Effective Python Development for Biologists: Tools and techniques for building biological programs By 作者: Dr Martin Jones ISBN-10 书号: 153910303X ISBN-13 书号: 9781539103035 出版日期: 2016-09-26 pages 页数: 296 Contents 1: Introduction 1 About this book » 1 Typography and formatting » 5 Getting in touch » 8 2: Environments for developing in Python 10 Introduction » 10 What you actually write code in » 10 Integrated development environments » 14 Managing Python and packages » 19 Working in a debugger » 25 Alternatives to pdb » 57 Recap » 59 3: Organizing and sharing code 61 Introduction » 61 Working with modules » 63 Distributing code » 80 Recap » 86 4: Testing your code 88 Introduction » 88 Testing with assert » 89 Automated testing with nose » 105 Types of assertions » 119 Designing for testing » 127 Special types of testing » 131 Recap » 137 5: Performance 139 Introduction » 139 Benchmarking » 140 Benchmarking memory » 147 Profiling » 160 Guidelines for performance optimization » 179 Specific tips for improving performance » 181 Further topics in performance » 194 Recap » 197 6: Building user interfaces 198 Why do we need a user interface? » 198 A simple program » 200 A simple interactive interface » 203 A simple command line interface » 207 Command line interfaces with argparse » 216 Alternatives to argparse » 241 Configuration files » 243 Web interfaces » 250 Graphical user interfaces » 257 Logging » 269 Logging messages » 273 Logging to a file » 276 Recap » 283

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.