Steven H.D. Haddock is a Research Scientist at the Monterey Bay Aquarium Research Institute and adjunct Associate Professor at the University of California, Santa Cruz, studying bioluminescence and biodiversity of gelatinous zooplankton. He started programming in BASIC on an Apple ][ and began his undergraduate studies in engineering before deciding to change fields. He took this programming background with him to his graduate studies in Marine Biology, where he quickly realized the advantages that computing skills offered and felt compelled to help foster these abilities in others. He has developed many utilities and devices for research, including instruments to monitor bioluminescence from fireflies, a freezer monitoring system, a web-based conference registration database, and a PCR calculator for smartphones.

Casey W. Dunn, a Professor at Yale University, does research that has a large computational component but always in conjunction with work in the field and lab. His first interest in computers stemmed from building electronics, and he further developed his computational skills working in Silicon Valley while an undergraduate. As his data sets grew larger and larger during grad school and his postdoc, he found himself reaching back to his computer background more often. In the course of his own research and helping other biologists with their computational challenges, he became concerned about the mismatch between training opportunities and the real day-to-day computational problems biologists face.

An essential tool that provides researchers with freedom from the most frustrating and time-consuming aspects of data processing so they can focus on the pleasures of scientific inquiry

• Before You Begin


• Part I: Text Files


• 1: Getting Set Up


• 2: Regular Expressions: Powerful Search and Replace


• 3: Exploring the Flexibility of Regular Expressions


• Part II: The Shell


• 4: Command-line Operations: The Shell


• 5: Handling Text in the Shell


• 6: Scripting with the Shell


• Part III: Programming


• 7: Components of Programming


• 8: Beginning Python Programming


• 9: Decisions and Loops


• 10: Reading and Writing Files


• 11: Merging Files


• 12: Modules and Libraries


• 13: Debugging Strategies


• Part IV: Combining Methods


• 14: Selecting and Combining Tools


• 15: Relational Databases


• 16: Advanced Shell and Pipelines


• Part V: Graphics


• 17: Graphical Concepts


• 18: Working with Vector Art


• 19: Working with Pixel Images


• Part VI: Advanced Topics


• 20: Working on Remote Computers


• 21: Installing Software


• 22: Electronics: Interacting with the Physical World