Bioinformatics using Python for Biologists

   IMPORTANT DATES for this Course
   Deadline for applications: April 2nd 2010
   Notification of acceptance dates:
        EARLY:  March 12th 2010
        NORMAL:  April 6th 2009
   Course date: April 19th to April 23rd 2010


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 is Adjunct Professor since 2005. She also gives invited lectures in other universities and in training courses. 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.

Mariagiovanna Mazzapioda graduated in Computer Science at the Sapienza University of Rome and finished her PhD course in Computing, Communications and Electronics at the University of Plymouth (UK) in 2010. From 2004 to 2009 she worked in evolutionary robotics and artificial life at the National Council of Research (ISTC-CNR) of Rome (Italy) developing a virtual world where artificial creatures live, develop and reproduce themselves during generations. In 2009 she moved to Bioinformatics and she is currently a postdoc in the Biocomputing Group of Sapienza University of Rome headed by Anna Tramontano. Her main research interests focus both on biological networks and on the development of tools for structural bioinformatics. Beside her main research activity, she collaborates as computer programmer in some side projects (C/C++, Python, R, Java).

Affiliation: Sapienza Universitá 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, ENSEMBLE records, blast output files, etc.
Biopython will be also introduced and applied to some of the mentioned examples.
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 someby 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 manage and analyse bioinformatics data.

Detailed Program

Instituto Gulbenkian de Ciência,

Apartado 14, 2781-901 Oeiras, Portugal

GTPB Homepage

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Last updated:  March 26th 2010