Biopython tools for protein analysis

By Sebastián Bassi (sbassi@genesdigitales.com).

This work is licensed under CC-BY-SA 3.0.

Note: This presentation requires Crunchy for iterative features to work. Most code snippets uses Biopython and it must be installed. Some scripts requires external files, these are in this data package (about 502Kb). This was tested with Biopython 1.50b and Python 2.5.2, but it should work with any recent Biopython version.

This presentation shows how Biopython can be used for protein analysis. This is not a tutorial, the aim of this laptop session is to show what can be done with Biopython. For tutorials, howtos, cookbook and learning material, please see More Information at the end of this laptop session.
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Python

Description

Official description: Python is a dynamic object-oriented programming language that can be used for many kinds of software development. It offers strong support for integration with other languages and tools, comes with extensive standard libraries, and can be learned in a few days.

Features

Easy to read:

#include stdout
int main()
{
std::cout << "Hello, world!\n";
}
with the output being: Hello, world!

The same program in Python would be:

print "Hello, world!"
Try it!:
>>> print "Hello, world!"

Multiplatform

Python runs on Windows, UNIX, GNU/Linux, Mac OS X, OS/2, Amiga, Palm Handhelds, and Nokia mobile phones. Python has also been ported to the Java and .NET virtual machines.

Batteries included

Includes libraries for a wide range of applications: See
Python Package Index

Free

OSI/GPL compilant. (Both as a freedom and as a beer!)

Who uses Python?

Google, NASA, IL&M, AstraZeneca, Rackspace, Facebook, Wikipedia, you name it...

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