September 03, 2017

Biopython with Peter Cock, Wibowo Arindrarto, and Tiago Antão

45 minutes

Summary

Advances in the techniques used for genome sequencing are providing us with more information to unlock the secrets of biology. But how does that data get processed and analyzed? With Python of course! This week I am joined by some of the core maintainers of Biopython to discuss what bioinformatics is, how Python is used to help power the research in the field, and how Biopython helps to tie everything together.

Preface

Hello and welcome to Podcast.__init__, the podcast about Python and the people who make it great.

I would like to thank everyone who supports us on Patreon. Your contributions help to make the show sustainable.

When you’re ready to launch your next project you’ll need somewhere to deploy it. Check out Linode at www.podastinit.com/linode?utm_source=rss&utm_medium=rss and get a $20 credit to try out their fast and reliable Linux virtual servers for running your awesome app.

Need to learn more about how to scale your apps or learn new techniques for building them? Pluralsight has the training and mentoring you need to level up your skills. Go to www.pythonpodcast.com/pluralsight?utm_source=rss&utm_medium=rss to start your free trial today.

Visit the site to subscribe to the show, sign up for the newsletter, read the show notes, and get in touch.

To help other people find the show please leave a review on iTunes, or Google Play Music, tell your friends and co-workers, and share it on social media.

If you work with data for your job or want to learn more about how open source is powering the latest innovations in data science then make your way to the Open Data Science Conference, happening in London in October and San Francisco in November. Follow the links in the show notes to register and help support the show in the process.

Your host as usual is Tobias Macey and today I’m interviewing Peter Cock, Wibowo Arindrarto, and Tiago Antão about biopython, a suite of python tools for computational molecular biology.

Interview

Introductions

How did you get introduced to Python?

Can you start by explaining what bioinformatics is and highlight some of the different areas of research?

What is biopython and how did it get started?

Biopython has a long history behind it. How has the project evolved over that time to meet the changing needs in terms of both research amd computation?

How does Biopython compare to the sibling Bio* projects in other programming languages?

What does a common workflow look like for someone who is working with biological data?

What are some of the most interesting or innovative uses of Biopython that you are aware of?

What are some of the most challenging aspects of developing and supporting Biopython?

What are some of the most exciting developments in bioinformatics, either recently or coming up?

How much domain knowledge is necessary for someone who wants to contribute to the project?

What are some of the most problematic limitations of Biopython and how do you work around them?

Keep In Touch

Peter

Website

Wibowo

Website

@_bow_ on Twitter

Tiago

Website

@tiagoantao on Twitter

Biopython

GitHub

Picks

Tobias

Keep it Low Conf

Peter

Jupyter Notebooks (formerly IPython) for producing notebooks combining code, graphical output and descriptive code. Can be seen as a modern take on Donald Knuth’s Literate programming?

Wibowo

Conda for installing software, including BioConda for community packaged software in bioinformatics.

Tiago

Brython project for writing Python 3 in your browser using JavaScript

Glacier National Park in North West Montana

Links

BioJava

BioRuby

BioPerl

BioJS

Open Bioinformatics Foundation

Software In The Public Interest

Oxford Nanopore Technology (for sequencing in the field etc)

The intro and outro music is from Requiem for a Fish The Freak Fandango Orchestra / CC BY-SA

...more

View all episodes

By Tobias Macey

4.4

100100 ratings