Practical Computing For Biologists
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| Author | : Steven H.D. Haddock |
| Publisher | : Sinauer |
| Total Pages | : 0 |
| Release | : 2011-04-22 |
| Genre | : Medical |
| ISBN | : 9780878933914 |
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 | : Ran Libeskind-Hadas |
| Publisher | : Cambridge University Press |
| Total Pages | : 289 |
| Release | : 2014-09-22 |
| Genre | : Science |
| ISBN | : 1316061337 |
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 | : Stefano Allesina |
| Publisher | : Princeton University Press |
| Total Pages | : 440 |
| Release | : 2019-01-15 |
| Genre | : Computers |
| ISBN | : 0691182752 |
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 | : Miguel Rocha |
| Publisher | : Springer Nature |
| Total Pages | : 188 |
| Release | : 2021-08-27 |
| Genre | : Technology & Engineering |
| ISBN | : 3030862585 |
This book features novel research papers spanning many different subfields in bioinformatics and computational biology, presenting the latest research on the practical applications to promote fruitful interactions between young researchers in different areas related to the field. Clearly, biology is increasingly becoming a science of information, requiring tools from the computational sciences. To address these challenges, we have seen the emergence of a new generation of interdisciplinary scientists with a strong background in the biological and computational sciences. PACBB'21 expects to contribute to this effort by encouraging a successful collaboration of researchers in different areas related to bioinformatics. The PACBB'21 technical program included 17 papers covering many different subfields in bioinformatics and computational biology. Therefore, this conference, held in Salamanca (Spain), definitely promotes the collaboration of scientists from different research groups and with different backgrounds (computer scientists, mathematicians, biologists) to reach breakthrough solutions for these challenges.
| Author | : Tim J. Stevens |
| Publisher | : Cambridge University Press |
| Total Pages | : 721 |
| Release | : 2015-02-12 |
| Genre | : Science |
| ISBN | : 1316194140 |
Do you have a biological question that could be readily answered by computational techniques, but little experience in programming? Do you want to learn more about the core techniques used in computational biology and bioinformatics? Written in an accessible style, this guide provides a foundation for both newcomers to computer programming and those interested in learning more about computational biology. The chapters guide the reader through: a complete beginners' course to programming in Python, with an introduction to computing jargon; descriptions of core bioinformatics methods with working Python examples; scientific computing techniques, including image analysis, statistics and machine learning. This book also functions as a language reference written in straightforward English, covering the most common Python language elements and a glossary of computing and biological terms. This title will teach undergraduates, postgraduates and professionals working in the life sciences how to program with Python, a powerful, flexible and easy-to-use language.
| Author | : Mitchell L Model |
| Publisher | : "O'Reilly Media, Inc." |
| Total Pages | : 526 |
| Release | : 2009-12-08 |
| Genre | : Science |
| ISBN | : 1449382908 |
Powerful, flexible, and easy to use, Python is an ideal language for building software tools and applications for life science research and development. This unique book shows you how to program with Python, using code examples taken directly from bioinformatics. In a short time, you'll be using sophisticated techniques and Python modules that are particularly effective for bioinformatics programming. Bioinformatics Programming Using Python is perfect for anyone involved with bioinformatics -- researchers, support staff, students, and software developers interested in writing bioinformatics applications. You'll find it useful whether you already use Python, write code in another language, or have no programming experience at all. It's an excellent self-instruction tool, as well as a handy reference when facing the challenges of real-life programming tasks. Become familiar with Python's fundamentals, including ways to develop simple applications Learn how to use Python modules for pattern matching, structured text processing, online data retrieval, and database access Discover generalized patterns that cover a large proportion of how Python code is used in bioinformatics Learn how to apply the principles and techniques of object-oriented programming Benefit from the "tips and traps" section in each chapter
| Author | : Cynthia Gibas |
| Publisher | : "O'Reilly Media, Inc." |
| Total Pages | : 452 |
| Release | : 2001 |
| Genre | : Computers |
| ISBN | : 9781565926646 |
This practical, hands-on guide shows how to develop a structured approach to biological data and the tools needed to analyze it. It's aimed at scientists and students learning computational approaches to biological data, as well as experienced biology researchers starting to use computers to handle data.
| Author | : Jim Fowler |
| Publisher | : John Wiley & Sons |
| Total Pages | : 235 |
| Release | : 2013-06-20 |
| Genre | : Science |
| ISBN | : 1118685644 |
Provides an excellent introductory text for students on the principles and methods of statistical analysis in the life sciences, helping them choose and analyse statistical tests for their own problems and present their findings. An understanding of statistical principles and methods is essential for any scientist but is particularly important for those in the life sciences. The field biologist faces very particular problems and challenges with statistics as "real-life" situations such as collecting insects with a sweep net or counting seagulls on a cliff face can hardly be expected to be as reliable or controllable as a laboratory-based experiment. Acknowledging the peculiarites of field-based data and its interpretation, this book provides a superb introduction to statistical analysis helping students relate to their particular and often diverse data with confidence and ease. To enhance the usefulness of this book, the new edition incorporates the more advanced method of multivariate analysis, introducing the nature of multivariate problems and describing the the techniques of principal components analysis, cluster analysis and discriminant analysis which are all applied to biological examples. An appendix detailing the statistical computing packages available has also been included. It will be extremely useful to undergraduates studying ecology, biology, and earth and environmental sciences and of interest to postgraduates who are not familiar with the application of multiavirate techniques and practising field biologists working in these areas.
| Author | : Vince Buffalo |
| Publisher | : "O'Reilly Media, Inc." |
| Total Pages | : 538 |
| Release | : 2015-07 |
| Genre | : Computers |
| ISBN | : 1449367518 |
Learn the data skills necessary for turning large sequencing datasets into reproducible and robust biological findings. With this practical guide, youâ??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 lifeâ??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, youâ??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
| Author | : Bryan P. Bergeron |
| Publisher | : Prentice Hall Professional |
| Total Pages | : 472 |
| Release | : 2003 |
| Genre | : Computers |
| ISBN | : 9780131008250 |
Comprehensive and concise, this handbook has chapters on computing visualization, large database designs, advanced pattern matching and other key bioinformatics techniques. It is a practical guide to computing in the growing field of Bioinformatics--the study of how information is represented and transmitted in biological systems, starting at the molecular level.
