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Issue 5: Winter 2012/2013

Informed: ELIXIR eNewsletter


Welcome to the winter 2012/2013 edition of Informed, the ELIXIR eNewsletter!

ELIXIR's mission is to build a sustainable European infrastructure for biological information, supporting life science research and its translation to medicine and the environment, the bio-industries and society. Informed provides you with the latest news and updates on developments within the ELIXIR initiative.

I hope you enjoy reading our newsletter, and welcome your comments.



Professor Søren Brunak
Chair, ELIXIR Interim Board

   

Portugal joins ELIXIR 

In late 2012, Portugal signed the ELIXIR Memorandum of Understanding (MoU) becoming the fourteenth country to join ELIXIR. The ELIXIR Interim Board was pleased to welcome Ricardo Migueis, from the Fundação para a Ciência et Technologia (FCT) in Lisbon, as the representative of ELIXIR’s newest member country on the occasion of the Third ELIXIR Interim Board Meeting held at the Wellcome Trust in London in October 2012.  Portugal's scientific community and national funding bodies made a concerted effort to conclude the signature of the ELIXIR MoU to enable Portugal’s timely participation at a critical juncture in the country’s construction of its National Roadmap for Research Infrastructures, due for completion in spring 2013.

FCT’s President, Dr Miguel Seabra expressed his support for his country’s participation as ELIXIR’s fourteenth member nation, saying “Our government and national funding agencies are keenly aware of the potential long-term benefits – both financial and scientific – of participating in ELIXIR.  As a pivotal research infrastructure, it sits at the crossroads of health, natural resources and marine biology – areas where Portugal has particular interests”.

More about Portugal and ELIXIR
ELIXIR preparatory phase comes to an end

ELIXIR officially entered its construction phase on 1 January 2013, marking the end of the 5 year EC-funded preparatory phase, which brought together 32 partners from 13 countries. With a contribution of €4.5 million from FP7, ELIXIR's preparatory phase was an incredibly productive and successful time for all stakeholders involved. In total, from the start of the preparatory phase in late 2007 to its end on 31 December 2012, ELIXIR partners held or took part in a total of over 550 meetings, workshops, conferences and events! These include meetings ranging from the scientific to the political, in places from as far north as Iceland to as far south as Crete. Meetings were held with a host of stakeholder organisations including academia, ministries and government bodies, funding agencies, charities, industry and the EU.

A big thank you to all preparatory phase partners for the time and effort they invested in progressing ELIXIR to this important transition.
What's coming up?

The first quarter of 2013 is proving to be no less busy than 2012, with a series of important meetings for ELIXIR taking place over the coming months.

In Amsterdam, on 21-22 March, scientific representatives of ELIXIR Member States will meet at a workshop organised by Netherlands' ELIXIR representatives to discuss, amongst other things, the recommendations made on ELIXIR Node Applications by the ELIXIR Scientific Advisory Board (SAB). This meeting will help ELIXIR Members develop a vision for the integration of ELIXIR services within Nodes across Europe.

On 25-26 March in Norwich, stakeholders involved in the UK ELIXIR Node, which will develop a training infrastructure, will attend a joint ELIXIR-UK/GOBLET Trainer's Workshop. The aim of the event is to provide a forum for sharing and exploring training experiences, collaborative ideas and best practice, in order to help establish a long-term community of trainers. ELIXIR-UK/Goblet event

The ELIXIR Consortium Agreement (ECA) Working Group aims to continue making good progress on developing ELIXIR's Consortium Agreement when it meets in Frankfurt on 15 January. The Working Group anticipates that a final draft of the ECA will be ready to submit to the Interim ELIXIR Board at the Fourth Interim Board meeting, which takes place in Copenhagen on 22-23 April 2013. Working towards this will be a major focus of the ECA Working Group over the coming months.

In Finland, on 21-22 January 2013, CSC and NBIC/DISC, which are the lead partner in the Finnish and Netherlands ELIXIR Nodes respectively, are hosting an IaaS (Infrastructure as a Service) meeting. The event is restricted to invited participants and the purpose is to collect experience to improve future IaaS service in the life science community. Iaas event in Finland

On 18 January, a small delegation of ELIXIR Interim Board members will meet officials from the European Commission's DG CONNECT in Brussels to discuss ELIXIR's role as an e-Infrastructure, which at the same time supports Europe's life scientists. 
Outcomes of Third Interim ELIXIR Board meeting

The Interim ELIXIR Board met for the third time in London on 22-23 October 2012. Over the course of the two day meeting, many important steps were agreed.

An initial discussion was held on the ELIXIR Consortium Agreement (ECA), which is the legal model which, once signed by five countries, will establish ELIXIR as a fully fledged research infrastructure. At present, participating Member States have signed a non-binding Memorandum of Understanding (MoU), which allows them to participate in the dicussions towards developing the ECA. It is expected that the final ECA will be signed later in 2013.

An operating budget for the ELIXIR Hub in 2013 was also agreed by Member States at the meeting. This will allow for the recruitment of staff at the ELIXIR Hub, who will work to connect and integrate current and future services developed by the ELIXIR Nodes. Recruitment for these posts will take place throughout 2013.
Scientific Advisory Board reviews Nodes 

On 14 December 2012, members of the ELIXIR Scientific Advisory Board (SAB) met for the first time in Hinxton, Cambridge. The SAB meets once a year to provide ELIXIR with independent scientific advice. The main purpose of the first SAB meeting was to conduct a review of the first round of ELIXIR Node Applications. These had been submitted by the following ELIXIR countries during the autumn of 2012: Czech Republic, Denmark, Estonia, Finland, Israel, Italy, Netherlands, Norway, Portugal, Slovenia, Spain, Sweden, Switzerland and the United Kingdom. This month, continuing our series of country focus articles, we look in more depth at the merging UK Node.

Over the coming weeks, the ELIXIR SAB will draft a series of recommendations for each ELIXIR Node application, which could provide the basis for further modification over the course of 2013. In April 2013, the ELIXIR Interim Board will make its final recommendation on each Node application. Nodes will officially come into effect once the ELIXIR Consortium Agreement (ECA) is signed.

At the SAB meeting, Dr Robert Gentleman of the biotechnology company Genentech, was elected to the Chair. Prof. Gunnar von Heijne of Stockholm University, Sweden, was elected Vice-Chair.

ELIXIR Scientific Advisory Board Members
Five pilot projects mark the start of technical integration

Technical specialists are making the first inroads into the development of pilot projects to trial aspects of ELIXIR’s data integration and storage. This important progression marks the transition from the preparatory phase to the construction phase of ELIXIR, with the work being funded through Member State contributions to the ELIXIR Hub budget.

Five pilot projects were identified and are underway;  The ELIXIR-facing cloud support and virtual machines project tests the cloud concept with willing Nodes, operating initially with Switzerland, through SIB Swiss Institute of Bioinformatics. It is envisaged that this pilot will enable groups to explore the advantages of having a virtual machine in close proximity to the extensive data repositories held at EMBL-EBI.  Finland’s IT Centre for Science (CSC) is involved in two separate pilot projects, one exploring the continuous transfer of major archive resources to a remote European location and another to simplify the authentication of data destined for the European Genotype Phenotype Archive (EGA)EMBL-EBI is working with Spain’s Centre for Genomic Regulation (CRG) to explore ways in which its emerging Node could share responsibility for production of the EGA in future and with SciLifeLab in Sweden to explore the challenge of linking data held in the Human Proteome Atlas with other protein resources.
Node Focus: The UK's emerging Node

The UK has made a substantial investment in genetics and genomics research and systems biology in recent years, much of this research and exploitation has been led by the UK Research Council's BBSRC, MRC, and NERC, together with the Wellcome Trust (WT). This has resulted in the generation of substantial data, and significant growth in demand for rapid access to all publically available biological databases and has been of direct benefit to the pharmaceutical and other industry sectors. 

In addition to an investment of €100M (£85M) towards to construction of the ELIXIR Hub and contributions towards the Hub's operational budget, the UK has also made resources available to establish the ELIXIR Node. Coordinated by the University of Oxford, the UK Node will bring together nine other key partners (Universities of Manchester, Liverpool, UCL, Edinburgh and Birmingham; The Genome Analysis Centre; the Environmental Omics Synthesis Centre; the Sanger Institute, and the University of Oxford e-Research Centre) with other participating organisations. This multi-centre approach seeks to make internationally recognised UK resources and expertise more widely available to European partners, to further enhance Europe’s research economy and the high quality of its science. The ELIXIR-UK Node application is supported by a £1M application to BBSRC, MRC and NERC for additional resources, for review in early 2013. 
 
The ELIXIR UK Node’s focus will be on training through specialised centres, in courses, and through e-learning, in partnership with other ELIXIR Nodes and agencies. ELIXIR-UK initiallyanticipates training postgraduate, postdoctoral and mid-career scientists, and will focus on the research-intensive bioscience and environment industries. Trainees from academia, industry and other user groups in ELIXIR member states will build interdisciplinary bridges between scientists newly empowered to integrate large data sets into their scientific programmes, and technologists and provide, and provide trusted and sustainable software.



Contact ELIXIR

For further information on ELIXIR please contact the team at:

EMBL-EBI
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD, United Kingdom

Tel: +44 (0)1223 494496
Email: asmith@ebi.ac.uk
www.elixir-europe.org

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