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Practical Computing for Biologists de Steven H. D. Haddock

Practical Computing for Biologists

Autor Steven H. D. Haddock, Casey W. Dunn
en Limba Engleză Paperback – 5 noi 2010

Considerăm acest volum un instrument indispensabil pentru nivelul de licență și master în științele vieții, fiind conceput special pentru a ajuta cercetătorii să depășească limitările programelor de calcul tabelar. Practical Computing for Biologists abordează o problemă critică în biologia modernă: gestionarea seturilor de date care cresc exponențial. Găsim în această carte o metodologie aplicată, dezvoltată de Steven H. D. Haddock și Casey W. Dunn pe baza propriei experiențe în cercetare, menită să automatizeze procesele repetitive de prelucrare a datelor.

Structura narativă este una pragmatică, ghidând cititorul prin 22 de capitole care acoperă linia de comandă Unix, programarea în Python, utilizarea bazelor de date și editarea grafică. Deși multe tehnici sunt esențiale pentru bioinformatică, aplicabilitatea lor este mult mai largă, vizând orice demers științific ce necesită rigoare computațională. Un element distinctiv al ediției publicate de Oxford University Press este atenția acordată utilizatorilor de sisteme de operare diferite; deși fluxul principal urmărește Mac OS X, instrucțiunile pentru Windows și Linux sunt integrate ergonomic în marginea textului.

Ca alternativă la Managing Your Biological Data with Python pentru cursurile de bioinformatică, acest manual are avantajul unei perspective mai vaste, incluzând nu doar programare, ci și noțiuni de hardware (electronică) și gestionare a serverelor la distanță. Față de UNIX and Perl to the Rescue!, care se concentrează pe Perl, volumul de față prioritizează Python, oferind o curbă de învățare adaptată nevoilor actuale din laboratoarele de cercetare.

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Specificații

ISBN-13: 9780878933914
ISBN-10: 0878933913
Pagini: 564
Dimensiuni: 230 x 193 x 26 mm
Greutate: 1.2 kg
Editura: Oxford University Press
Colecția OUP USA
Locul publicării:New York, United States

De ce să citești această carte

Recomandăm această carte oricărui biolog care s-a simțit limitat de Excel în procesarea datelor experimentale. Veți câștiga competențe practice în automatizarea analizelor prin Unix și Python, transformând orele de muncă manuală în procese de câteva secunde. Este resursa ideală pentru a trece de la simpla colectare a datelor la o analiză computațională robustă, fără a necesita experiență prealabilă în programare.

Despre autor

Steven H. D. Haddock și Casey W. Dunn sunt cercetători activi care și-au dedicat cariera studierii biodiversității și evoluției marine, utilizând metode computaționale avansate. Steven Haddock este cercetător la MBARI (Monterey Bay Aquarium Research Institute), specializat în bioluminescență și zooplancton, în timp ce Casey Dunn este profesor la Universitatea Yale, recunoscut pentru contribuțiile sale în filogenomică. Experiența lor directă în dezvoltarea de instrumente software pentru propriile laboratoare conferă cărții o notă autentică, soluțiile propuse fiind testate în scenarii reale de cercetare biologică.

Descriere

Published by Sinauer Associates, an imprint of Oxford University Press. 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 electronicsWhile 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.

Recenzii

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.
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.
My copy of Practical Computing for Biologists arrived last week, and I've 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.
When considering my research and use of time, this book has been the most important book I've 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.

Notă biografică

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.