Bioinformatics Data Skills: Reproducible and Robust Research with Open Source Tools 1st Edition

by Vince Buffalo (Author)

19 customer reviews

ISBN-13: 978-1449367374

ISBN-10: 1449367372

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This practical book teaches the skills that scientists need for turning large sequencing datasets into reproducible and robust biological findings. Many biologists begin their bioinformatics training by learning scripting languages like Python and R alongside the Unix command line. But there's a huge gap between knowing a few programming languages and being prepared to analyze large amounts of biological data.
Rather than teach bioinformatics as a set of workflows that are likely to change with this rapidly evolving field, this book demsonstrates the practice of bioinformatics through data skills. Rigorous assessment of data quality and of the effectiveness of tools is the foundation of reproducible and robust bioinformatics analysis. Through open source and freely available tools, you'll learn not only how to do bioinformatics, but how to approach problems as a bioinformatician.

Go from handling small problems with messy scripts to tackling large problems with clever methods and tools
Focus on high-throughput (or "next generation") sequencing data
Learn data analysis with modern methods, versus covering older theoretical concepts
Understand how to choose and implement the best tool for the job
Delve into methods that lead to easier, more reproducible, and robust bioinformatics analysis

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Editorial Reviews

About the Author

Vince Buffalo is currently a first-year graduate student studying population genetics in Graham Coop's lab at UC Davis in the Population Biology Graduate Group. Before starting his PhD in population genetics, Vince worked professionally as a bioinformatician in the Bioinformatics Core at the UC Davis Genome Center and in the Department of Plant Sciences. An obsessive programmer since he was a young teenager, Vince was drawn to the statistical and computational problems of genomics. He works on open source bioinformatics tools in his work and free time, and enjoys fly fishing and cooking when away from the computer.

Paperback: 538 pages
Publisher: O'Reilly Media; 1 edition (July 23, 2015)
Language: English
ISBN-10: 1449367372
ISBN-13: 978-1449367374
Product Dimensions: 7 x 1.2 x 9.2 inches
Shipping Weight: 2 pounds (View shipping rates and policies)
Average Customer Review: 19 customer reviews
Amazon Best Sellers Rank: #66,943 in Books (See Top 100 in Books)
- #14 in Books > Computers & Technology > Computer Science > Bioinformatics
- #49 in Books > Engineering & Transportation > Engineering > Bioengineering > Biochemistry
- #150 in Books > Computers & Technology > Programming > Software Design, Testing & Engineering > Software Development

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Robert Shear

A carefully written intermediate text with valuable advice for all who work with large data sets in biology.

June 9, 2016

Format: PaperbackVerified Purchase

The book is a gem. The clear and unambiguous description of technical details sets it apart from many similar volumes. The author's wise advice on good practice could save many a researcher time and trouble in the long run.

5 people found this helpful

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October 13, 2016

Format: PaperbackVerified Purchase

Chose this book for a class in bioinformatics,

Pros: great range of topics covered: bash shell, git, ssh, working with data, data compression

Cons: the author is a little long winded and and it does not have great examples

2 people found this helpful

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Piotr

Great resource for learning your way around linux based systems ...

April 3, 2017

Format: PaperbackVerified Purchase

Great resource for learning your way around linux based systems in relation to bioinformatics/genomic analysis tools. Everything is followed through step-by-step and doesn't leave you wondering why something was done, while at the same time it doesn't keep teaching you past commands unnecessarily.

One person found this helpful

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September 9, 2017

Format: PaperbackVerified Purchase

Bioinformatic Data skills ...but aware this is a book for bioinformaticians but not for wet lab scientists

One person found this helpful

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Zachary Shields

Great book for learning NGS data analysis, not for true beginners.

October 23, 2015

Format: PaperbackVerified Purchase

I feel strongly obligated to commend this book. This is a wonderful compendium that helps those who already know a bit of Python/R languages to quickly pick up speed in dealing with next-gen sequencing data. Many of the practical tips are not easily available elsewhere. Some potential buyers may be distanced noticing the fact that the author is a new graduate student in population genetics. Please don't worry. The author is also a senior bioinformatician who is so generously sharing his truly practical insights and skills with NGS data. Fresh and up-to-date! On the other hand, it's only fair to note this book is not for those who are truly beginners to bioinformatics, especially those without any Linux/Python/R skills.

14 people found this helpful

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Nathan B. Smith

Bioinformatics and Data Science: Great learning experience!

January 24, 2017

Format: PaperbackVerified Purchase

Data science is the hottest ticket in town for tech jobs these days. Bioinformatics is a great practical use of data science. What better way to learn data science?

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Mr T

Good starting point for an amateur (but not novice)

August 15, 2017

Format: PaperbackVerified Purchase

A good text for the amateur bioinformatician or the journeyman looking to improve their overall approach. Not meant for the novice with little command line experience. The book provides an overview of many broad topics as opposed to specific tools, and the author does a good job of emphasizing reproducibility, which is surprisingly poorly practiced in the field. Recommended.

2 people found this helpful

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April 15, 2017

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The book is well written

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