Bioinformatics Programming Using Python

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 t

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

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 nu

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 nu

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 simp

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 simp

All social and policy researchers need to synthesize data into a visual representation. Producing good visualizations combines creativity and technique. This book teaches the techniques and basics to produce a variety of visualizations, allowing readers to communicate data and analyses in a creative and effective way. Visuals for tables, time series, maps, text, and networks are carefully explained and organized, showing how to choose the right plot for the type of data being analysed and displayed. Examples are drawn from public policy, public safety, education, political tweets, and public health. The presentation proceeds step by step, starting from the basics, in the programming languages R and Python so that readers learn the coding skills while simultaneously becoming familiar with the advantages and disadvantages of each visualization. No prior knowledge of either Python or R is required. Code for all the visualizations are available from the book's website.

All social and policy researchers need to synthesize data into a visual representation. Producing good visualizations combines creativity and technique. This book teaches the techniques and basics to produce a variety of visualizations, allowing readers to communicate data and analyses in a creative and effective way. Visuals for tables, time series, maps, text, and networks are carefully explained and organized, showing how to choose the right plot for the type of data being analysed and displayed. Examples are drawn from public policy, public safety, education, political tweets, and public health. The presentation proceeds step by step, starting from the basics, in the programming languages R and Python so that readers learn the coding skills while simultaneously becoming familiar with the advantages and disadvantages of each visualization. No prior knowledge of either Python or R is required. Code for all the visualizations are available from the book's website.

Specifically designed for linguists, this book provides an introduction to programming using Python for those with little to no experience of coding. Python is one of the most popular and widely-used programming languages as it's also available for free and runs on any operating system. All examples in the text involve language data and can be adapted or used directly for language research. The text focuses on key language-related issues: searching, text manipulation, text encoding and internet data, providing an excellent resource for language research. More experienced users of Python will also benefit from the advanced chapters on graphical user interfaces and functional programming.

Specifically designed for linguists, this book provides an introduction to programming using Python for those with little to no experience of coding. Python is one of the most popular and widely-used programming languages as it's also available for free and runs on any operating system. All examples in the text involve language data and can be adapted or used directly for language research. The text focuses on key language-related issues: searching, text manipulation, text encoding and internet data, providing an excellent resource for language research. More experienced users of Python will also benefit from the advanced chapters on graphical user interfaces and functional programming.

Essentials of Programming in Mathematica® provides an introduction suitable for readers with little or no background in the language as well as for those with some experience using programs such as C, Java, or Perl. The author, an established authority on Mathematica® programming, has written an example-driven text that covers the language from first principles, as well as including material from natural language processing, bioinformatics, graphs and networks, signal analysis, geometry, computer science, and many other applied areas. The book is appropriate for self-study or as a text for a course in programming in computational science. Readers will benefit from the author's tips, which provide insight and suggestions on small and large points. He also provides more than 350 exercises from novice through to advanced level with all of the solutions available online.

Presents a guide for object-oriented programming for readers to become comfortable building classes and using those found in popular code libraries.

Starting from first principles, this book covers all of the foundational material needed to develop a clear understanding of the Mathematica language, with a practical emphasis on solving problems. Concrete examples throughout the text demonstrate how Mathematica can be used to solve problems in science, engineering, economics/finance, computational linguistics, geoscience, bioinformatics, and a range of other fields. The book will appeal to students, researchers and programmers wishing to further their understanding of Mathematica. Designed to suit users of any ability, it assumes no formal knowledge of programming so it is ideal for self-study. Over 290 exercises are provided to challenge the reader's understanding of the material covered and these provide ample opportunity to practice using the language. Mathematica notebooks containing examples, programs and solutions to exercises are available from www.cambridge.org/wellin.

Offering a new perspective, this textbook demystifies the operation of electric machines by providing an integrated understanding of electromagnetic fields, electric circuits, numerical analysis, and computer programming. It presents fundamental concepts in a rigorous manner, emphasising underlying physical modelling assumptions and limitations, and provides detailed explanations of how to implement the finite element method to explore these concepts using Python. It includes explanations of the conversion of concepts into algorithms, and algorithms into code, and examples building in complexity, from simple linear-motion electromagnets to rotating machines. Over 100 theoretical and computational end-of-chapter exercises test understanding, with solutions for instructors and downloadable Python code available online. Ideal for graduates and senior undergraduates studying electric machines, electric machine design and control, and power electronic converters and power systems engineerin

Python is today's fastest growing programming language. This engaging and refreshingly different guide breaks down the skills into clear step-by-step chunks and explains the theory using brief easy-to-understand language. Rather than bamboozling readers with pages of mind-numbing technical jargon, this book includes 150 practical challenges, putting the power in the reader's hands. Through creating programs to solve these challenges the reader will quickly progress from mastering the basics to confidently using subroutines, a graphical user interface, and linking to external text, csv and SQL files. This book is perfect for anyone who wants to learn how to program with Python. In particular, students starting out in computer science and teachers who want to improve their confidence in Python will find here a set of ready-made challenges for classroom use.

A no-nonsense introduction to software design using the Python programming language. Written for people with no programming experience, this book starts with the most basic concepts and gradually adds new material. Some of the ideas students find most challenging, like recursion and object-oriented programming, are divided into a sequence of smaller steps and introduced over the course of several chapters. The focus is on the programming process, with special emphasis on debugging. The book includes a wide range of exercises, from short examples to substantial projects, so that students have ample opportunity to practise each new concept. Exercise solutions and code examples are available from thinkpython.com, along with Swampy, a suite of Python programs that is used in some of the exercises.

A no-nonsense introduction to software design using the Python programming language. Written for people with no programming experience, this book starts with the most basic concepts and gradually adds new material. Some of the ideas students find most challenging, like recursion and object-oriented programming, are divided into a sequence of smaller steps and introduced over the course of several chapters. The focus is on the programming process, with special emphasis on debugging. The book includes a wide range of exercises, from short examples to substantial projects, so that students have ample opportunity to practise each new concept. Exercise solutions and code examples are available from thinkpython.com, along with Swampy, a suite of Python programs that is used in some of the exercises.

Constraint logic programming lies at the intersection of logic programming, optimisation and artificial intelligence. It has proved a successful tool in many areas including production planning, transportation scheduling, numerical analysis and bioinformatics. Eclipse is one of the leading software systems that realise its underlying methodology. Eclipse is exploited commercially by Cisco, and is freely available and used for teaching and research in over 500 universities. This book has a two-fold purpose. It's an introduction to constraint programming, appropriate for one-semester courses for upper undergraduate or graduate students in computer science or for programmers wishing to master the practical aspects of constraint programming. By the end of the book, the reader will be able to understand and write constraint programs that solve complex problems. Second, it provides a systematic introduction to the Eclipse system through carefully-chosen examples that guide the reader throu

Real-world data sets are messy and complicated. Written for students in social science and public management, this authoritative but approachable guide describes all the tools needed to collect data and prepare it for analysis. Offering detailed, step-by-step instructions, it covers collection of many different types of data including web files, APIs, and maps; data cleaning; data formatting; the integration of different sources into a comprehensive data set; and storage using third-party tools to facilitate access and shareability, from Google Docs to GitHub. Assuming no prior knowledge of R and Python, the author introduces programming concepts gradually, using real data sets that provide the reader with practical, functional experience.

Real-world data sets are messy and complicated. Written for students in social science and public management, this authoritative but approachable guide describes all the tools needed to collect data and prepare it for analysis. Offering detailed, step-by-step instructions, it covers collection of many different types of data including web files, APIs, and maps; data cleaning; data formatting; the integration of different sources into a comprehensive data set; and storage using third-party tools to facilitate access and shareability, from Google Docs to GitHub. Assuming no prior knowledge of R and Python, the author introduces programming concepts gradually, using real data sets that provide the reader with practical, functional experience.

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 req

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 req

Networks are everywhere: networks of friends, transportation networks and the Web. Neurons in our brains and proteins within our bodies form networks that determine our intelligence and survival. This modern, accessible textbook introduces the basics of network science for a wide range of job sectors from management to marketing, from biology to engineering, and from neuroscience to the social sciences. Students will develop important, practical skills and learn to write code for using networks in their areas of interest - even as they are just learning to program with Python. Extensive sets of tutorials and homework problems provide plenty of hands-on practice and longer programming tutorials online further enhance students' programming skills. This intuitive and direct approach makes the book ideal for a first course, aimed at a wide audience without a strong background in mathematics or computing but with a desire to learn the fundamentals and applications of network science.