I am glad to announce the second edition of Python for Bioinformatics. In today's data driven biology, programming knowledge is essential in turning ideas into testable hypothesis. Based on my 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. Most of the code can be executed online using a collection of Jupyter Notebooks hosted at https://notebooks.azure.com/library/py3.us. All source code is available at GitHub (https://github.com/Serulab/Py4Bio) The intended audience of this book are bioinformatics students and graduates who are not software developers but needs to learn how to program. Software developers can also take advantage of the book, since there is also advanced and reference material.
Table of contents Section I: Programming Chapter 1: ■ Introduction Chapter 2 ■ First Steps with Python Chapter 3 ■ Basic Programming: Data Types Chapter 4 ■ Programming: Flow Control Chapter 5 ■ Handling Files Chapter 6 ■ Code Modularizing Chapter 7 ■ Error Handling Chapter 8 ■ Introduction to Object Orienting Programming (OOP) Chapter 9 ■ Introduction to Biopython Section II: Advanced Topics Chapter 10 ■ Web Applications Chapter 11 ■ XML Chapter 12 ■ Python and Databases Chapter 13 ■ Regular Expressions Chapter 14 ■ Graphics in Python Section III: Python Recipes with Commented Source Code Chapter 15 ■ Sequence Manipulation in Batch Chapter 16 ■ Web Application for Filtering Vector Contamination Chapter 17 ■ Searching for PCR Primers Using Primer3 Chapter 18 ■ Calculating Melting Temperature from a Set of Primers Chapter 19 ■ Filtering Out Specific Fields from a GenBank File Chapter 20 ■ Inferring Splicing Sites Chapter 21 ■ Web Server for Multiple Alignment Chapter 22 ■ Drawing Marker Positions Using Data Stored in a Database Chapter 23 ■ DNA Mutations with Restrictions (On-Line only) Section IV: Appendices Appendix A ■ INTRODUCTION TO VERSION CONTROL Appendix B ■ PYTHONANYWHERE Appendix C ■ REFERENCE Where to buy? In Amazon (http://amzn.to/2vWazcL) or at the publisher web site (https://goo.gl/t2uoyN), save 20% with the promo code AZR94 (valid only in the publisher site and up to December 2017). For more information, include book mailing list, visit http://py3.us/ -- https://mail.python.org/mailman/listinfo/python-list
