The Gulbenkian Training Programme in Bioinformatics
Introductory Bioinformatics - IB08 Course WebsiteIMPORTANT DATES
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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.
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. |
Instituto Gulbenkian de Ciência,
Apartado14, 2781-901 Oeiras, Portugal