BPB11

Bioinformatics using Python for Biologists

   IMPORTANT DATES for this Course
   Deadline for applications: April 11th 2011
   Notification of acceptance dates:
        EARLY: March 12th 2011
        NORMAL: April 14th 2011
   Course date: May 2nd to May 6th 2011

Instructors:

Allegra Via graduated in Theoretical Physics at Sapienza University of Rome and obtained her PhD in Cellular and Molecular Biology in 2002. Since 1998 she works in Computational Biology and regularly teaches Bioinformatics and Python Programming Language to bioinformaticians and biologists. She was Postdoctoral Fellow at the University of Rome 'Tor Vergata' where she has been Adjunct Professor in 2005-2010. Since the academic year 2010-2011 she teaches at Sapienza University of Rome. She also gives invited lectures in other universities and in training courses, namely the first edition of the BPB course for GTPB in 2010. Currently she works as researcher in the Biocomputing Group of Sapienza University of Rome headed by Anna Tramontano. Her main research interests include protein structural bioinformatics and protein function prediction and analysis. Besides her research activity, she wrote two book chapters related to Internet for Cell and Molecular Biologists and is currently writing a book on Python programming for Biology and Bioinformatics, which is under consideration by Taylor&Francis (publisher).

Fabrizio Ferrè graduated in Molecular Biology at Tor Vergata University of Rome, where he also got his Ph.D. in Cellular and Molecular Biology in 2002. He spent his postdoctoral research activity at Boston College, Harvard Medical School and Sapienza University of Rome Since the beginning of the Ph.D training he applied and developed computational techniques for the analysis of biomedical data, ranging from protein structural analysis and function prediction to the analysis of genomic data. Since 2009 he teaches the Computational Genomics course at the Tor Vergata University. He wrote several peer-reviewed research articles on scientific journals, and participated in the writing of books aimed at introducting bioinformatic resources to the biomedical researcher.

Affiliation: Sapienza Università di Roma, Roma, IT

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.

Detailed Program

Instituto Gulbenkian de Ciência,

Apartado 14, 2781-901 Oeiras, Portugal

GTPB Homepage

IGC Homepage

Last updated: February 13th 2011