Introduction

We will start by installing the required software. This will include the Python distribution, some fundamental Python libraries, and external bioinformatics software. Here, we will also be concerned with the world outside Python. In bioinformatics and Big Data, R is also a major player; therefore, you will learn how to interact with it via rpy2 a Python/R bridge. We will also explore the advantages that the IPython framework can give us in order to efficiently interface with R. This chapter will set the stage for all the computational biology that we will perform in the rest of the book.

As different users have different requirements, we will cover two different approaches on how to install the software. One approach is using the Anaconda Python (http://docs.continuum.io/anaconda/) distribution and another approach to install the software via Docker (a server virtualization method based on containers sharing the same operating system kernel—https://www.docker.com/). We will also provide some help on how to use the standard Python installation tool, pip, if you use the standard Python distribution. If you have a different Python environment that you are comfortable with, feel free to continue using it. If you are using a Windows-based OS, you are strongly encouraged to consider changing your operating system or use Docker via boot2docker.