Practical Computing for Biologists by Steven H.D. Haddock (English) Paperback Bo

Description: Practical Computing for Biologists by Steven H.D. Haddock, Casey W. Dunn Published by Sinauer Associates, an imprint of Oxford University Press.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. FORMAT Paperback LANGUAGE English CONDITION Brand New Publisher Description 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 morepowerfully 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 thetechniques 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 editinggraphics *Databases *Performing analyses on remote servers *Working withelectronicsWhile 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 fromthe most frustrating and time-consuming aspects of data processing so you can focus on the pleasures of scientific inquiry.RESOURCESForStudentsThe Companion Website includes downloads, community forums, tips and examples, and textbook errata and updates.For InstructorsThe Instructors Resource Library features all of the textbooks figures and tables, provided in ready-to-use PowerPoint presentations. Notes 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 Author Biography 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 MarineBiology, 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 instrumentsto monitor bioluminescence from fireflies, a freezer monitoring system, a web-based conference registration database, and a PCR calculator for smartphones. In addition to teaching invertebrate zoology and writing a booklet to teach the technique of blue-water scuba diving, he has given tutorials in computing to students and administrators. His interest in education extends to his Bioluminescence Web Page /~biolum/) and the Jellywatch.org citizen-science website.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 thecourse 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 biologistsface. In addition to teaching invertebrate biology, evolution, and development, his educational activities include the websites siphonophores.org and creaturecast.org. Dr. Dunn is the recipient of the National Science Foundations 2011 Alan T. Waterman Award, recognizing an outstanding young researcher in any field of science or engineering supported by NSF. Table of Contents Before You BeginPart I: Text Files1. Getting Set Up2. Regular Expressions: Powerful Search & Replace3. Exploring the Flexibility of Regular ExpressionsPart II: The Shell4. Command-line Operations: The Shell5. Handling Text in the Shell6. Scripting with the ShellPart III: Programming7. Components of Programming8. Beginning Python Programming9. Decisions and Loops10. Reading and Writing Files11. Merging Files12. Modules and Libraries13. Debugging StrategiesPart IV: Combining Methods14. Selecting and Combining Tools15. Relational Databases16. Advanced Shell and PipelinesPart V: Graphics17. Graphical Concepts18. Working with Vector Art19. Working with Pixel ImagesPart VI: Advanced Topics20. Working on Remote Computers21. Installing Software22. Electronics: Interacting with the Physical WorldAppendices Review "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"The book covers a wide range of subjects that truly justifies the title of practical computing. In addition to the usual programming-related topics, it also includes a thorough introduction to the programming environment, approaches to combining different programs together, a description of the basic text manipulation tools such as regular expressions, and even an introduction to dealing with digital art and images. As such the book is great value for themoney, being at least three books in one."--Olga G. Troyanskaya, Cell"My copy of Practical Computing for Biologists arrived last week, and Ive been very impressed. It is a well-written, well-paced guide to basic computing skills for scientists and engineers of all stripes (not just biologists). It is beautifully produced: full-color printing and great graphical design make this book a joy to read. If I ever do turn Software Carpentry into a book, I might skip the topics PCB covers and just tell people to go and buyit."--Greg Wilson, software-carpentry.org"When considering my research and use of time, this book has been the most important book Ive read in the last year, and perhaps the last decade. Striking a perfect balance by guiding you through tutorials and nudging your own self-exploration, the book has just enough guided direction to not annoy or overwhelm. It has helped (and is still helping) me to do what I was doing before, but more efficiently."--Cyme & Cystidium Promotional Shows how to use computing tools to work more powerfully and effectively Long Description 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 morepowerfully 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 thetechniques 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 editinggraphics *Databases *Performing analyses on remote servers *Working withelectronicsWhile 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 fromthe most frustrating and time-consuming aspects of data processing so you can focus on the pleasures of scientific inquiry.RESOURCESForStudentsThe Companion Website includes downloads, community forums, tips and examples, and textbook errata and updates.For InstructorsThe Instructors Resource Library features all of the textbooks figures and tables, provided in ready-to-use PowerPoint presentations. Review Text "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"The book covers a wide range of subjects that truly justifies the title of practical computing. In addition to the usual programming-related topics, it also includes a thorough introduction to the programming environment, approaches to combining different programs together, a description of the basic text manipulation tools such as regular expressions, and even an introduction to dealing with digital art and images. As such the book is great value for themoney, being at least three books in one." --Olga G. Troyanskaya, Cell"My copy of Practical Computing for Biologists arrived last week, and Ive been very impressed. It is a well-written, well-paced guide to basic computing skills for scientists and engineers of all stripes (not just biologists). It is beautifully produced: full-color printing and great graphical design make this book a joy to read. If I ever do turn Software Carpentry into a book, I might skip the topics PCB covers and just tell people to go and buyit." --Greg Wilson, software-carpentry.org"When considering my research and use of time, this book has been the most important book Ive read in the last year, and perhaps the last decade. Striking a perfect balance by guiding you through tutorials and nudging your own self-exploration, the book has just enough guided direction to not annoy or overwhelm. It has helped (and is still helping) me to do what I was doing before, but more efficiently." --Cyme & Cystidium Review Quote "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 "The book covers a wide range of subjects that truly justifies the title of practical computing. In addition to the usual programming-related topics, it also includes a thorough introduction to the programming environment, approaches to combining different programs together, a description of the basic text manipulation tools such as regular expressions, and even an introduction to dealing with digital art and images. As such the book is great value for the money, being at least three books in one." --Olga G. Troyanskaya, Cell "My copy of Practical Computing for Biologists arrived last week, and Ive been very impressed. It is a well-written, well-paced guide to basic computing skills for scientists and engineers of all stripes (not just biologists). It is beautifully produced: full-color printing and great graphical design make this book a joy to read. If I ever do turn Software Carpentry into a book, I might skip the topics PCB covers and just tell people to go and buy it." --Greg Wilson, software-carpentry.org "When considering my research and use of time, this book has been the most important book Ive read in the last year, and perhaps the last decade. Striking a perfect balance by guiding you through tutorials and nudging your own self-exploration, the book has just enough guided direction to not annoy or overwhelm. It has helped (and is still helping) me to do what I was doing before, but more efficiently." --Cyme & Cystidium Description for Bookstore 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 Details ISBN0878933913 Author Casey W. Dunn ISBN-10 0878933913 ISBN-13 9780878933914 Format Paperback Media Book Language English Short Title PRAC COMPUTING FOR BIOLOGISTS DEWEY 570.285 Illustrations Yes Country of Publication United States Affiliation Yale University Imprint Oxford University Press Inc Place of Publication New York Publisher Oxford University Press Inc Series Sinauer NZ Release Date 2010-11-05 US Release Date 2010-11-05 Year 2010 Publication Date 2010-11-05 UK Release Date 2010-11-05 Audience Tertiary & Higher Education AU Release Date 2010-11-04 Pages 564 We've got this At The Nile, if you're looking for it, we've got it. 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