EMBO Practical course 2010

18-23, October 2010
EBI-EMBL, Hinxton, Cambridge, UK

Registration opens on 1^st Jun 2010
Registration closes on 3^rd Sep 2010
Selected candidates will be notified by 15^th Sep 2010

Organisers

• Gabriella Rustici, EBI-EMBL - Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
• Wolfgang Huber, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
• John Quackenbush, Department of Biostatistics, 44 Binney Street, Dana-Faber Cancer Institute Smith 822A, Boston, MA 02115, USA
• Alvis Brazma, EBI-EMBL - Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK

Description

The main objective of this course is to introduce the participants to advanced bioinformatics, statistical methodologies and software tools for analyzing and managing transcriptomics data.

This course is aimed at advanced PhD students and post-doctoral researchers who are applying or planning to apply microarray, next generation sequencing technologies and bioinformatics methods in their research. Participants who have already performed microarray based experiments are encouraged to bring their own data to analyze it during the last practical session of the course.

Over the past few years, microarrays have become an established technology in molecular biology, used in an increasing number of laboratories, for studying a cell's transcriptome — the collection of all RNA transcripts produced at a specific time. The newly emerging next generation sequencing methods promise to change the landscape of gene-expression analysis, posing new analytical challenges.

A growing wealth of data analysis tools is available to researchers of different levels of expertise, and several courses on data analysis are given annually by EMBO and other organizations. Nevertheless, data analysis is still a major bottleneck for many researchers which are still applying inadequate statistical methods for the interpretation of their results. At the same time new, increasingly more sophisticated methodologies are introduced and new analysis methods are being developed.

The aim of this course is to familiarize the participants with such advanced methodologies and provide hands-on training on the latest analytical approaches.    

The European Bioinformatics Institute (EBI) is one of the acknowledged leaders in microarray informatics and data analysis. The co-organizers of this course are internationally acknowledged experts in the transcriptomics field. All trainers involved have extensive experience in teaching data analysis at both introductory and advanced levels.

References and links

• http://www.ebi.ac.uk/microarray/
• Bioconductor Case Studies. Series: Use R! Hahne, F; Huber, W.; Gentleman, R.; Falcon, S. Springer, 2008, 284 p.
• Microarray Technology in Practice. Russell, S.; Meadows, L.A., Russell, R.R. Academic Press, 2008, 464 p.
• Bioinformatics and Computational Biology Solutions Using R and Bioconductor. Series: Statistics for Biology and Health, Gentleman, R.; Carey, V.; Huber, W.; Irizarry, R.; Dudoit, S. (Eds.). Springer, 2005, 460 p.
• Microarray Gene Expression Data Analysis – a Beginner’s Guide. Causton H., Quackenbush J., Brazma A. Wiley-Blackwell, 2003, 160 p.

Content

The proposed course will consist of:

• Lectures from distinguished speakers;
• Demonstrations of microarray and next-generation sequencing data analysis software and other relevant bioinformatics resources;
• Practical sessions using the demonstrated software/resources to analyze both data provided by the trainers and the participants own data;
• Discussion of the results obtained during the practical sessions;
• Poster presentations from the participants describing their research in the transcriptomics field.

There will be 8-10 lectures (~25% of the course) which will give insight into how biological knowledge can be generated from microarray and sequencing experiments, illustrating different ways of analyzing such data.

The practical sessions (~75% of the course) will consist of computer exercises that will enable the participants to apply statistical methods to the analysis of microarray and sequencing data, under the guidance of the lecturers and teaching assistants. On the last day, participants will have the chance to analyze their own data and discuss the results with the trainers.

List of speakers

• Benilton Carvalho, Cancer Research UK
• Angela Goncalves, EBI
• Hedi Peterson, University of Tartu
• Jonh Quackenbush, Dana-Faber Cancer Institute
• Oscar Rueda, Cancer Research UK
• Roslin Russell, Cancer Research UK
• Gabriella Rustici, EBI

Target Audience

There will be up to 40 students accepted. This is determined by the size of the IT Training Room at the EBI. The student selection will be done by the co-organizers of the course in consultations with EMBO.

The student selection criteria will be:

• relevance of their current work to the objectives of the course
• scientific excellence of the previous research
• quality of the applications
• geographical distribution
• recommendations from EMBO

Students at early stages of their career will be accepted if they can demonstrate the relevance of their work to the objectives of the course. Students who will have performed microarray experiments will be preferred. Students are encouraged to bring data from their own microarray experiments to analyze during the course.

Applicants from industry will not be considered (similar courses for industry are given by the EBI separately, without EMBO funding). Staff from the host institution (EBI) will not be taken as students. Students from the UK will not be given any preference.

Financial Support

The costs of participant accommodation and catering is paid by EMBO on room sharing basis (two persons per room). The travel costs have to be covered by the participants (financial support may be possible for participants from Eastern European countries).

Information for commercial applicants only

Our course funders request that we charge a higher registration fee to commercial delegates, and may also set some limits on the number of commercial delegates at each course. Please see below for registration details.

Commercial/SME Registration Fee = £900.00 (1000 €)

EBI Industry Programme Member Registration Fee = £375.00 (accommodation costs only)

There is no registration fee for academics.