Practical Computing For Biologists

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Practical Computing for Biologists

Steven H.D. Haddock,Casey W. Dunn
Practical Computing for Biologists Book PDF

Author : Steven H.D. Haddock,Casey W. Dunn
Publisher : Sinauer
Page : 0 pages
File Size : 41,8 Mb
Release : 2011-04-22
Category : Medical
ISBN : 0878933913

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Practical Computing for Biologists by Steven H.D. Haddock,Casey W. Dunn Pdf

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.

Computing Skills for Biologists

Stefano Allesina,Madlen Wilmes
Computing Skills for Biologists Book PDF

Author : Stefano Allesina,Madlen Wilmes
Publisher : Princeton University Press
Page : 440 pages
File Size : 42,8 Mb
Release : 2019-01-15
Category : Computers
ISBN : 9780691182759

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Computing Skills for Biologists by Stefano Allesina,Madlen Wilmes Pdf

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

Computing for Biologists

Ran Libeskind-Hadas,Eliot Bush
Computing for Biologists Book PDF

Author : Ran Libeskind-Hadas,Eliot Bush
Publisher : Cambridge University Press
Page : 289 pages
File Size : 55,9 Mb
Release : 2014-09-22
Category : Science
ISBN : 9781316061336

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Computing for Biologists by Ran Libeskind-Hadas,Eliot Bush Pdf

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.

Python Programming for Biology

Tim J. Stevens,Wayne Boucher
Python Programming for Biology Book PDF

Author : Tim J. Stevens,Wayne Boucher
Publisher : Cambridge University Press
Page : 721 pages
File Size : 40,8 Mb
Release : 2015-02-12
Category : Science
ISBN : 9780521895835

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Python Programming for Biology by Tim J. Stevens,Wayne Boucher Pdf

This book introduces Python as a powerful tool for the investigation of problems in computational biology, for novices and experienced programmers alike.

Bioinformatics Computing

Bryan P. Bergeron
Bioinformatics Computing Book PDF

Author : Bryan P. Bergeron
Publisher : Prentice Hall Professional
Page : 472 pages
File Size : 53,6 Mb
Release : 2003
Category : Computers
ISBN : 0131008250

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Bioinformatics Computing by Bryan P. Bergeron Pdf

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.

Developing Bioinformatics Computer Skills

Cynthia Gibas,Per Jambeck
Developing Bioinformatics Computer Skills Book PDF

Author : Cynthia Gibas,Per Jambeck
Publisher : "O'Reilly Media, Inc."
Page : 452 pages
File Size : 44,6 Mb
Release : 2001
Category : Computers
ISBN : 1565926641

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Developing Bioinformatics Computer Skills by Cynthia Gibas,Per Jambeck Pdf

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.

Practical Statistics for Field Biology

Jim Fowler,Lou Cohen,Philip Jarvis
Practical Statistics for Field Biology Book PDF

Author : Jim Fowler,Lou Cohen,Philip Jarvis
Publisher : John Wiley & Sons
Page : 235 pages
File Size : 46,5 Mb
Release : 2013-06-20
Category : Science
ISBN : 9781118685648

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Practical Statistics for Field Biology by Jim Fowler,Lou Cohen,Philip Jarvis Pdf

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.

Bioinformatics Data Skills

Vince Buffalo
Bioinformatics Data Skills Book PDF

Author : Vince Buffalo
Publisher : "O'Reilly Media, Inc."
Page : 538 pages
File Size : 47,9 Mb
Release : 2015-07
Category : Computers
ISBN : 9781449367510

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Bioinformatics Data Skills by Vince Buffalo Pdf

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

Practical Applications of Computational Biology & Bioinformatics, 14th International Conference (PACBB 2020)

Gabriella Panuccio,Miguel Rocha,Florentino Fdez-Riverola,Mohd Saberi Mohamad,Roberto Casado-Vara
Practical Applications of Computational Biology Bioinformatics 14th International Conference PACBB 2020 Book PDF

Author : Gabriella Panuccio,Miguel Rocha,Florentino Fdez-Riverola,Mohd Saberi Mohamad,Roberto Casado-Vara
Publisher : Springer
Page : 216 pages
File Size : 49,8 Mb
Release : 2021-07-24
Category : Technology & Engineering
ISBN : 3030545709

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Practical Applications of Computational Biology & Bioinformatics, 14th International Conference (PACBB 2020) by Gabriella Panuccio,Miguel Rocha,Florentino Fdez-Riverola,Mohd Saberi Mohamad,Roberto Casado-Vara Pdf

This book highlights the latest research on practical applications of computational biology and bioinformatics, and addresses emerging experimental and sequencing techniques that are posing new challenges for bioinformatics and computational biology. Successfully applying these techniques calls for new algorithms and approaches from fields such as statistics, data mining, machine learning, optimization, computer science, and artificial intelligence. In response to these challenges, we have seen the rise of a new generation of interdisciplinary scientists with a strong background in the biological and computational sciences.These proceedings include 21 papers covering many different subfields of bioinformatics and computational biology. Focusing on interdisciplinary applications that combine e.g. bioinformatics, chemoinformatics, and system biology, they are intended to promote the collaboration of scientists from different research groups and with different backgrounds (computer scientists, mathematicians, biologists) to reach breakthrough solutions and overcome the challenges outlined above.

Computational Biology

Röbbe Wünschiers
Computational Biology Book PDF

Author : Röbbe Wünschiers
Publisher : Springer Science & Business Media
Page : 284 pages
File Size : 45,5 Mb
Release : 2012-12-06
Category : Science
ISBN : 9783642185526

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Computational Biology by Röbbe Wünschiers Pdf

-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

Bioinformatics for Biologists

Pavel Pevzner,Ron Shamir
Bioinformatics for Biologists Book PDF

Author : Pavel Pevzner,Ron Shamir
Publisher : Cambridge University Press
Page : 0 pages
File Size : 47,7 Mb
Release : 2011-09-15
Category : Science
ISBN : 1107648874

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Bioinformatics for Biologists by Pavel Pevzner,Ron Shamir Pdf

The computational education of biologists is changing to prepare students for facing the complex datasets of today's life science research. In this concise textbook, the authors' fresh pedagogical approaches lead biology students from first principles towards computational thinking. A team of renowned bioinformaticians take innovative routes to introduce computational ideas in the context of real biological problems. Intuitive explanations promote deep understanding, using little mathematical formalism. Self-contained chapters show how computational procedures are developed and applied to central topics in bioinformatics and genomics, such as the genetic basis of disease, genome evolution or the tree of life concept. Using bioinformatic resources requires a basic understanding of what bioinformatics is and what it can do. Rather than just presenting tools, the authors - each a leading scientist - engage the students' problem-solving skills, preparing them to meet the computational challenges of their life science careers.

A Computer Scientist's Guide to Cell Biology

William W. Cohen
A Computer Scientist s Guide to Cell Biology Book PDF

Author : William W. Cohen
Publisher : Springer Science & Business Media
Page : 104 pages
File Size : 45,6 Mb
Release : 2007-07-23
Category : Computers
ISBN : 9780387482781

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A Computer Scientist's Guide to Cell Biology by William W. Cohen Pdf

This book is designed specifically as a guide for Computer Scientists needing an introduction to Cell Biology. The text explores three different facets of biology: biological systems, experimental methods, and language and nomenclature. The author discusses what biologists are trying to determine from their experiments, how various experimental procedures are used and how they relate to accepted concepts in computer science, and the vocabulary necessary to read and understand current literature in biology. The book is an invaluable reference tool and an excellent starting point for a more comprehensive examination of cell biology.

Computational Biology

Röbbe Wünschiers
Computational Biology Book PDF

Author : Röbbe Wünschiers
Publisher : Springer Science & Business Media
Page : 453 pages
File Size : 46,8 Mb
Release : 2013-01-30
Category : Science
ISBN : 9783642347498

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Computational Biology by Röbbe Wünschiers Pdf

This greatly expanded 2nd edition provides a practical introduction to - data processing with Linux tools and the programming languages AWK and Perl - data management with the relational database system MySQL, and - data analysis and visualization with the statistical computing environment R for students and practitioners in the life sciences. Although written for beginners, experienced researchers in areas involving bioinformatics and computational biology may benefit from numerous tips and tricks that help to process, filter and format large datasets. Learning by doing is the basic concept of this book. Worked examples illustrate how to employ data processing and analysis techniques, e.g. for - finding proteins potentially causing pathogenicity in bacteria, - supporting the significance of BLAST with homology modeling, or - detecting candidate proteins that may be redox-regulated, on the basis of their structure. All the software tools and datasets used are freely available. One section is devoted to explaining setup and maintenance of Linux as an operating system independent virtual machine. The author's experiences and knowledge gained from working and teaching in both academia and industry constitute the foundation for this practical approach.

Catalyzing Inquiry at the Interface of Computing and Biology

National Research Council,Division on Engineering and Physical Sciences,Computer Science and Telecommunications Board,Committee on Frontiers at the Interface of Computing and Biology
Catalyzing Inquiry at the Interface of Computing and Biology Book PDF

Author : National Research Council,Division on Engineering and Physical Sciences,Computer Science and Telecommunications Board,Committee on Frontiers at the Interface of Computing and Biology
Publisher : National Academies Press
Page : 469 pages
File Size : 43,6 Mb
Release : 2006-01-01
Category : Science
ISBN : 9780309096126

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Catalyzing Inquiry at the Interface of Computing and Biology by National Research Council,Division on Engineering and Physical Sciences,Computer Science and Telecommunications Board,Committee on Frontiers at the Interface of Computing and Biology Pdf

Advances in computer science and technology and in biology over the last several years have opened up the possibility for computing to help answer fundamental questions in biology and for biology to help with new approaches to computing. Making the most of the research opportunities at the interface of computing and biology requires the active participation of people from both fields. While past attempts have been made in this direction, circumstances today appear to be much more favorable for progress. To help take advantage of these opportunities, this study was requested of the NRC by the National Science Foundation, the Department of Defense, the National Institutes of Health, and the Department of Energy. The report provides the basis for establishing cross-disciplinary collaboration between biology and computing including an analysis of potential impediments and strategies for overcoming them. The report also presents a wealth of examples that should encourage students in the biological sciences to look for ways to enable them to be more effective users of computing in their studies.

Practical Applications of Computational Biology & Bioinformatics, 15th International Conference (PACBB 2021)

Miguel Rocha,Florentino Fdez-Riverola,Mohd Saberi Mohamad,Roberto Casado-Vara
Practical Applications of Computational Biology Bioinformatics 15th International Conference PACBB 2021 Book PDF

Author : Miguel Rocha,Florentino Fdez-Riverola,Mohd Saberi Mohamad,Roberto Casado-Vara
Publisher : Springer Nature
Page : 188 pages
File Size : 43,8 Mb
Release : 2021-08-27
Category : Technology & Engineering
ISBN : 9783030862589

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Practical Applications of Computational Biology & Bioinformatics, 15th International Conference (PACBB 2021) by Miguel Rocha,Florentino Fdez-Riverola,Mohd Saberi Mohamad,Roberto Casado-Vara Pdf

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.