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European bioinformatics early-stage training in advanced research

Final Activity Report Summary - BIOSTAR (European Bioinformatics Early-Stage Training in Advanced Research)

The objectives of BIOSTAR were to provide the participants not only with bioinformatics training to the highest possible level in Europe, but also that they should benefit fully from all aspects of working within a team at a leading international research institute.
1. Integration into a research team at EBI: The participants became fully integrated members in their respective host teams. They took part in the weekly group meetings and had the opportunity to discuss and present their own work within this supportive environment.
2. A short research project: Each participant was given a research project to work on during his/her stay at EBI. In the majority of cases, these led to a publication or a meeting abstract.
3. Mentoring by the EBI group leader: The group leaders, who are all at the forefront in their respective fields, directly supervised the BIOSTAR participants on a one-to-one basis.
4. Presentation skill training: Depending on their experience, the participants were given the opportunity to present their works either to their team or in a larger context. As most participants were non-native speakers of English they were also able to improve significantly their communication skills.
5. Attendance at training courses: EBI organises training workshops and international conferences, and the participants were given access to these during their stay, as well as to activities organised on the Wellcome Trust Genome Campus at Hinxton.

As well as research training, the objective was for all participants to receive full training where appropriate in different aspects of the molecular data resources hosted at EBI. Technical training was also to be given as appropriate, depending on the person's background and previous experience.

The training site was advertised on the EBI web site, and by emails to relevant university department. Recruitment was not anticipated to be a problem, as EBI receives numerous queries of this type even when no fellowships are advertised. In total, approximately 170 enquiries were received, and we were able to offer fellowships to 35 people. One of the objectives of the project had been to attract more women into bioinformatics, with 30 % set as the target. A ratio of 10 women out of a total of 35 (= 28.5 %) can be regarded as a considerable success in a very male-dominated field.

The research projects covered the full range of scientific fields at the EBI, and it would be impossible to even summarise the results in this limited space. The projects ranged from a more molecular level such as transcription factor binding, DNA alignment, and protein families, to a systems biology level such as mathematical modelling of biological systems. A few examples are listed below:
- creation of a set of multiple sequence alignments that could be used to benchmark DNA alignment programmes;
- identification and characterisation of the regulatory function of 1 369 human transcription factors;
- construction of a probe alignment and annotation algorithm for the analysis of strains of yeast;
- a computational project which aims to infer transcriptional regulators from genome-scale data using machine learning techniques;
- insights into the BioModels database and the practice of mathematical modelling of biological systems in the Computational Neurobiology Group.

Feedback from the participants was consistently positive, and focussed not only on the scientific benefits but also on the whole experience of working in a highly competitive research environment. The participants also stressed the technical skills acquired, and the insight into what resources were available. To quote some participants:
- 'My work greatly improved, I learned a lot about how to deal with big amounts of data of different types.'
- 'My stay helped me to find a unique direction for my project because I was able to interact with people in an exceptional research group.'
- 'My stay at EBI gave me the opportunity to learn cutting edge bioinformatics methods for high-throughput sequencing data analysis.'

The great majority were PhD students, and considered their time at EBI as crucial to the success of their doctoral studies.