BPB12 - Bioinformatics using Python for Biologists

General info

Date: 25 Jun 2012 - 29 Jun 2012
Location: Oeiras, PT
Website: http://gtpb.igc.gulbenkian.pt/bicourses/BPB12
Keywords: Programming, Information extraction, parsing
Organiser: Instituto Gulbenkian de Ciência
Contact(s): bicourses@igc.gulbenkian.pt

Description

Course description
Python is an object-oriented programming language that is ideal for biological data analysis. The course will start with very basic language concepts and instructions and will cover all the main language aspects, including variables, types, modules, functions, exceptions, control of flux, input, output, and classes. All the examples and practical sessions will focus on solving particular biological problems. In particular, examples and practical sessions will cover:

working with DNA and protein sequences
data retrieval from files and their manipulation
running applications, such as BLAST, locally and from a script
finding motifs in sequences
parsing Swiss-Prot files, PDB files, ENSEMBL records, blast output files, etc.

-Biopython will be also introduced and applied to some of the mentioned examples.-

The course is meant to be highly interactive and the students will continuously put theory into practice while learning. By the end of the course, the students will have a good understanding of Python basics and will have acquired the skills to manage any type of bioinformatics record and to run applications from scripts. Unix/linux basic skills will be provided at the beginning of the course.

Target Audience
End-users of bioinformatics databases and tools that aim at developing hands-on capabilities for biological data analysis, ie writing their own or adapting somebody else's Python scripts in an autonomous way.

Course Pre-requisites
Basic familiarity with bioinformatics data resources such as Uniprot/Swiss-Prot, Blast, ENSEMBL, PDB, etc. The course is directed to biologists with little or no programming experience and aims at making them capable to use Python to autonomously manage and analyse biological data.

Teachers