The Biopython Project is an amazing initiative that helps scientists use Python for bioinformatics – and it’s exceptionally easy to learn!
You can access online services, parse (read) different file types, analyze, and do a bunch of fun stuff with your data with Biopython. The people behind the project have put in a lot of effort to ensure that using the package is easy and effortless to use.
Python is one of the easiest programming languages to learn – which adds to the simplicity of using Biopython. So there’s no reason to shy away from that blinking screen. Get on your text editor and start coding!
Getting a Cozy Habitat for your (Bio)Python
The first step to installing Biopython is setting up Python on your computer. Biopython works best on Python 2.7, but they also have a new release that supports Python 3.x (if that’s what you prefer).
If you’re new to this, just install Python 2.7.
Your computer comes pre-installed with Python. To check the version, simply type:
python —version
in your Terminal.
Some people prefer to install python in a separate directory to use for their own development projects (to avoid any problems that may occur if you accidentally delete something – although this is extremely rare). If you want to do this, simply install Homebrew (it’ll take care of everything and more). Then, you can install Python.
Side note: I cannot recommend pip enough. It’s a python package manager. It’s really handy for installing all the different python packages you may need in the future. To install it, simply type
sudo easy_install pip
in your Terminal window.
Bringing the BioPython home
So we’ve set the stage and you’re already getting comfortable with the Terminal – you’ll be writing your first Python program soon!
Now that you have Python, it’s time to install the dependencies for Biopython. Dependencies save programmers time so that they don’t have to rewrite code.
Biopython relies on the NumPy package (among others; but this is the only one you need to install right now).
Go to your terminal window and type:
sudo pip install biopython
(Told you pip is amazing!)
And you’re done!
If you run in to any problems with installation, you can check out the official documentation.
Now that everything is installed, you can write your first Python program. I strongly recommend the Atom Text editor, but you can use whichever editor you like.
And to help you get started with writing that code? We’ve got you covered.
Just before Life Technologies purchased the start-up company Ion Torrent, the fledgling company was dealing with a torrent of another kind—worldwide media interest in its new sequencing technology, which promised to bring the price of next-generation, massively parallel sequencing down to $1,000 per run. Since that dramatic announcement in the summer of 2011, Life Technologies…
You don’t need to be told about how next generation sequencing technologies have revolutionized the way we study the genome and the epigenome. Whether you want to look at transcription (RNA-seq), translation (Ribo-seq) genomes (DNA-seq), interactions of proteins and DNA (ChIP-Seq) or to study epigenetic features such as methylation (whole genome bilsulfite sequencing) there are…
It was not long since the commercialization of NGS (a little more than ten years ago) that scientists went beyond the basics and got creative with the new technology to study much more than just the sequence of DNA. In this article we highlight some of the different NGS technologies and methods available out there….
Plants are just not green gods—they can be more. You can cost-effectively express your recombinant complex proteins in a plant system. More interestingly, plants are ideal systems for producing functional monoclonal antibodies, enzymes, and vaccine components! They can also be used for protein localization studies. To save time, you can transiently express your protein using…
10 Things Every Molecular Biologist Should Know
The eBook with top tips from our Researcher community.
