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Bioinformatics with Python Cookbook by Tiago Antao pdf download

Bioinformatics with Python Cookbook by Tiago Antao.
Learn how to use modern Python bioinformatics libraries and applications to do cutting-edge research in computational biology.

Whether you are reading this book as a computational biologist or a Python programmer, you will probably relate to the "explosive  growth, exciting times" expression. The recent growth of Python is strongly connected with its status as the main programming  language for big data. On the other hand, the deluge of data in biology, mostly from genomics and proteomics makes  bioinformatics one of the forefront applications of data science. There is a massive need for bioinformaticians to analyze all this data; of course, one of the main tools is Python. We will not only talk about the programming language, but also the whole community and software ecology behind it. When you choose Python to analyze your data, you will also get an extensive set of libraries, ranging from statistical analysis to plotting, parallel programming, machine learning, and bioinformatics. However, when you choose Python, you expect more than this; the community has a tradition of providing good documentation, reliable libraries, and frameworks. It is also friendly and supportive of all its participants.

In this book, we will present practical solutions to modern bioinformatics problems using Python. Our approach will be hands-on, where we will address important topics, such as next-generation sequencing, genomics, population genetics, phylogenetics, and proteomics among others. At this stage, you probably know the language reasonably well and are aware of the basic analysis  methods in your field of research. You will dive directly into relevant complex computational biology problems and learn how to tackle them with Python. This is not your first Python book or your first biology lesson; this is where you will find reliable and pragmatic solutions to realistic and complex problems.

Bioinformatics with Python Cookbook by Tiago Antao pdf download

Table Of Contents:
Chapter 1: Python and the Surrounding Software Ecology 
Chapter 2: Next-generation Sequencing 
Chapter 3: Working with Genomes 
Chapter 4: Population Genetics 
Chapter 5: Population Genetics Simulation 
Chapter 6: Phylogenetics 1
Chapter 7: Using the Protein Data Bank
Chapter 8: Other Topics in Bioinformatics
Chapter 9: Python for Big Genomics Datasets 

What you need for this book?
Modern bioinformatics analysis is normally performed on a Linux server. Most of our recipes will also work on Mac OS X. It will also work on Windows in theory, but this is not recommended. If you do not have a Linux server, you can use a free virtual machine emulator such as VirtualBox to run it on a Windows/Mac computer. An alternative that we explore in the book is to use Docker as a container, which can be used on Windows and Mac via  boot2docker.

As modern bioinformatics is a big data discipline, you will need a reasonable amount of memory; at least 4 GB on a native Linux machine, probably 8 GB on a Mac/Windows system, but more would be better. A broadband Internet connection will also be necessary to download the real and hands-on datasets used in the book.

Python is a requirement. All the code will work with version 2, although you are highly encouraged to use version 3 whenever possible. Many free Python libraries will also be required and these will be presented in the book. Biopython, NumPy, SciPy, and Matplotlib are used in almost all chapters. Although the IPython Notebook is not strictly required, it's highly encouraged. Different chapters will also require various bioinformatics tools. All the tools used in the book are freely available and thorough instructions are provided in the relevant chapters of this book.

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.

Book Details:
⏩Author: Tiago Antao
⏩Puplisher: Packt Publishing Ltd
⏩Puplication Date: June 25, 2015
⏩Language: English
⏩Size: 5.77 MB 
⏩Pages: 306
⏩Format: PDF

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