Introductory Bioinformatics (second course)

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   IMPORTANT DATES for this Course
   Deadline for applications: December 4th 2014
  Latest notification of acceptance: December 5th 2014
   Course date: December 9th - December 12th 2014

Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants.


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. David pioneered Bioinformatics Training at the IGC in 1986, in the scope of a MSc course. He collaborates in GTPB regularly since its inception in 1999, several times per year.

Affiliation: University of Cambridge, Department of Genetics, 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, that provided user skills to more than 3200 course attendees throughout its twelve years of existance. In 2002, in cooperation with Mario Silva from FCUL, he designed a graduate Programme in Bioinformatics. He currently teaches Bioinformatics both in graduate and undergraduate programmes.

Affiliation: Instituto Gulbenkian de Ciência, Oeiras, PT

Javier Santoyo-Lopez has a PhD in Biological Sciences from the University "Autonoma deMadrid", (Madrid, Spain) and an MSc in Bioinformatics from the University of Abertay Dundee (Dundee,Scotland, UK). He worked as a Molecular Biologist at the Centre of Molecular Biology "Severo Ochoa" (Madrid, Spain) and then he moved to the field of Bioinformatics working in renowned international centres like the Wellcome Trust Biocentre (Dundee, Scotland, UK), the Sanger Institute (Hinxton, England, UK) or the Spanish National Cancer Centre (Madrid, Spain). In his previous appointment he was the Scientific Coordinator of the Genomics and Bioinformatics Platform of Andalusia (Seville, Spain) supervising the Medical Genome Project (MGP). This was a large scale NGS project that sequenced the exome ofmore than 300 Spanish healthy individuals, to find population variants, and also sequenced a large number of individuals affected by rare diseases, to discover the genetic cause of the disease. Currently he is the BioinformaticsOperations Manager at Edinburgh Genomics, one of the largest Genomics facilities in the UK.

Affiliation Edinburgh Genomics, The University of Edinburgh, Ashworth Laboratories, Edinburgh, Scotland, UK


The course sets out to introduce an extensive range of computing facilities vital for molecular biological research. This will be achieved 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.

The last day of the this course will be dedicated to a soft introduction to Next Generation Sequencing (NGS) data analysis.


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 4 day long training, they will also know how to implement this methodology elsewhere, 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

Instituto Gulbenkian de Ciência,

Apartado 14, 2781-901 Oeiras, Portugal

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Last updated:  Nov 4th 2014