Introductory Bioinformatics

   IMPORTANT DATES for this Course
   Deadline for applications: Mar 5th 2012
        EARLY:  Mar 1st 2012
        NORMAL:   Mar 6th 2012
   Course date: March 12th to March 16th 2012


David P Judge is a Computer Scientist that teaches Bioinformatics since 1985. He runs the Bioinformatics Training 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, the Wellcome Trust Sanger Institute and the Instituto Gulbenkian de Ciência through GTPB. He teaches Bioinformatics in several international training programmes and is regularly invited to teach in many places in Europe, Asia, Africa and America. His course notes and exercises are well known in the international community of Bioinformatics professionals and users, many of which (difficult to count) have had their first contact with Bioinformatics through him.

Affiliation: University of Cambridge, Department of Genetics, Cambridge, UK

Phil Cunningham is the Senior Bioinformatics Officer at King's College University of London.

Phil has been supporting KCL Biomedical scientists for well over 20 years after graduating in Biochemistry at Sussex University (1969). During his post graduate studies at Sussex he was introduced to computers (1971) and has been involved in "biological computing" ever since. A Post Graduate Certificate in Education (1976) ensured a fuller awareness of the extra difficulties involved in teaching (as opposed to learning) scientific material and this has proved invaluable in the last decade and a half whilst teaching bioinformatics to KCL undergraduates. Since the beginning of GTPB, Phil has also taught in several courses in Portugal, and also at the University of Minho, Braga.

Affiliation: King's College University of London Department of Biochemistry, London, 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, that provided user skills to more than 1800 course attendees throughout its twelve years of existance. In 2002, in cooperation with Mario Silva from FCUL, he designed a graduate Programme in Bioinformatics. In 2006 he launched a new public service based on a High Performance Computing platform, with a grant from FCT. He currently teaches Bioinformatics both in graduate and undergraduate programmes.

Affiliation: Instituto Gulbenkian de Ciência, Oeiras, PT

Course description


The course sets out to introduce an extensive range of computing facilities vital for molecular biological research. This will be acheived primarily through "hands on" exercises based around an investigation of a well documented human disease. How information can be obtained both by analysis of raw sequence data and by interrogation of information resources will be demonstrated. In order to enable the participants to perform sequence analisys on short read sequences, we will hold a day of Next Generation Sequencing data analysis (NGS) for beginners.


The course is a user course. How to use the various tools is thus the prime objective. However, where it is useful, the operation of the programs will be discussed as far as is required. Participants will know how to set up the programs in an informed fashion, and to fully understand the output generated. On completion of this 5 day long training, they will also know how to implement this methodology elsehwere, using public domain software and data resources.

The course will provide participants with an awareness of a wide range of bioinformatics tools and sufficient experience to use those tools in basic investigations.

Target Audience

This course is intended for those wishing to investigate how they might begin to exploit the ever expanding abundance of computing resources for molecular biologists.

Course Pre-requisites

Basic understanding of molecular biology and no particular computing expertise will be assumed.

Detailed Program

In collaboration with INTERBIO

Sponsorship available for members of the following INTERBIO Nodes:
- Université Paul Sabatier Toulouse - UPS (Midi-Pyrénées - France) (www.ups-tlse.fr)
- Fundación Privada BioRegió de Catalunya - BIOCAT (Catalonia - Spain), (www.biocat.cat)
- Institut Européen de Chimie et Biologie - IECB (Aquitaine - France), (www.iecb.u-bordeaux.fr)
- Fundación de la Comunidad Valenciana para la Innovación Urbana y Economía del Conocimiento - FIVEC (Valencia - Spain), (www.fivec.org).

If you wish to apply as a member of one of these institutions, please contact your local INTERBIO representative.

Instituto Gulbenkian de Ciência,

Apartado 14, 2781-901 Oeiras, Portugal

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Last updated:  Feb 20th 2012