Search Results for "python-for-biologists-a-complete-programming-course-for-beginners"

Python for Biologists

Python for Biologists

  • Author: Martin Jones
  • Publisher: Createspace Independent Publishing Platform
  • ISBN: 9781492346135
  • Category: Computers
  • Page: 229
  • View: 7173
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Python for biologists is a complete programming course for beginners that will give you the skills you need to tackle common biological and bioinformatics problems.

Python Programming for Biology

Python Programming for Biology

  • Author: Tim J. Stevens,Wayne Boucher
  • Publisher: Cambridge University Press
  • ISBN: 0521895839
  • Category: Computers
  • Page: 711
  • View: 5705
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This book introduces Python as a powerful tool for the investigation of problems in computational biology, for novices and experienced programmers alike.

Python for Complete Beginners

Python for Complete Beginners

  • Author: Martin Jones
  • Publisher: Createspace Independent Publishing Platform
  • ISBN: 9781514376980
  • Category: Computer programming
  • Page: 248
  • View: 1430
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"This book is an introduction to the Python programming language for complete beginners – those who have never written a program before, or who are just getting started with programming"-back cover.

Advanced Python for Biologists

Advanced Python for Biologists

  • Author: Martin O. Jones
  • Publisher: Createspace Independent Pub
  • ISBN: 9781495244377
  • Category: Computers
  • Page: 267
  • View: 9105
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Advanced Python for Biologists is a programming course for workers in biology and bioinformatics who want to develop their programming skills. It starts with the basic Python knowledge outlined in Python for Biologists and introduces advanced Python tools and techniques with biological examples. You'll learn: - How to use object-oriented programming to model biological entities - How to write more robust code and programs by using Python's exception system - How to test your code using the unit testing framework - How to transform data using Python's comprehensions - How to write flexible functions and applications using functional programming - How to use Python's iteration framework to extend your own object and functions Advanced Python for Biologists is written with an emphasis on practical problem-solving and uses everyday biological examples throughout. Each section contains exercises along with solutions and detailed discussion.

Bioinformatics Programming Using Python

Bioinformatics Programming Using Python

Practical Programming for Biological Data

  • Author: Mitchell L Model
  • Publisher: "O'Reilly Media, Inc."
  • ISBN: 9781449382902
  • Category: Computers
  • Page: 528
  • View: 4830
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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

Beginning Perl for Bioinformatics

Beginning Perl for Bioinformatics

An Introduction to Perl for Biologists

  • Author: James Tisdall
  • Publisher: "O'Reilly Media, Inc."
  • ISBN: 9780596550479
  • Category: Computers
  • Page: 386
  • View: 5845
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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

Getting Started with R

Getting Started with R

  • Author: Andrew P. Beckerman,Owen L. Petchey,Dylan Z. Childs
  • Publisher: Oxford University Press
  • ISBN: 0198787839
  • Category: Science
  • Page: 240
  • View: 9818
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R is rapidly becoming the standard software for statistical analyses, graphical presentation of data, and programming in the natural, physical, social, and engineering sciences. Getting Started with R is now the go-to introductory guide for biologists wanting to learn how to use R in their research. It teaches readers how to import, explore, graph, and analyse data, while keeping them focused on their ultimate goals: clearly communicating their data in oral presentations, posters, papers, and reports. It provides a consistent workflow for using R that is simple, efficient, reliable, and reproducible. This second edition has been updated and expanded while retaining the concise and engaging nature of its predecessor, offering an accessible and fun introduction to the packages dplyr and ggplot2 for data manipulation and graphing. It expands the set of basic statistics considered in the first edition to include new examples of a simple regression, a one-way and a two-way ANOVA. Finally, it introduces a new chapter on the generalised linear model. Getting Started with R is suitable for undergraduates, graduate students, professional researchers, and practitioners in the biological sciences.

Computing for Biologists

Computing for Biologists

Python Programming and Principles

  • Author: Ran Libeskind-Hadas,Eliot Bush
  • Publisher: Cambridge University Press
  • ISBN: 1316061337
  • Category: Science
  • Page: N.A
  • View: 7321
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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 for Bioinformatics

Python for Bioinformatics

  • Author: Jason Kinser
  • Publisher: Jones & Bartlett Learning
  • ISBN: 0763751863
  • Category: Computers
  • Page: 417
  • View: 407
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Python for Bioinformatics provides a clear introduction to the Python programming language and instructs beginners on the development of simple programming exercises. Important Notice: The digital edition of this book is missing some of the images or content found in the physical edition.

R Programming for Bioinformatics

R Programming for Bioinformatics

  • Author: Robert Gentleman
  • Publisher: CRC Press
  • ISBN: 9781420063684
  • Category: Mathematics
  • Page: 328
  • View: 8808
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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.

Bioinformatics Programming in Python

Bioinformatics Programming in Python

A Practical Course for Beginners

  • Author: Ruediger-Marcus Flaig
  • Publisher: John Wiley & Sons
  • ISBN: 3527644903
  • Category: Medical
  • Page: 428
  • View: 625
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This first introductory book designed to train novice programmers is based on a student course taught by the author, and has been optimized for biology students without previous experience in programming. By interspersing theory chapters with numerous small and large programming exercises, the author quickly shows readers how to do their own programming, and throughout uses anecdotes and real-life examples from the biosciences to 'spice up' the text. This practical book thus teaches essential programming skills for life scientists who want -- or need -- to write their own bioinformatics software tools.

Practical Computing for Biologists

Practical Computing for Biologists

  • Author: Steven Harold David Haddock,Casey W. Dunn
  • Publisher: Sinauer Associates Incorporated
  • ISBN: 9780878933914
  • Category: Computers
  • Page: 538
  • View: 1985
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To help with the increasingly large data sets that many scientists deal with, this book illustrates how to use many freely available computing tools to work more powerfully and effectively. The book was born out of the authors' experiences developing tools for their research and to fix other biologist's computational problems.

Python for Bioinformatics, Second Edition

Python for Bioinformatics, Second Edition

  • Author: Sebastian Bassi
  • Publisher: CRC Press
  • ISBN: 1351976958
  • Category: Mathematics
  • Page: 424
  • View: 7787
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In today's data driven biology, programming knowledge is essential in turning ideas into testable hypothesis. Based on the author’s extensive experience, Python for Bioinformatics, Second Edition helps biologists get to grips with the basics of software development. Requiring no prior knowledge of programming-related concepts, the book focuses on the easy-to-use, yet powerful, Python computer language. This new edition is updated throughout to Python 3 and is designed not just to help scientists master the basics, but to do more in less time and in a reproducible way. New developments added in this edition include NoSQL databases, the Anaconda Python distribution, graphical libraries like Bokeh, and the use of Github for collaborative development.

UNIX and Perl to the Rescue!

UNIX and Perl to the Rescue!

A Field Guide for the Life Sciences (and Other Data-rich Pursuits)

  • Author: Keith Bradnam,Ian Korf
  • Publisher: Cambridge University Press
  • ISBN: 1107000688
  • Category: Computers
  • Page: 428
  • View: 1872
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An accessible guide to learning the key features of Unix and Perl, written with the non-programmer in mind.

Genomics and Bioinformatics

Genomics and Bioinformatics

An Introduction to Programming Tools for Life Scientists

  • Author: Tore Samuelsson
  • Publisher: Cambridge University Press
  • ISBN: 1107378338
  • Category: Science
  • Page: N.A
  • View: 4405
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With the arrival of genomics and genome sequencing projects, biology has been transformed into an incredibly data-rich science. The vast amount of information generated has made computational analysis critical and has increased demand for skilled bioinformaticians. Designed for biologists without previous programming experience, this textbook provides a hands-on introduction to Unix, Perl and other tools used in sequence bioinformatics. Relevant biological topics are used throughout the book and are combined with practical bioinformatics examples, leading students through the process from biological problem to computational solution. All of the Perl scripts, sequence and database files used in the book are available for download at the accompanying website, allowing the reader to easily follow each example using their own computer. Programming examples are kept at an introductory level, avoiding complex mathematics that students often find daunting. The book demonstrates that even simple programs can provide powerful solutions to many complex bioinformatics problems.

Bioinformatics Data Skills

Bioinformatics Data Skills

Reproducible and Robust Research with Open Source Tools

  • Author: Vince Buffalo
  • Publisher: "O'Reilly Media, Inc."
  • ISBN: 1449367518
  • Category: Computers
  • Page: 538
  • View: 4738
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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

Bioinformatics for Beginners

Bioinformatics for Beginners

Genes, Genomes, Molecular Evolution, Databases and Analytical Tools

  • Author: Supratim Choudhuri
  • Publisher: Elsevier
  • ISBN: 0124105106
  • Category: Medical
  • Page: 238
  • View: 9741
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Bioinformatics for Beginners: Genes, Genomes, Molecular Evolution, Databases and Analytical Tools provides a coherent and friendly treatment of bioinformatics for any student or scientist within biology who has not routinely performed bioinformatic analysis. The book discusses the relevant principles needed to understand the theoretical underpinnings of bioinformatic analysis and demonstrates, with examples, targeted analysis using freely available web-based software and publicly available databases. Eschewing non-essential information, the work focuses on principles and hands-on analysis, also pointing to further study options. Avoids non-essential coverage, yet fully describes the field for beginners Explains the molecular basis of evolution to place bioinformatic analysis in biological context Provides useful links to the vast resource of publicly available bioinformatic databases and analysis tools Contains over 100 figures that aid in concept discovery and illustration

Effective Python Development for Biologists

Effective Python Development for Biologists

Tools and Techniques for Building Biological Programs

  • Author: Martin Jones
  • Publisher: Createspace Independent Publishing Platform
  • ISBN: 9781539103035
  • Category:
  • Page: 300
  • View: 8010
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Python is rapidly becoming the standard language for many talks in scientific research, and is particularly popular in biology and bioinformatics. One of the great strengths of Python is the ecosystem of tools and libraries that have grown up around it. This book introduces the novice biologist programmer to tools and techniques that make developing Python code easier and faster and will help you to write more reliable, performant programs. Written by a biologist, it focusses on solving the problems that students and researchers encounter every day: How do I make my program run faster? How can I be sure that my results are correct? How do I share this program with my colleagues? How can I speed up the process of writing my code? Chapters include: Environments for development - learn how you can take advantage of different tools for actually writing code, including those designed specifically for scientific work. Organising and sharing code - learn how Python's module and packaging system works, how to effectively reuse code across multiple projects, and how to share your programs with colleagues and the wider world. Testing - learn how automated testing can make your code more reliable, how to catch bugs before they impact your work, and how to edit code with confidence. Performance - learn how to make your code run quickly even on large datasets, how to understand the scaling behaviour of your code, and explore the trade offs involved in designing code. User interfaces - learn how to make your code more user friendly, how to design effective interfaces, and how to automate record-keeping with Python's logging system. About the author Martin started his programming career by learning Perl during the course of his PhD in evolutionary biology, and started teaching other people to program soon after. Since then he has taught introductory programming to hundreds of biologists, from undergraduates to PIs, and has maintained a philosophy that programming courses must be friendly, approachable, and practical. In his academic career, Martin mixed research and teaching at the University of Edinburgh, culminating in a two year stint as Lecturer in Bioinformatics. He now runs programming courses for biological researchers as a full time freelancer. Praise for Martin's previous books "Great, great book. I think this is the perfect book for any biologist to who wants to start learning to code with Python... I didn't know a command-line from a hole in the ground when I first opened up this book, and mere days later I was impressing my colleagues with my own DNA analysis programs." "Zero to writing useful programs in a weekend... Python for Biologists arrived last Thursday, 6/16/16, I spent the whole weekend glued to my laptop in a 2 1/2 day frenzy of coding, and I just finished it -- and came on Amazon to order the next one!" "One of the BEST coding books I've used in a long time. Direct applications in bioinformatics. I bought the advanced python book too." "The most useful guide to Python I've found...I've tried a few Python books, and this is by far the best for me."

A Concise Introduction to Programming in Python

A Concise Introduction to Programming in Python

  • Author: Mark J. Johnson
  • Publisher: CRC Press
  • ISBN: 1498759696
  • Category: Computers
  • Page: 217
  • View: 2572
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Suitable for newcomers to computer science, A Concise Introduction to Programming in Python provides a succinct, yet complete, first course in computer science using the Python programming language. The book features: Short, modular chapters with brief and precise explanations, intended for one class period Early introduction of basic procedural constructs such as functions, selection, and repetition, allowing them to be used throughout the course Objects are introduced in the middle of the course, and class design comes toward the end Examples, exercises, and projects from a wide range of application domains, including biology, physics, images, sound, mathematics, games, and textual analysis No external libraries are required, simplifying the book’s use in common lab spaces Each chapter introduces a main idea through a concrete example and a series of exercises. Designed to teach programming in a concise, yet comprehensive way, this book provides a timely introduction for students and anyone interested in learning Python.

Learning Python

Learning Python

Powerful Object-Oriented Programming

  • Author: Mark Lutz
  • Publisher: "O'Reilly Media, Inc."
  • ISBN: 1449355692
  • Category: Computers
  • Page: 1648
  • View: 3319
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Get a comprehensive, in-depth introduction to the core Python language with this hands-on book. Based on author Mark Lutz’s popular training course, this updated fifth edition will help you quickly write efficient, high-quality code with Python. It’s an ideal way to begin, whether you’re new to programming or a professional developer versed in other languages. Complete with quizzes, exercises, and helpful illustrations, this easy-to-follow, self-paced tutorial gets you started with both Python 2.7 and 3.3— the latest releases in the 3.X and 2.X lines—plus all other releases in common use today. You’ll also learn some advanced language features that recently have become more common in Python code. Explore Python’s major built-in object types such as numbers, lists, and dictionaries Create and process objects with Python statements, and learn Python’s general syntax model Use functions to avoid code redundancy and package code for reuse Organize statements, functions, and other tools into larger components with modules Dive into classes: Python’s object-oriented programming tool for structuring code Write large programs with Python’s exception-handling model and development tools Learn advanced Python tools, including decorators, descriptors, metaclasses, and Unicode processing