Practical Computing for Biologists

ISBN-13: 9780878933914 / Angielski / Miękka / 2010 / 564 str.

Yale University) Dunn Casey W. (

Opis

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.

Practical Computing for Biologists shows you how to use many freely available computing tools to work more powerfully and effectively. The book 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. Twenty-two chapters organized into six parts address these topics (and more; see Contents):

*Searching with regular expressions

*The Unix command line

*Python programming and debugging

*Creating and editing graphics

*Databases

*Performing analyses on remote servers

*Working with electronics

While most of the concepts and examples apply to any operating system, the main narrative focuses on Mac OS X. Where there are differences for Windows and Linux users, parallel instructions are provided in the margin and in an appendix. The book is designed to be used as a self-guided resource for researchers, a companion book in a course, or as a primary textbook. Practical Computing for Biologists will free you from the most frustrating and time-consuming aspects of data processing so you can focus on the pleasures of scientific inquiry.

RESOURCES

For Students

The Companion Website includes downloads, community forums, tips and examples, and textbook errata and updates.

For Instructors

The Instructor's Resource Library features all of the textbook's figures and tables, provided in ready-to-use PowerPoint presentations.

Recenzje

Practical Computing for Biologists is a clear guide to methods that unlock the power of the personal computer. Although the breadth of subjects covered is certainly an asset of this volume, what really makes the book stand out is how well the authors clearly describe each technique and its applicability to biological sciences. It is a great launching point for any necessary further investigation of computational techniques. Matthew Aiello-Lammens, The Quarterly Review of Biology

Spis treści

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.

O autorze

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.