Includes bibliographical references and index.

Part 1: Text files -- Getting set up -- Regular expressions: powerful search and replace -- Exploring the flexibility of regular expressions -- Part 2: The shell -- Command-line operations: the shell -- Handling text in the shell -- Scripting with the shell -- Part 3: Programming -- Components of programming -- Beginning python programming -- Decisions and loops -- Reading and writing files -- Merging files -- Modules and libraries -- Debugging strategies -- Part 4: Combing methods -- Selecting and combining tools -- Relational databases -- Advanced shell and pipelines -- Part 5: Graphics -- Graphical concepts -- Working with vector art -- Working with pixel images -- Part 6: Advanced topics -- Working on remote computers -- Installing software -- Electronics: interacting with the physical world. To help with the increasingly large data sets that many scientists deal with, this book illustrates how to use many freely available computing tools to work more powerfully and effectively. The book was born out of the authors' experiences developing tools for their research and to fix other biologist's computational problems.