GTPB

The Gulbenkian Training Programme in Bioinformatics


GTPB runs at the Instituto Gulbenkian de Ciência on a yearly basis since 1999.
More than 950 course attendees in 9 years
Pedro Fernandes, GTPB organizer



Introductory Bioinformatics - IB08

Course Website

IMPORTANT DATES
Deadline for applications: March 18th 2008
Course date: April 7th - April 11th 2008



Instructors:

David P Judge is a Computer Scientist that teaches Bioinformatics since 1985. He runs the Bioinformatics Teaching Facilty housed at the Department of Genetics in the University of Cambridge, providing the necessary environment for graduate and undergraduate courses, on top of a comprehensive training programme in cooperation with the European Bioinformatics Institute and the Wellcome Trust Sanger Institute. He teaches Bioinformatics in many international training programmes and regularly in many places in Europe, Asia, Africa and America. His course notes and exercises are well known in the international community of Bioinformatics users.
University of Cambridge, Cambridge, UK
Pedro Fernandes graduated in Electronics and Telecommunications Engineering at IST (U.T. Lisboa). He worked in Biomedical Engineering, Biophysics and Physiology and changed to Bioinformatics in 1990. He established the first user community in Portugal around the national service provided by the portuguese node of the EMBnet. In 1998 he created the Gulbenkian Training Programme in Bioinformatics, providing user skills to more then 950 course attendees throughout its nine years of existance. In 2002 he designed a Masters Programme in Bioinformatics in cooperation with Mario Silva from the University of Lisboa. In 2006 he launched a new service based on a High Performance Computing platform. He teaches Bioinformatics both in graduate and undergraduate programmes.
Instituto Gulbenkian de Ciência, Oeiras, PT

Course Description

This five day introductory course is designed for newcomers to Bioinformatics. It also suits people that have some experience and wish to know how to use High Performance Computers (HPC) to speed-up their analysis. Its aim is to provide hands-on experience with sequence analysis tools in a way that reveals the power and the limitations of the methods. The majority of the course will be taught using the iNquiry software suite, now installed in the HPC Cluster "hermes" at the IGC. That includes EMBOSS, FASTA, multiple varieties of BLAST, etc. with a very friendly web interface.

Topics covered:
Internet Biological Data Resources
Sequence alignment - pairwise and multiple
Nucleotide sequence analysis - restriction mapping, primer design etc.
Protein sequence analysis - motifs, domains, patterns, profiles
3D visualization of protein structures

Attendees will be trained in software for: Identification of Coding Regions in genomic DNA; Gene Prediction; Primer Selection; Restriction Mapping; Sequence database similarity searching; Multiple sequence analysis; Pattern and motif searching; Protein sequence biophysical properties; Preliminary protein secondary structure prediction;


Timetable (provisional):

April 7th

Day 1

09:30 -11:00

Introduction, What is Bioinformatics?

11:00 -11:30

Coffee Break

11:30 -12:30

Sequence Analysis in High Performance Computing patforms

12:30 - 14:00

Lunch Break

14:00 - 16:00

Information Resources available through the Internet

16:00 - 16:30

Tea Break

16:30 - 18:00

Practical

April 8th

Day 2

09:30 -11:00

Pairwise Alignments

11:00 - 11:30

Coffee Break

11:30 - 12:30

Database Searching Methods

12:30 - 14:00

Lunch Break

14:00 - 16:00

Dynamic Programming

16:00 - 16:30

Tea Break

16:30 - 18:00

Practical

April 9th

Day 3

09:30 -11:00

Multiple Sequence Alignments

11:00 - 11:30

Coffee Break

11:30 - 12:30

Protein Sequence Analysis

12:30 - 14:00

Lunch Break

14:00 - 16:00

Practical

16:00 - 16:30

Tea Break

16:30 - 18:00

Practical

April 10th

Day 4

09:30 -11:00

Dynamic Programming

11:00 -11:30

Coffee Break

11:30 - 12:30

Protein Sequence Analysis

12:30 - 14:00

Lunch Break

14:00 - 16:00

Practical

16:00 - 16:30

Tea Break

16:30 - 18:00

Practical

April 11th

Day 5

09:30 -11:00

Patterns and Profiles

11:00 -11:30

Coffee Break

11:30 -12:30

Practical

12:30 - 14:00

Lunch Break

14:00 - 16:00

Analysis of Mutations

16:00 - 16:30

Tea Break

16:30 - 18:00

Practical, Wrap-up Session


Pre-requisites: Basic Molecular Biology and Biochemistry. Elementary computing skills.

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Instituto Gulbenkian de Ciência, Apartado14, 2781-901 Oeiras, Portugal


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Last updated:Apr 2nd 2008