Bioinformatics with Python Cookbook First Published Edition

by Tiago Antao (Author)

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ISBN-13: 978-1782175117

ISBN-10: 1782175113

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Bioinformatics with Python Cookbook: Learn how to use modern Python bioinformatics libraries and applications to do cutting-edge research in computational biology, 2nd Edition
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Learn how to use modern Python bioinformatics libraries and applications to do cutting-edge research in computational biology

About This Book

Discover and learn the most important Python libraries and applications to do a complex bioinformatics analysis
Focuses on the most modern tools to do research with next generation sequencing, genomics, population genetics, phylogenomics, and proteomics
Uses real-world examples and teaches you to implement high-impact research methods

Who This Book Is For

If you have intermediate-level knowledge of Python and are well aware of the main research and vocabulary in your bioinformatics topic of interest, this book will help you develop your knowledge further.

What You Will Learn

Gain a deep understanding of Python's fundamental bioinformatics libraries and be exposed to the most important data science tools in Python
Process genome-wide data with Biopython
Analyze and perform quality control on next-generation sequencing datasets using libraries such as PyVCF or PySAM
Use DendroPy and Biopython for phylogenetic analysis
Perform population genetics analysis on large datasets
Simulate complex demographies and genomic features with simuPOP

In Detail

If you are either a computational biologist or a Python programmer, you will probably relate to the expression "explosive growth, exciting times". Python is arguably the main programming language for big data, and the deluge of data in biology, mostly from genomics and proteomics, makes bioinformatics one of the most exciting fields in data science.

Using the hands-on recipes in this book, you'll be able to do practical research and analysis in computational biology with Python. We cover modern, next-generation sequencing libraries and explore real-world examples on how to handle real data. The main focus of the book is the practical application of bioinformatics, but we also cover modern programming techniques and frameworks to deal with the ever increasing deluge of bioinformatics data.

Vince Buffalo
97
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Tiago Antao
23
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Product details

Publisher ‏ : ‎ Packt Publishing; First Published edition (June 25, 2015)
Language ‏ : ‎ English
Paperback ‏ : ‎ 306 pages
ISBN-10 ‏ : ‎ 1782175113
ISBN-13 ‏ : ‎ 978-1782175117
Item Weight ‏ : ‎ 1.16 pounds
Dimensions ‏ : ‎ 7.5 x 0.69 x 9.25 inches

Best Sellers Rank: #3,103,262 in Books (See Top 100 in Books)
- #761 in Bioinformatics (Books)
- #3,312 in Python Programming
- #7,860 in Computer Programming Languages

Customer Reviews:
7 ratings

About the author

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Tiago Antao

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Tiago Antao has a long career in the field of scientific computing, have been a researcher at the Universities of Oxford and Cambridge. He is a co-author of several Python-based scientific software packages like Biopython.

He currently works in the software development industry focusing on developing high performance software solutions using Python.

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G. A. Patino

The bioinformatics Python book for the biomedical scientist

Reviewed in the United States on July 27, 2015

This book is a great addition to the library of texts to learn advanced Python applications in biomedical sciences. One big drawback of the Python environment in this field is the paucity of textbooks beyond the most basic level. In this sense, the book by Antao is a welcome contribution.
Two things you need to know right away about the book: 1) This is not a bioinformatics book, as it covers only the Python implementation of the algorithms but not their theoretical background. Furthermore, the techniques covered are intermediate and advanced bioinformatics topics (e.g. next-generation sequencing, population genetics, protein structure visualization). 2) By the same token, is not an introductory Python book, knowledge about the language and its most common scientific packages (NumPy, SciPy, and Matplotlib) is assumed (on the other hand, Chapter 1 - covering the installation of the software - is a little wasted because of this).
The materials in each chapter are presented clearly and in a concise manner. Is very easy to follow what Python packages are being used and the differences in syntax between Python 2 and 3. The selected examples are very relatable to the biomedical scientist, making it a nice change of pace from all the finance examples commonly encountered in most Python books. The code runs smoothly without any changes, and the explanations of the commands are good although a little short every now and then.
In summary, this is a great book if you are looking to implement advanced bioinformatics techniques in Python. The writing style of the author makes it very user-friendly and if he decided to write another book covering how to implement basic bioinformatic techniques (probably a Biopython manual) I wouldn't hesitate to add it to my library.

6 people found this helpful

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Loris

Good cookbook for bioinformaticians

Reviewed in the United States on August 29, 2015

This book is an excellent bioinformatics cookbook and it covers a vast range of topics, ranging from next generation sequencing to population genetics and phylogenetics. However to take fully advantage of the book is highly recommended to have both a medium-high knowledge of python and some experience in bioinformatics. Each chapter provides python code to reproduce the analyses the author performs. Even though the author explains the code in details, the code often is not trivial and a certain experience with python is required. Similarly, a previous knowledge of bioinformatic technologies is desirable as the book often uses a terminology (such as fastq, bam, vcf, etc.) that won’t be familiar to those that haven’t any experience in bioinformatics.

The book is well organized and structured. The first chapter helps the reader to set up a python environment through Anaconda or Docker. In the following chapter the author starts to talk about bioinformatics and the first topic he touches is NGS (next generation sequencing). I found this chapter very interesting as it shows how to deal efficiently with the usually huge fastq files and how to perform simple but useful analyses such as quality control of the sequencing reads by position. In the same chapter the author talks about the variant call format (VCF) and how to work with it through libraries such as pyVCF. The next chapter is dedicated to whole genome sequences in fasta format and to genome annotations in GFF/GTF formats. The following chapters are about population genetics and phylogenetics. Even though I’m not an expert of these fields and I was not aware of the formats used (such as genepop) I could enjoy the reading and the code was straightforward enough to be easily understandable. Then the author explains how to use PDB (the protein data bank) and the software PyMol. A very interesting (and in my opinion important) chapter is the last one where the author discusses how to deal efficiently with big genomics datasets. Here the authors talks about concurrency and ipython parallel computing, and shows how it is possible to speed up your python code by using libraries such as Cython and Numba.

Overall the book is well written and organized and is a good cookbook for bioinformaticians.

7 people found this helpful

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Yannick Pouliot

A pleasure to explore

Reviewed in the United States on October 13, 2015

I've been in computational biology for a long time, and I find this to be one of the most impressive practical and comprehensive books I've come across (and I go through a lot!) It provides an incredibly wide survey of different domains of computational biology (e.g., protein structure, genomics, and much more), combined with lots of good Python programming advice (e.g., use of IPython/Jupyter notebooks, provided by the author). And it's about as up to date as imaginable -- quite a tour de force!

4 people found this helpful

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Stefanobia

Per mio figlio

Reviewed in Italy on December 1, 2016

Verified Purchase

Non sono in grado di recensire il prodotto in quanto non ho queste conoscenze, libro perfetto senza nessun segno o danneggiamento

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Bioinformatics with Python Cookbook

Reviewed in Spain on November 10, 2018

Verified Purchase

En mi caso, con poca experiencia en bioinformática, este libro me ha proporcionado una visión general de como se usa python en este campo.

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JoseJaime

Must read

Reviewed in Mexico on January 13, 2016

Verified Purchase

Awesome, clear, updated. This is an must be readed textbook for bioinformaticians and biologist that want to tackle bioinformatics with Python.
Python basis are mandatory.

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Bioinformatics with Python Cookbook First Published Edition

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About This Book

Who This Book Is For

What You Will Learn

In Detail

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About the author

Tiago Antao

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