Practical Computing for Biologists

About this book

Increasingly, scientists find themselves facing exponentially larger data sets and analyses without suitable tools to deal with them. Many biologists end up using spreadsheet programs for most of their data-processing tasks and spend hours clicking around or copying and pasting, and then repeating the process for other data files.

This book shows how to use many freely available computing tools to work more powerfully and effectively. It was born out of the authors' own experience in developing tools for their research and helping other biologists with their computational problems. Although many of the techniques are relevant to molecular bioinformatics, the motivation for the book is much broader, focusing on topics and techniques that are applicable to a range of scientific endeavors.

Contents

Before You Begin PART I: TEXT FILES Getting Set Up Regular Expressions: Powerful Search & Replace Exploring the Flexibility of Regular Expressions PART II: THE SHELL Command-line Operations: The Shell Handling Text in the Shell Scripting with the Shell PART III: PROGRAMMING Components of Programming Beginning Python Programming Decisions and Loops Reading and Writing Files Merging Files Modules and Libraries Debugging Strategies PART IV: COMBINING METHODS Selecting and Combining Tools Relational Databases Advanced Shell and Pipelines PART V: GRAPHICS Graphical Concepts Working with Vector Art Working with Pixel Images PART VI: ADVANCED TOPICS Working on Remote Computers Installing Software Electronics: Interacting with the Physical World APPENDICES Working with other Operating Systems Regular Expression Search Terms Shell Commands Python Quick Reference Template Programs Binary, Hex, and ASCII SQL Commands Index

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Biography

STEVEN HADDOCK is a Research Scientist at the Monterey Bay Aquarium Research Institute and adjunct Associate Professor at the University of California, Santa Cruz, USA, studying bioluminescence and biodiversity of gelatinous zooplankton.

CASEY DUNN, an Assistant Professor at Brown University, USA, does research that has a large computational component but always in conjunction with work in the field and lab.