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

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• 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