Bioinformatics using Python for Biologists

Downloadable poster in PDF
A Testimonial: Participating in "Bioinformatics using Python for Biologists" in 2010 has caused very sharp improvements in my research career.
- Tiago Magalhães, PhD, University College Dublin

   IMPORTANT DATES for this Course
   Deadline for applications: May 28th 2013
   Notification of acceptance dates:
        EARLY:  May 13th 2013
        NORMAL:  May 29th 2013
   Course date: June 3rd to June 7th 2013


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.
Allegra Via has created the first BPB course in GTPB in 2010. The 2010 and 2011 and 2012 issues of this course were fully booked (20 seats) and the participant satisfaction was excellent (above 86%).

Affiliation: Sapienza Università di Roma, Roma, IT

Kristian Rother is a Python developer and freelance trainer for scientists. He gives workshops on software and scientific communication. He likes to develop and test methods for making trainings effective and interesting. Kristian graduated in biochemistry in 2002 and obtained his PhD in biology at the Humboldt University Berlin in 2006. Until 2011, he worked on RNA 3D modeling at the Adam Mickiewicz University Poznan, Poland. He has a professional SCRUM Master and is Club Executive at Toastmasters International. Kristian Rother is currently collaborating with Allegra Via in the writing of the book "Managing your biological data with Python", which is under consideration by the publisher Taylor & Francis.

Affiliation: Academis Training, Berlin, DE

Course description

Python is an object-oriented programming language that is ideal for biological data analysis. The course will start from zero knowledge, and will cover all basic concepts of Python, including variables, calculating, reading and writing files, control flow, modules, functions, exceptions. All examples and practical sessions will focus on solving biological problems.

In particular the 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 scrip
- finding motifs in sequence
- parsing Swiss-Prot files, PDB files, ENSEMBL records, blast output files, etc.
- Biopython

The course will be highly interactive and the students will continuously put theory into practice while learning. By the end of the course, the participants will have a good understanding of Python basics and will have acquired the skills to manage any type of bioinformatics database record and to run applications from scripts. Basic Unix/linux 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:  May 2nd 2013