Biopython
Ahmed G. A. Ali
Agenda
Open Bio Foundation
What is Python
Some Advantages of Python for Biologists
DEMOs (Many of them )
Nothing more !!!!
Open Bio Foundation
It is an open-source for Bioinformatics.
BioC++, BioPerl, BioJava, Biopython, BioRuby, BioSQL
BioWhateverYouWant
What does it do?
Managing the Bio* projects (Servers, Webpages, FTP sites
…etc.)
Hold annual meetings – Bioinformatics Open Source
Conference (BOSC)
Organizing ”hackathon” events for developers to get
together and work
What is Python
"Python is an interpreted, interactive, object-oriented programming language“ Form
http://www.python.org/
Python is often compared to Tcl, Perl, Ruby, Scheme or Java. Some of its key
distinguishing features include:
very clear, readable syntax
strong introspection capabilities
intuitive object orientation
natural expression of procedural code
full modularity, supporting hierarchical packages
exception-based error handling
very high level dynamic data types
extensive standard libraries and third party modules for virtually every task
extensions and modules easily written in C, C++ (or Java for Jython, or
.NET languages for IronPython)
embeddable within applications as a scripting interface
From: http://www.python.org/about/
What is Python
Python is powerful... and fast
Python plays well with others
Python can integrate with COM, .NET, and CORBA objects.
For Java libraries, use Jython, an implementation of Python for the Java
Virtual Machine.
For .NET, try IronPython , Microsoft's new implementation of Python
for .NET, or Python for .NET.
Python is also supported for the Internet Communications Engine (ICE)
and many other integration technologies.
Python is friendly... and easy to learn
Python is Open
From: http://www.python.org/about/
What is Python
Python runs everywhere
All major operating systems: Windows, Linux/Unix, OS/2, Mac, Amiga,
among others.
here are even versions that run on .NET, the Java virtual machine, and
Nokia Series 60 cell phones.
From: http://www.python.org/about/
Some Advantages of Python for Biologists
Easy to write quick programs
Very easy to interact with files and the operating system
Nice libraries for dealing with web pages, databases, other
useful things
Many useful libraries for Scientists
Numerical Python – fast, multidimensional arrays; math, math,
math (http://www.pfdubois.com/numpy/ )
Scientific Python – statistics, python MPI interfaces (
http://starship.python.net/~hinsen/ScientificPython/ )
Of course, Biopython...
Slide By: Brad Chapman
Open-Bio + Python = Biopython
Official blurb: international association of developers of
freely available Python tools for computational molecular
biology; established in 1999.
http://biopython.org
Library of functionality for dealing with common
problems biologists programming in python might face.
Slide By: Brad Chapman
What Can Biopython Do
Slide By: Brad Chapman
DEMO 1- Sequences.
Goals:
1. To Use the Bio Library to create a Sequence Object.
2. Using the Bio Libraries, Transcript the sequence.
3. Using the Bio Libraries, Translate the sequence.
DEMO-2 FASTA File ‘Something Real’
Goals:
1. Opening a FASTA File and parsing it using the Bio Libraries.
2. Calculating some Statistics for each gene like:
1. The count of every nucleotide.
2. The length of the sequence.
3. The CG percentage.
3. Saving the results in an Excel compatible file
DEMO-3 NCBI BLAST
Goals
1. To use the Bio libraries to call the NCBI Blast and query it.
2. Save the results in xml format.
3. Parse the results and view them.
4. And that is All
DEMO-4 Pubmed Search
Goals
1. Calling the Entrez Web Services using the Bio Libraries.
2. Searching the Pubmed Database using Esearch, and Efetch.
3. Saving the results in different formats(XML, HTML)
Let’s go Home
