Luxembourg, Sep 2001

Pedro FernandesInst. Gulbenkian de Ciência, Oeiras, Portugal

EMBEREMBERA European Multimedia

Bioinformatics Educational Resource

Teaching BioinformaticsTeaching BioinformaticsBioinformatics is a cross-field between Biology, IT and Computing.

The main objective of Bioinformatics is to gain knowledge on Bio-Medical issues. It uses computing methods to process the biological information that emerges from the detailed analysis of molecules (proteins, DNA, RNA), thus inferring on their structure and properties (functions) and helping to answer biological questions.

The information flood that occurred in the last 50 years, more recently giving us access to complete genomes, created new challenges. We need, more than ever, that our students, scientists and medical staff become knowledgeable in this area. Practical and interactive learning is needed.

Our community: EMBnet Our community: EMBnet • European Molecular Biology Network

• network of European Bioinformatics providers• 30 National Nodes mandated by local government• 10 Specialist Nodes • 32000+ user community

• EMBnet was established in 1988• activities include provision of databases and

software via login accounts, user support & training• mainly supported by EC funds and Node

subscriptions

The BackgroundThe Background• Still too few university courses available

• skill shortage in a high-demand area• need to educate people of the active communities

(high spread of age, motivation, objectives)

• EMBER was conceived as a collaborative project to• draw on skills & expertise of EMBnet teachers • exploit EMBnet’s existing pool of teaching materials• draw together existing EMBnet partners • provide a stand-alone multimedia Bioinformatics course

The EMBER ConsortiumThe EMBER Consortium• University of Manchester (Coordinator)• Swiss Institute of Bioinformatics - Switzerland• University of Nijmegen - The Netherlands• South African National Bioinformatics Institute - South Africa• European Bioinformatics Institute - UK• Instituto Gulbenkian de Ciência - Portugal• University of Bruxelles - Belgium• Institute for Marine Biosciences - Canada• Research Institute for Genetic Engineering & Biotechnology -

Turkey• Expert Centre for Taxonomic Identification -The Netherlands

The Gulbenkian Training Program in Bioinformatics

• Teaches about 120 students/year

• Runs 2 basic courses and 4 specialized courses

• Quality control relies on self-assessment

• Pleasent, interactive environment

EMBER picks-up onEMBER picks-up on

Existing on-line

Bioinformatics

practical

An accompanying

Textbook

The ProjectThe Project

• EMBER will• collate, evaluate & amalgamate existing materials• revise & update these where necessary• add new material in line with perceived needs

• Use the updated and new material to• extend the existing introductory text-book• extend the existing Web practical (produced professionally)• develop a parallel (Web-independent) course on CD-ROM

• EMBER will be suitable for delivery• as part of conventional face-to-face courses• or in stand-alone, self-paced settings (e.g., the workplace)

Evaluating Skills Shortage Evaluating Skills Shortage (June 2001)(June 2001)

• 188 targets (both academic and industrial) were selected according to their involvement in Bioinformatics, Biotechnology, Drug Discovery, etc.

• They were inquired on what they consider pre-requisite knowledge in order to admit students or employees (20 topics).

Results show that:

.

• Basic Statistics and Information Theory need more emphasis.

• The curriculum we designed matches the needs quite well.

• Our choice of advanced topics needs some adjustment.

Evaluating Skills Shortage Evaluating Skills Shortage (June 2001)(June 2001)

•Molecular BiologyBasic concepts, Genomic and Proteomic structure

•Core BioinformaticsBiological Databases, Sequence Analysis,

Functional Genomics•Advanced Bioinformatics

Molecular Evolution and PhylogenyProtein Structure PredictionThe TranscriptomeThe Proteome

•InformaticsInformation TheoryBasic StatisticsDatabase TechnologiesKnowledge RepresentationBiocomputing

The “Ideal” SyllabusThe “Ideal” Syllabus