina and Madlen Wilmes present a valuable toolbox for the effective analysis of biological data. Based on the authors’ experiences teaching scientific computing at the University of Chicago, this textbook emphasizes the automation of repetitive tasks and the construction of pipelines for data organization, analysis, visualization, and publication. Stressing practice rather than theory, the book’s examples and exercises are drawn from actual biological data and solve cogent problems spanning the entire breadth of biological disciplines, including ecology, genetics, microbiology, and molecular biology. Beginners will benefit from the many examples explained step-by-step, while more seasoned researchers will learn how to combine tools to make biological data analysis robust and reproducible. The book uses free software and code that can be run on any platform. Computing Skills for Biologists is ideal for scientists wanting to improve their technical skills and instructors looking to teach the main computing tools essential for biology research in the twenty-first century. Excellent resource for acquiring comprehensive computing skills Both novice and experienced scientists will increase efficiency by building automated and reproducible pipelines for biological data analysis Code examples based on published data spanning the breadth of biological disciplines Detailed solutions provided for exercises in each chapter Extensive companion website
Author | : Ran Libeskind-Hadas |
Publisher | : Cambridge University Press |
Total Pages | : 289 |
Release | : 2014-09-22 |
Genre | : Science |
ISBN | : 1316061337 |
Download Computing for Biologists Book in PDF, ePub and Kindle
Computing is revolutionizing the practice of biology. This book, which assumes no prior computing experience, provides students with the tools to write their own Python programs and to understand fundamental concepts in computational biology and bioinformatics. Each major part of the book begins with a compelling biological question, followed by the algorithmic ideas and programming tools necessary to explore it: the origins of pathogenicity are examined using gene finding, the evolutionary history of sex determination systems is studied using sequence alignment, and the origin of modern humans is addressed using phylogenetic methods. In addition to providing general programming skills, this book explores the design of efficient algorithms, simulation, NP-hardness, and the maximum likelihood method, among other key concepts and methods. Easy-to-read and designed to equip students with the skills to write programs for solving a range of biological problems, the book is accompanied by numerous programming exercises, available at www.cs.hmc.edu/CFB.
Author | : Steven H.D. Haddock |
Publisher | : Sinauer |
Total Pages | : 0 |
Release | : 2011-04-22 |
Genre | : Medical |
ISBN | : 9780878933914 |
Download Practical Computing for Biologists Book in PDF, ePub and Kindle
Practical Computing for Biologists shows you how to use many freely available computing tools to work more powerfully and effectively. The book was born out of the authors' own experience in developing tools for their research and helping other biologists with their computational problems. Many of the techniques are relevant to molecular bioinformatics but the scope of the book is much broader, covering topics and techniques that are applicable to a range of scientific endeavours. Twenty-two chapters organized into six parts address the following topics (and more; see Contents): • Searching with regular expressions • The Unix command line • Python programming and debugging • Creating and editing graphics • Databases • Performing analyses on remote servers • Working with electronics While the main narrative focuses on Mac OS X, most of the concepts and examples apply to any operating system. Where there are differences for Windows and Linux users, parallel instructions are provided in the margin and in an appendix. The book is designed to be used as a self-guided resource for researchers, a companion book in a course, or as a primary textbook. Practical Computing for Biologists will free you from the most frustrating and time-consuming aspects of data processing so you can focus on the pleasures of scientific inquiry.
Author | : Shawn T. O'Neil |
Publisher | : |
Total Pages | : 0 |
Release | : 2017-12-21 |
Genre | : Science |
ISBN | : 9780870719264 |
Download A Primer for Computational Biology Book in PDF, ePub and Kindle
A Primer for Computational Biology aims to provide life scientists and students the skills necessary for research in a data-rich world. The text covers accessing and using remote servers via the command-line, writing programs and pipelines for data analysis, and provides useful vocabulary for interdisciplinary work. The book is broken into three parts: Introduction to Unix/Linux: The command-line is the "natural environment" of scientific computing, and this part covers a wide range of topics, including logging in, working with files and directories, installing programs and writing scripts, and the powerful "pipe" operator for file and data manipulation. Programming in Python: Python is both a premier language for learning and a common choice in scientific software development. This part covers the basic concepts in programming (data types, if-statements and loops, functions) via examples of DNA-sequence analysis. This part also covers more complex subjects in software development such as objects and classes, modules, and APIs. Programming in R: The R language specializes in statistical data analysis, and is also quite useful for visualizing large datasets. This third part covers the basics of R as a programming language (data types, if-statements, functions, loops and when to use them) as well as techniques for large-scale, multi-test analyses. Other topics include S3 classes and data visualization with ggplot2.
Author | : Peter J. Denning |
Publisher | : MIT Press |
Total Pages | : 266 |
Release | : 2019-05-14 |
Genre | : Computers |
ISBN | : 0262536560 |
Download Computational Thinking Book in PDF, ePub and Kindle
An introduction to computational thinking that traces a genealogy beginning centuries before the digital computer. A few decades into the digital era, scientists discovered that thinking in terms of computation made possible an entirely new way of organizing scientific investigation; eventually, every field had a computational branch: computational physics, computational biology, computational sociology. More recently, “computational thinking” has become part of the K–12 curriculum. But what is computational thinking? This volume in the MIT Press Essential Knowledge series offers an accessible overview, tracing a genealogy that begins centuries before digital computers and portraying computational thinking as pioneers of computing have described it. The authors explain that computational thinking (CT) is not a set of concepts for programming; it is a way of thinking that is honed through practice: the mental skills for designing computations to do jobs for us, and for explaining and interpreting the world as a complex of information processes. Mathematically trained experts (known as “computers”) who performed complex calculations as teams engaged in CT long before electronic computers. The authors identify six dimensions of today's highly developed CT—methods, machines, computing education, software engineering, computational science, and design—and cover each in a chapter. Along the way, they debunk inflated claims for CT and computation while making clear the power of CT in all its complexity and multiplicity.
Author | : James Tisdall |
Publisher | : "O'Reilly Media, Inc." |
Total Pages | : 388 |
Release | : 2001-10-22 |
Genre | : Computers |
ISBN | : 0596550472 |
Download Beginning Perl for Bioinformatics Book in PDF, ePub and Kindle
With its highly developed capacity to detect patterns in data, Perl has become one of the most popular languages for biological data analysis. But if you're a biologist with little or no programming experience, starting out in Perl can be a challenge. Many biologists have a difficult time learning how to apply the language to bioinformatics. The most popular Perl programming books are often too theoretical and too focused on computer science for a non-programming biologist who needs to solve very specific problems.Beginning Perl for Bioinformatics is designed to get you quickly over the Perl language barrier by approaching programming as an important new laboratory skill, revealing Perl programs and techniques that are immediately useful in the lab. Each chapter focuses on solving a particular bioinformatics problem or class of problems, starting with the simplest and increasing in complexity as the book progresses. Each chapter includes programming exercises and teaches bioinformatics by showing and modifying programs that deal with various kinds of practical biological problems. By the end of the book you'll have a solid understanding of Perl basics, a collection of programs for such tasks as parsing BLAST and GenBank, and the skills to take on more advanced bioinformatics programming. Some of the later chapters focus in greater detail on specific bioinformatics topics. This book is suitable for use as a classroom textbook, for self-study, and as a reference.The book covers: Programming basics and working with DNA sequences and strings Debugging your code Simulating gene mutations using random number generators Regular expressions and finding motifs in data Arrays, hashes, and relational databases Regular expressions and restriction maps Using Perl to parse PDB records, annotations in GenBank, and BLAST output
Author | : Röbbe Wünschiers |
Publisher | : Springer Science & Business Media |
Total Pages | : 291 |
Release | : 2012-12-06 |
Genre | : Science |
ISBN | : 3642185525 |
Download Computational Biology Book in PDF, ePub and Kindle
-Teaches the reader how to use Unix, which is the key to basic computing and allows the most flexibility for bioinformatics applications -Written specifically with the needs of molecular biologists in mind -Easy to follow, written for beginners with no computational knowledge -Includes examples from biological data analysis -Can be use either for self-teaching or in courses
Author | : Alan J. Cann |
Publisher | : John Wiley & Sons |
Total Pages | : 199 |
Release | : 2013-04-25 |
Genre | : Science |
ISBN | : 1118685709 |
Download Maths from Scratch for Biologists Book in PDF, ePub and Kindle
Numerical ability is an essential skill for everyone studying the biological sciences but many students are frightened by the 'perceived' difficulty of mathematics, and are nervous about applying mathematical skills in their chosen field of study. Having taught introductory maths and statistics for many years, Alan Cann understands these challenges and just how invaluable an accessible, confidence building textbook could be to the fearful student. Unable to find a book pitched at the right level, that concentrated on why numerical skills are useful to biologists, he wrote his own. The result is Maths from Scratch for Biologists , a highly instructive, informal text that explains step by step how and why you need to tackle maths within the biological sciences. Features: * An accessible, jargon-busting approach to help readers master basic mathematical, statistical and data handling techniques in biology * Numerous end of chapter problems to reinforce key concepts and encourage students to test their newly acquired skills through practise * A handy, time-saving glossary * A supplementary website with numerous problems and self-test exercises