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Contenu archivé le 2024-04-19

Computer Network for Bioinformatics in Europe: Securing Europe's Bioinformatics Infrastructure


Bioinformatics is now recognised as an essential element in biotechnology R&D with more than 100 databases being used on a regular basis. These databases have to be created, updated, validated and disseminated; and the user has to be offered simple and supported access. EMBnet, the European Molecular Biology Network, provides the European infrastructure for this need through a well managed physical and intellectual network of bioinformatics centres operating in a coordinated fashion.
For this grant period, EMBnet set itself four main practical tasks:
1 to develop and deliver Education and Training courses;
2 to seek pragmatic solutions to perceived technical problems through an applied Research and Development programme based on user needs;
3 to publicise the existence of the network, its activities and the general advances in bioinformatics to as many potential users as possible, and
4 to further establish a well managed annd structured organisation capable of reacting to user needs.
Each activity was led by an elected Project committee, reporting to the full membership at each annual meeting.

1 Education and Training
The goal was to ensure that European molecular biologists and biotechnologists were adequately trained for the effective use of bioinformatic software and databases and to keep users abreast of the new developments in bioinformatics. This was achieved by a series of training courses both for basic sequence analysis and more specialized topics. It was also fostered by developing World Wide Web based biocomputing tutorials and uniform programme documentation, which can now be found at In addition, the nodes contributed several hundred pages of course material available through the WWW, so now all EMBnet nodes are able to organize up to date user courses in national languages.

2 Research and Development
The focus was on infrastructural needs not covered either by industrial nor by EU-funded initiatives. The networking perfomance was constantly monitored. New user interfaces and database transfer protocols were developed and installed. 'Seed money' was provided to such important initiatives as BioImage (microscopic image database), the SRS sequence retrieval system, and the EGCG (Extended GCG software package). As a result, several of these are ready for the Demonstration Project phase or, like BioImage has already obtained funding from separate EU grants.
Many of the nodes developed bionformatics methods which were then made publicly available through the EGCG program package or through WWW servers. These new services form a rapidly growing, distributed core infrastructure through which, for example, Swedes, Italians and Greeks can all access facilities made available in France.An e-mail help-line ( was established which offers fast-feedback on-line technical support on bioinformatics. In addition, virtually all nodes have local e-mail of telephone helpdesks operating in national languages.

3. Publicity and Public Relations
EMBnet produces a quaterly newsletter, '' dealing with issues of interest to European bionformatics, with sections on theory, software and databawse development. It is produced both for WWW ( and as printable postscript versions. '' is distributed through a number of European nodes but its readership is wider than Europe. The WWW pages are accessed more than 50,000 times a year.
The P&PR Committee has overseen the production of a new EMBnet brochure which is available in hard copy and on the WWW. An EMBnet Quick Guide, contianing each node's basic information has also been produced. Posters have been produced and circulated throughout Europe. A descriptive article ('EMBnet: an institute without walls') has been published by one member of this commitee in the authoritative journal 'Trends in Biochemical Sciences'. The nodes themelves produced a large number of scientific publications.

4. Coordination and management
EMBnet is a public foundation registered in The Netherlands. The coordinating activity is overseen by the Executive Board which executes the decisions of the Annual General Meetings. Two such meetings were held during this grant period, in Madrid (1995) and in Helsinki (1996). Both were organised in association with a scientific meeting which brought together top scientists and EMBnet node managers, together with local staff and scientists to examine a topic of bioinformatic relevance.
EMBnet's membership is steadily increasing; the Sanger Centre joined as a specialist node in 1995. The following year Pharmacia-Upjohn (Sweden) joined as an industrial associate node as well as three new non-EU national nodes (Russia, Australia, China). Other nodes have expressed interest including South Africa, Canada, Cuba, Turkey and University College of London. While the non-EU nodes are not participants of EU grants, they contribute to EMBnet with their expertise, membership fees and by increasing the group's visibility in international bioinformatics.

The past grant period was marked by an unparallelled increase in the use biological computation. During this time, the exponential increase of the DNA databases began to be seen as a matter of immediate importance with implications about the requirement for computer disk storage. The call from the pharmaceutical industry for adequately trained bioinformaticians became increasingly strident. EMBnet has and will continue to make real contributions to overcoming these challenges. However, the organisation and its constituent nodes can only achieve this through intensive cross-border collaboration and a sharing of expertise and experience. EMBnet has become a distributed core infrastructure and a technical resource of European dimensions that complements the central information resources. The infrastructure for communication and information transfer within EMBnet is now established but needs to be maintained in order to provide solutions to tomorrow's problems.


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CSC - Cost-sharing contracts


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6525 ED Nijmegen

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