Through many examples and exercises, this book helps simplify bioinformatics programming using Python. It's an ideal guide for biologists who want to learn either basic scripting or substantial programming for various computational tasks, and for programmers who want to learn bioinformatics programming.
Bioinformatics Programming with Python can be used as a reference, for self-instruction, or as a companion book to help you through undergraduate courses in computer science, biology, and other life sciences. With the level of detail this book provides, it's also perfect for Professional Master's graduate courses in Bioinformatics.
Mitchell L. Model has worked in a wide range of platforms, languages, technologies and domains. For much of his career he has been an independent consultant, providing training, mentoring, tools, and support to software development groups learning to use new technologies and practices. During the past 15 years his work has focused on bioinformatics.
Preface; Introduction; Python; Notes; Conventions Used in This Book; We'd Like to Hear from You; Using Code Examples; Safari® Books Online; Acknowledgments; Chapter 1: Primitives; 1.1 Simple Values; 1.2 Expressions; 1.3 Tips, Traps, and Tracebacks; Chapter 2: Names, Functions, and Modules; 2.1 Assigning Names; 2.2 Defining Functions; 2.3 Using Modules; 2.4 Tips, Traps, and Tracebacks; Chapter 3: Collections; 3.1 Sets; 3.2 Sequences; 3.3 Mappings; 3.4 Streams; 3.5 Collection-Related Expression Features; 3.6 Tips, Traps, and Tracebacks; Chapter 4: Control Statements; 4.1 Conditionals; 4.2 Loops; 4.3 Iterations; 4.4 Exception Handlers; 4.5 Extended Examples; 4.6 Tips, Traps, and Tracebacks; Chapter 5: Classes; 5.1 Defining Classes; 5.2 Class and Method Relationships; 5.3 Tips, Traps, and Tracebacks; Chapter 6: Utilities; 6.1 System Environment; 6.2 The Filesystem; 6.3 Working with Text; 6.4 Persistent Storage; 6.5 Tips, Traps, and Tracebacks; Chapter 7: Pattern Matching; 7.1 Fundamental Syntax; 7.2 The Actions of the re Module; 7.3 Results of re Functions and Methods; 7.4 Putting It All Together: Examples; 7.5 Tips, Traps, and Tracebacks; Chapter 8: Structured Text; 8.1 HTML; 8.2 XML; 8.3 Tips, Traps, and Tracebacks; Chapter 9: Web Programming; 9.1 Manipulating URLs: urllib.parse; 9.2 Opening Web Pages: webbrowser; 9.3 Web Clients; 9.4 Web Servers; 9.5 Tips, Traps, and Tracebacks; Chapter 10: Relational Databases; 10.1 Representation in Relational Databases; 10.2 Using Relational Data; 10.3 Tips, Traps, and Tracebacks; Chapter 11: Structured Graphics; 11.1 Introduction to Graphics Programming; 11.2 Structured Graphics with tkinter; 11.3 Structured Graphics with SVG; 11.4 Tips, Traps, and Tracebacks; Python Language Summary; Language Components; Types and Expressions; Statements; Notes; Collection Type Summary; Types and General Operations; Specific Collection Types; Iteration Templates; Colophon;
Show moreThrough many examples and exercises, this book helps simplify bioinformatics programming using Python. It's an ideal guide for biologists who want to learn either basic scripting or substantial programming for various computational tasks, and for programmers who want to learn bioinformatics programming.
Bioinformatics Programming with Python can be used as a reference, for self-instruction, or as a companion book to help you through undergraduate courses in computer science, biology, and other life sciences. With the level of detail this book provides, it's also perfect for Professional Master's graduate courses in Bioinformatics.
Mitchell L. Model has worked in a wide range of platforms, languages, technologies and domains. For much of his career he has been an independent consultant, providing training, mentoring, tools, and support to software development groups learning to use new technologies and practices. During the past 15 years his work has focused on bioinformatics.
Preface; Introduction; Python; Notes; Conventions Used in This Book; We'd Like to Hear from You; Using Code Examples; Safari® Books Online; Acknowledgments; Chapter 1: Primitives; 1.1 Simple Values; 1.2 Expressions; 1.3 Tips, Traps, and Tracebacks; Chapter 2: Names, Functions, and Modules; 2.1 Assigning Names; 2.2 Defining Functions; 2.3 Using Modules; 2.4 Tips, Traps, and Tracebacks; Chapter 3: Collections; 3.1 Sets; 3.2 Sequences; 3.3 Mappings; 3.4 Streams; 3.5 Collection-Related Expression Features; 3.6 Tips, Traps, and Tracebacks; Chapter 4: Control Statements; 4.1 Conditionals; 4.2 Loops; 4.3 Iterations; 4.4 Exception Handlers; 4.5 Extended Examples; 4.6 Tips, Traps, and Tracebacks; Chapter 5: Classes; 5.1 Defining Classes; 5.2 Class and Method Relationships; 5.3 Tips, Traps, and Tracebacks; Chapter 6: Utilities; 6.1 System Environment; 6.2 The Filesystem; 6.3 Working with Text; 6.4 Persistent Storage; 6.5 Tips, Traps, and Tracebacks; Chapter 7: Pattern Matching; 7.1 Fundamental Syntax; 7.2 The Actions of the re Module; 7.3 Results of re Functions and Methods; 7.4 Putting It All Together: Examples; 7.5 Tips, Traps, and Tracebacks; Chapter 8: Structured Text; 8.1 HTML; 8.2 XML; 8.3 Tips, Traps, and Tracebacks; Chapter 9: Web Programming; 9.1 Manipulating URLs: urllib.parse; 9.2 Opening Web Pages: webbrowser; 9.3 Web Clients; 9.4 Web Servers; 9.5 Tips, Traps, and Tracebacks; Chapter 10: Relational Databases; 10.1 Representation in Relational Databases; 10.2 Using Relational Data; 10.3 Tips, Traps, and Tracebacks; Chapter 11: Structured Graphics; 11.1 Introduction to Graphics Programming; 11.2 Structured Graphics with tkinter; 11.3 Structured Graphics with SVG; 11.4 Tips, Traps, and Tracebacks; Python Language Summary; Language Components; Types and Expressions; Statements; Notes; Collection Type Summary; Types and General Operations; Specific Collection Types; Iteration Templates; Colophon;
Show moreDr. Mitchell L Model is a computer scientist with a background in philosophy. He specializes in object technology, knowledge representation, user interfaces, distributed computing, and software development and is an inveterate software tool builder. Mitchell held academic appointments at Brown and Brandeis Universities and worked at a number of early-phase startup companies. For much of his career he has been an independent consultant, providing training, mentoring, and support to software development groups learning to use new technologies and practices. He has written and taught many professional programming and technology courses. Mitchell is also the author of one of the first C++-based data structure books -- Data Structures, Data Abstraction: A Contemporary Introduction Using C++, published in 1994 by Prentice-Hall. Since 1993 Mitchell has been working primarily in bioinformatics, becoming captivated by the complexities of the biological phenomena which it addresses. He was the senior technologist in Millennium Pharmaceutical's large bioinformatics department from 1993 through 2001, playing a major role in growing the department and guiding the development of its diverse software portfolio. He was a Visiting Associate Professor with Wesleyan University's Integrative Genomics group. More recently he has been teaching courses in Northeastern University's Professional Masters in Bioinformatics program. Mitchell's first programming experience was writing machine code for an IBM 1620 in 1966, which ignited a lifelong fascination with computing. He traces his interest in data structures and his visual style of thinking about them to the Tinkertoys of his childhood. Lisp was Mitchell's first professional home, Smalltalk his second. He spent long periods of exile in C++ before returning to Smalltalk in the early 1990's. In the last ten years he has worked extensively in Java, JavaScript, and Python, as well as a number of web and database technologies. He particularly appreciates the way Python elegantly combines an easy to read and write syntax, the functional style of Lisp, the object-oriented purity of Smalltalk, well-designed statement constructs, a wonderful library of well-documented modules, and a terrific user community. Mitchell's personal interests include jazz, photography, typography, design, geology, and a host of more obscure scientific subjects. His commitment is to teaching, always seeking new ways to effectively communicate the conceptual beauty of computer science. What gives him the greatest satisfaction is coaching students and professionals in the art of software development to enable them to work more effectively and creatively.
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