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A European Network for Integrated Genome Annotation

Final Report Summary - BIOSAPIENS (A European Network for Integrated Genome Annotation)

At the outset, the network consisted of 25 laboratories from 14 different European countries. To launch the project 37 members of the consortium, representing all contractors gathered for the first annual general meeting held in Rome on 26 - 27 February 2004. Individual work packages held meetings to coordinate their research activities and interactions and to discuss the work programme, including deliverables and milestones. Working together towards these goals has strengthened the community and generated a cooperative approach to genome annotation. Each work package required close contact and interaction between partners. Already in the first year, the remarkable progress was made to develop the technical integration needed to facilitate the distributed annotation effort, using the Distributed annotation system (DAS) technology. Each laboratory installed a DAS server and provided annotations as appropriate that can be viewed at any site through a DAS client. At the end of the first year, working DAS servers had been installed in 15 laboratories, each providing some test annotations. This integrated system provided the proof of principle required in the first year, that the infrastructure was appropriate to provide basic distributed annotation.

During this first year, an extensive outreach programme included press releases, workshops to promote BIOSAPIENS, presentations to scientists and the general public on the importance of genome annotations and a meeting of representatives of European Master's courses in bioinformatics. The visibility and impact of bioinformatics in Europe was improved through the many meetings and workshops BIOSAPIENS organised and helped to support, including:
- CAPRI: Critical Assessment of Predictions on Interactions;
- CASP6: Critical Assessment of Techniques for Protein Structure Prediction; Bologna Winter School in Bioinformatics;
- Pre-SIG meeting on Genome Annotation' at ISMB/ECCB2004.
To foster worldwide interactions, the BIOSAPIENS network was described at several other international meetings in Europe and United States, with encouraging interactions between computational biologists and experimentalists as one of the objectives. During this period, the first meeting with our scientific advisory board was held in Rome. This group comprises almost exclusively of experimentalists, and the aim of this meeting was to explain our goals and receive their advice.

The extensive outreach programme continued in the fourth year, and included workshops to promote BIOSAPIENS, available at A major event was the Special Interest Group workshop on Automated Genome Annotation, which was organised prior to the ECCB / ISMB meeting in Vienna in July 2007. We continued our support for the Bologna Winter School with another - BIOSAPIENS corner (please see online). The consortium was also involved in the production of a book, dedicated to the BIOSAPIENS methods and developments, with Dmitrij Frishman as editor. The book was published by Springer in 2008.

The BIOSAPIENS steering committee and consortium had played major parts in 2006 in the preparation of a proposal for the ESFRI programme. The European Life Sciences Infrastructure for Biological Information (ELIXIR) was successful and work started in January 2008. To assess the impact on young scientists involved in the project, a questionnaire was sent out in early 2009 to all post-doctoral researchers (or equivalent). They were asked where they were working now, what their experience of being involved in a large European project had been, and how many publications they had got out of their time with BIOSAPIENS .

Of the 22 people who replied (out of 61), 10 were still at the same institution, but in several cases their positions had been made permanent and / or they had become independent researchers with their own funding. Four had gone to work for high-tech companies in the field of bioinformatics, and seven to other universities, including Columbia University and Yale. One post doc had left the field and become a manager in public health care, but still felt that working in a large collaboration had helped her in her career.