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Biopython: Ahmed G. A. Ali

The document discusses Biopython, an open-source library for biological computation with Python. It begins by introducing the Open Bio Foundation, which manages various bioinformatics projects. It then provides an overview of the Python programming language, highlighting advantages for biologists like its clear syntax, extensive libraries, and ability to integrate with other languages. Key features of Biopython are described, including tools for working with biological sequences, parsing FASTA files, performing NCBI BLAST searches, and querying PubMed. Several demonstrations are outlined to showcase capabilities of Biopython.

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Samir Sabry
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201 views

Biopython: Ahmed G. A. Ali

The document discusses Biopython, an open-source library for biological computation with Python. It begins by introducing the Open Bio Foundation, which manages various bioinformatics projects. It then provides an overview of the Python programming language, highlighting advantages for biologists like its clear syntax, extensive libraries, and ability to integrate with other languages. Key features of Biopython are described, including tools for working with biological sequences, parsing FASTA files, performing NCBI BLAST searches, and querying PubMed. Several demonstrations are outlined to showcase capabilities of Biopython.

Uploaded by

Samir Sabry
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PPTX, PDF, TXT or read online on Scribd
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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 

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