Essential Computing Skills For Biologists

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Essential Computing Skills for Biologists

Wang Ziling,Zhang Lishu
Essential Computing Skills for Biologists Book PDF

Author : Wang Ziling,Zhang Lishu
Publisher : World Scientific
Page : 304 pages
File Size : 46,6 Mb
Release : 2013-10-10
Category : Computers
ISBN : 9781848169265

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Essential Computing Skills for Biologists by Wang Ziling,Zhang Lishu Pdf

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.

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 : 43,6 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 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 : 48,7 Mb
Release : 2019
Category : Ability
ISBN : 9780691167299

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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 : 40,9 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.

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 : 46,6 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.

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 : 41,6 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.

Computational Thinking for Life Scientists

Benny Chor,Amir Rubinstein
Computational Thinking for Life Scientists Book PDF

Author : Benny Chor,Amir Rubinstein
Publisher : Cambridge University Press
Page : 220 pages
File Size : 50,6 Mb
Release : 2022-08-31
Category : Computers
ISBN : 9781108195461

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Computational Thinking for Life Scientists by Benny Chor,Amir Rubinstein Pdf

Computational thinking is increasingly gaining importance in modern biology, due to the unprecedented scale at which data is nowadays produced. Bridging the cultural gap between the biological and computational sciences, this book serves as an accessible introduction to computational concepts for students in the life sciences. It focuses on teaching algorithmic and logical thinking, rather than just the use of existing bioinformatics tools or programming. Topics are presented from a biological point of view, to demonstrate how computational approaches can be used to solve problems in biology such as biological image processing, regulatory networks, and sequence analysis. The book contains a range of pedagogical features to aid understanding, including real-world examples, in-text exercises, end-of-chapter problems, colour-coded Python code, and 'code explained' boxes. User-friendly throughout, Computational Thinking for Life Scientists promotes the thinking skills and self-efficacy required for any modern biologist to adopt computational approaches in their research with confidence.

A Primer for Computational Biology

Shawn T. O'Neil
A Primer for Computational Biology Book PDF

Author : Shawn T. O'Neil
Publisher : Unknown
Page : 0 pages
File Size : 55,8 Mb
Release : 2017-12-21
Category : Science
ISBN : 0870719262

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A Primer for Computational Biology by Shawn T. O'Neil Pdf

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.

Bioinformatics Biocomputing and Perl

Michael Moorhouse,Paul Barry
Bioinformatics Biocomputing and Perl Book PDF

Author : Michael Moorhouse,Paul Barry
Publisher : John Wiley & Sons
Page : 506 pages
File Size : 42,9 Mb
Release : 2005-09-27
Category : Medical
ISBN : 9780470026458

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Bioinformatics Biocomputing and Perl by Michael Moorhouse,Paul Barry Pdf

Bioinformatics, Biocomputing and Perl presents a modern introduction to bioinformatics computing skills and practice. Structuring its presentation around four main areas of study, this book covers the skills vital to the day-to-day activities of today’s bioinformatician. Each chapter contains a series of maxims designed to highlight key points and there are exercises to supplement and cement the introduced material. Working with Perl presents an extended tutorial introduction to programming through Perl, the premier programming technology of the bioinformatics community. Even though no previous programming experience is assumed, completing the tutorial equips the reader with the ability to produce powerful custom programs with ease. Working with Data applies the programming skills acquired to processing a variety of bioinformatics data. In addition to advice on working with important data stores such as the Protein DataBank, SWISS-PROT, EMBL and the GenBank, considerable discussion is devoted to using bioinformatics data to populate relational database systems. The popular MySQL database is used in all examples. Working with the Web presents a discussion of the Web-based technologies that allow the bioinformatics researcher to publish both data and applications on the Internet. Working with Applications shifts gear from creating custom programs to using them. The tools described include Clustal-W, EMBOSS, STRIDE, BLAST and Xmgrace. An introduction to the important Bioperl Project concludes this chapter and rounds off the book.

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 : 48,6 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.

Bioinformatics Data Skills

Vince Buffalo
Bioinformatics Data Skills Book PDF

Author : Vince Buffalo
Publisher : "O'Reilly Media, Inc."
Page : 538 pages
File Size : 40,6 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

Implementing Reproducible Research

Victoria Stodden,Friedrich Leisch,Roger D. Peng
Implementing Reproducible Research Book PDF

Author : Victoria Stodden,Friedrich Leisch,Roger D. Peng
Publisher : CRC Press
Page : 450 pages
File Size : 43,7 Mb
Release : 2018-12-14
Category : Mathematics
ISBN : 9781315360393

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Implementing Reproducible Research by Victoria Stodden,Friedrich Leisch,Roger D. Peng Pdf

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.

Computer Simulation and Data Analysis in Molecular Biology and Biophysics

Victor Bloomfield
Computer Simulation and Data Analysis in Molecular Biology and Biophysics Book PDF

Author : Victor Bloomfield
Publisher : Springer Science & Business Media
Page : 325 pages
File Size : 55,8 Mb
Release : 2009-06-05
Category : Science
ISBN : 9781441900838

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Computer Simulation and Data Analysis in Molecular Biology and Biophysics by Victor Bloomfield Pdf

This book provides an introduction to two important aspects of modern bioch- istry, molecular biology, and biophysics: computer simulation and data analysis. My aim is to introduce the tools that will enable students to learn and use some f- damental methods to construct quantitative models of biological mechanisms, both deterministicandwithsomeelementsofrandomness;tolearnhowconceptsofpr- ability can help to understand important features of DNA sequences; and to apply a useful set of statistical methods to analysis of experimental data. The availability of very capable but inexpensive personal computers and software makes it possible to do such work at a much higher level, but in a much easier way, than ever before. TheExecutiveSummaryofthein?uential2003reportfromtheNationalAcademy of Sciences, “BIO 2010: Transforming Undergraduate Education for Future - search Biologists” [12], begins The interplay of the recombinant DNA, instrumentation, and digital revolutions has p- foundly transformed biological research. The con?uence of these three innovations has led to important discoveries, such as the mapping of the human genome. How biologists design, perform, and analyze experiments is changing swiftly. Biological concepts and models are becoming more quantitative, and biological research has become critically dependent on concepts and methods drawn from other scienti?c disciplines. The connections between the biological sciences and the physical sciences, mathematics, and computer science are rapidly becoming deeper and more extensive.

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 : 44,6 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.

Bioinformatics Computing

Bryan P. Bergeron
Bioinformatics Computing Book PDF

Author : Bryan P. Bergeron
Publisher : Prentice Hall Professional
Page : 472 pages
File Size : 44,8 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.