Bioinformatics Programming Using Python by Mitchell L Model Review by Dr. Sukanta Ganguly
This book is a good Python Programming tutorial. It does a good job of explaining the concepts of Python programming to individuals who would like to learn Python. The book is written in eleven chapters. It has two appendix titles ‘A’ and ‘B’.
It starts with the chapter titled ‘Primitives’ where the primitives and operators supported in Python are explained. The second chapter titled ‘Names, Functions and Modules’ does what the title states. Here the author explains the ways to define methods, functions, variables, comments and use of existing modules. The next chapter titled ‘Collections’ explains the collection primitives like sets, sequences, mappings, streams, etc. The chapter following that titled ‘Control Statements’ shows to use the control statements in Python. The following chapter titled ‘Classes’ and it explains how to create/define classes in Python with attributes, instances, decompositions, inheritance, etc. The next chapter is titled ‘Utilities’. Here the author explains the use of command line utilities, data, time constructs, file system operations, text block operations, persistent factors like ‘dbm’, ‘pickle’, etc.
The next few chapters get a little more interesting starting with the chapter titled ‘Pattern Matching’, where some basics of pattern matching is covered. Very minor bioinformatics’ concepts like DNA/RNA sequences are shown here. The next chapter titled ‘Structured Text’ explains some high level basics of structured files like HTML and XML. Continuing on the Web path the next chapter is titled ‘Web Programming’. Here the author explains the usage of a few existing modules urllib, webbrowser, etc. Simplistic views of web client and web server are also shown in this chapter. The next chapter addresses database queries and is titled ‘Relational Databases’. It presents some simple ways of database query from Python with Web driven front end. A few pages of limited and/or restricted enzyme database query example is demonstrated here. The last chapter is titled ‘Structured Graphics’. It shows some GUI toolkits, talks about tkinter and SVG file formats.
Over all the book tries to cover a lot in python but lacks depth in anything apart from just explaining Python programming. Less little of Bioinformatics is actually shown, explained or demonstrated in this book.