European Life-science Infrastructure for Biological Information
To achieve this, we will address the following tasks and issues:
1 Define the scope of the infrastructure, its role and benefits
2 Define an appropriate governance and legal structure
3 Define a long term funding structure to provide a sustainable infrastructure
4 Define the requirements for the European Data Centre in the next 5-10 years and makes plans to meet these needs
5 Involve all relevant stakeholders, including users, data providers, tools providers to ensure that the infrastructure meets their needs
6 Explore integration and interoperability between core and specialised data resources and the development of standards in newly emerging fields
7 Define the critical interdisciplinary links that need to be forged between the ‘biological’ and related scientific disciplines, including medicine, agriculture and the environment
8 Define the needs of related European industries
9 Define a training strategy to ensure that Europe effectively exploits all the available information
The specific activities of the preparatory phase will include:
A Holding stakeholder meetings to bring together national representatives, key scientific opinion and funding organisations.
B Establishing working parties, supported by technical feasibility studies where appropriate, to address the tasks and issues above with final reports at month 18.
C Consolidating these reports into a management and funding proposal to be sent to member states and funding agencies with draft MoU by month 38 and to seek agreement on the MoU and establish an Interim ELIXIR Board by month 50.
D To establish the detailed organization of ELIXIR; and to draft and work toward the signing of the ELIXIR International Consortium Agreement
EUROPEAN MOLECULAR BIOLOGY LABORATORY
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Janet Thornton (Prof.)
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Grant agreement ID: 211601
1 November 2007
31 December 2012
€ 5 868 924,92
€ 4 500 000
EUROPEAN MOLECULAR BIOLOGY LABORATORY
Building a life-science infrastructure
Grant agreement ID: 211601
1 November 2007
31 December 2012
€ 5 868 924,92
€ 4 500 000
EUROPEAN MOLECULAR BIOLOGY LABORATORY
Final Report Summary - ELIXIR (European Life-science Infrastructure for Biological Information)
The mission of ELIXIR is to construct and operate a sustainable infrastructure for biological information in Europe to support life science research and its translation to medicine and the environment, the bio-industries and society.
The ELIXIR preparatory phase demonstrated an urgent need for a pan-European infrastructure for biological data, consisting of biomolecular data collections and the means to deploy and access them. In order to achieve its mission ELIXIR will need to construct, operate and enhance the following components of its infrastructure in accordance with the requirements of the community and the direction of the ELIXIR Board.
The ELIXIR data infrastructure
The ELIXIR compute infrastructure
The ELIXIR tools and standards infrastructure
The ELIXIR infrastructure to support the other ESFRI Biomolecular science infrastructures
The ELIXIR infrastructure for training
The ELIXIR international collaboration infrastructure
The aim of the ELIXIR preparatory phase has been to develop a Business Case for the infrastructure, outlining the scope of the infrastructure, its role and benefits; and detailing its governance, legal and long term funding structure, based on the recommendations of the Preparatory Phase work packages and through engaging with other BMS projects to develop a model for provision of infrastructure to support the other BMS projects; and to consult with European Funding agencies and governments in the member states to begin drafting and negotiation of an ‘International’ Consortium Agreement for the establishment of ELIXIR.
ELIXIR will be organised as a distributed topology comprising a Hub, located at the EMBL-EBI, housed in a new building, currently being constructed on the Wellcome Trust Genome campus (Due for completion Autumn 2013), acting as the coordination point, responsible for the scientific and technical coordination of, ELIXIR Nodes, located at centres of excellence in ELIXIR Member states throughout Europe, providing data resources; bio-computing capacity; infrastructure for data integration; and services for the research community, including training and standards development.
Project Context and Objectives:
The ELIXIR preparatory phase project aimed to achieve ELIXIR’s mission to construct and operate a sustainable infrastructure for biological information in Europe by addressing the following:
1. Defining the scope of the infrastructure, its role and benefits
2. Defining an appropriate governance and legal structure
3. Defining a long term funding structure to provide a sustainable infrastructure
4. Defining the requirements for the European Data Centre in the next 5-10 years and make plans to meet these needs
5. Involving all relevant stakeholders, including users, data providers, and tools providers to ensure that the infrastructure meets their needs
6. Exploring integration and interoperability between core and specialised data resources and the development of standards in newly emerging fields
7. Defining the critical interdisciplinary links that need to be forged between the ‘biological’ and related scientific disciplines, including medicine, agriculture and the environment
8. Defining the needs of related European industries
9. Defining a training strategy to ensure that Europe effectively exploits all the available information
10. Developing a Business Case for the infrastructure, outlining the scope of the infrastructure, its role and benefits; and detailing its governance, legal and long term funding structure, based on the recommendations of the Preparatory Phase work packages
11. Consulting with European Funding agencies and governments in the member states to develop and agree a Memoranda of Understanding.
12. Engaging with other BMS projects to develop a model for provision of infrastructure to support the other BMS projects
13. Consult with European Funding agencies and governments in the member states to draft an International Consortium Agreement
Although ELIXIR was originally described in the ESFRI documentation as an upgrade to the core European bioinformatics infrastructure that is located at the European Bioinformatics Institute, ELIXIR management has always recognised the need for substantial investment in a distributed infrastructure.
In the course of the ELIXIR preparatory phase, it has become abundantly clear that, whilst an upgrade to the core infrastructure is vital, the ambitions of the community are much greater than this. Stakeholders within the member states are convinced that if Europe is to gain maximum benefit from the data being produced by the modern techniques of high throughput biology, then it is going to be necessary to enhance the bioinformatics infrastructure within the member states as well. It is also clear that this has to be co-ordinated in order to ensure that member-state infrastructures will interoperate with each other and with the core and also to minimise duplication of effort. It appears to be universally accepted that these activities also fall within the remit of ELIXIR.
The proposed model for ELIXIR has been derived as the result of multiple consultations and project work during ELIXIR’s preparatory phase and takes into account stakeholder recommendations elicited and analysed during project work. These have been set in the international context of bioinformatics research and services, and in the context of the scientific and technological challenges that face European bioinformatics.
The preparatory phase looked into the needs of bioinformatics users, the best strategy for providing data resources, issues of data integration and interoperability with other ESFRI BMS research infrastructures, training strategy and infrastructure for tools integration. It produced feasibility studies for archiving and aggregating images associated with cell-based assays, supercomputing facilities for genomic data, and European resources for systems biology. It investigated interdisciplinary interactions between biological information and medical/health and nutritional information, as well as with chemical, plant, agricultural and environmental research. The legal and organisational model, as well as the most suitable funding strategy for ELIXIR, were also investigated and defined.
Recommendations from user communities were of vital importance in configuring the proposed model for ELIXIR, because the ultimate indicator for ELIXIR’s success will be its acceptance and use by researchers in academia and industry. Users throughout Europe, including industry (which accounts for approximately 20% of public access to the EMBL-EBI’s data resources), clearly expressed a substantial need for an extended infrastructure to provide and maintain databases, especially those with primary data originating from Europe.
Data resources are the foundation of that infrastructure. A survey identified about 500 existing biological databases in Europe and has collected detailed information from over 200 databases hosted by about 100 institutions. The palette of available databases ranges from large projects for major core data sets, with upwards of 20 staff members, to specialist collections that are the part-time effort of individual researchers. The total European effort currently involves at least 350 staff Europe-wide with reported annual direct costs of about €30 million. However, even conservative estimates would put the total expenditure (including indirect costs) at more than €50 million per annum. The EMBL-EBI’s user community alone accessed its website from approximately 3 million IP addresses in 2010, and is generating some 150 million web hits a month.
One of the biggest recent breakthroughs in the life sciences has been the development of DNA sequencing technologies, to reveal the genetic code of life. Knowledge of DNA sequences has become indispensable for basic biological research as well as in numerous applied fields such as diagnostics, drug development, biotechnology, forensic biology and systems biology.
Over the past decade, innovative technical solutions developed to meet the high demand for low-cost sequencing have resulted in high-throughput sequencing technologies that parallelise the sequencing process, producing billions of bases of nucleotide data per experiment. The wide uptake of this so-called ‘next-generation’ sequencing and other ultrahigh throughput technologies by life scientists has led to unprecedented growth in the amount of data generated.
Next-generation DNA sequencing has become so widely used that it is believed to be a ‘disruptive technology’: it is so much better than the technology that it replaces that users have difficulty adapting to it. Modern sequencers are capable of analysing the equivalent of a human genome every 14 minutes at a cost of US $5,000. This rate is 400 times greater than in the year 2000, when the draft human genome was first published. It is expected that further developments will result in sequencers between a thousand times and a million times more productive over the next ten years. The observed expansion of data volume has been supra-exponential.
Data coming from novel gene sequencing technologies are only one of the data challenges faced by today’s life scientists, the other being the integration of different data in meaningful, research-supportive ways. Life science research is becoming increasingly collaborative and complex, using several different technologies to understand organisms and diseases at the systems level.
ELIXIR’s vision for the future is to provide researchers in academia and industry with seamless access to biological information that will revolutionise discovery in the life sciences, by integrating data at different levels of analysis, for example from molecular biology to clinical practice. The enormity of these tasks necessitates cross-border cooperation on a scale unprecedented to biological and biomedical research. The most obvious solution is the development of a pan-European initiative that will enable European countries to pool their resources in a coordinated manner.
ELIXIR will, for the first time, enable pan-European coordination of all scientific and technical issues related to handling the biomolecular data resources. This is essential to be able to meet the challenges that Europe faces regarding the collection, storage and dissemination of biomedical data.
The ELIXIR preparatory phase demonstrated an urgent need for a pan-European infrastructure for biological data, consisting of biomolecular data collections and the means to deploy and access them and that in order to achieve its mission ELIXIR would need to construct, operate and enhance the following components of its infrastructure in accordance with the requirements of the community and the direction of the ELIXIR Board.
- The ELIXIR Hub and connected ELIXIR Nodes infrastructure
- The ELIXIR data infrastructure
- The ELIXIR compute infrastructure
- The ELIXIR tools and standards infrastructure
- The ELIXIR infrastructure to support the other ESFRI Biomolecular science infrastructures
- The ELIXIR infrastructure for training
- The ELIXIR international collaboration infrastructure
In the ELIXIR preparatory phase it has been clearly indicated that the organisational and operational model for such an infrastructure should be organised as a distributed topology comprising a Hub, acting as the coordination point, responsible for the scientific and technical coordination of the ELIXIR Nodes distributed throughout Europe, with the Hub being located at EMBL-EBI, and ELXIR Nodes will be located at centres of excellence in the ELIXIR Member States.
The data infrastructure should include the data resources plus the infrastructure for the tools that are used to access and interpret the data. Currently EMBL-EBI, strengthened by with many strong collaborators throughout Europe and beyond, has acted effectively as a central European hub for core data. Many smaller, specialised data resources have emerged, but these are rarely coordinated with the core data and are often difficult for researchers to find. Indeed, the increasing plethora of niche databases makes the bioinformatics landscape needlessly complex for its users. In the face of the data deluge, limited resources and lack of coordination, EMBL-EBI will rapidly become unable to meet the full European demand.
The future pan-European data infrastructure should therefore:
- Enhance the existing collective data capacity to meet rising demand (the “data deluge”)
- Build a distributed infrastructure that enables full data integration so that the collective, expanding capacity across the continent is used optimally;
- Establish universal principles for optimising the use of existing data capacity (such as assessing which data should be stored and made available to users);
- Present a transparent single interface to a distributed infrastructure.
To date, life scientists have rarely needed to use European e-infrastructures, which have been mostly developed to provide services for the physical sciences. As a consequence, the existing compute architecture has been optimised for the requirements of physical science communities, which typically address compute-intensive problems. In contrast, biologists require data-rich, massively parallel queries. However, this is now changing because biologists are generating data at previously unprecedented rates, comparable to those generated by the physical sciences. Unless an increase of an order of magnitude in compute infrastructure capacity occurs (including storage and processor power) in a manner suitable to meet demand for life sciences, it is anticipated that the existing European data infrastructure will not be adequate to respond to challenges driven by the data deluge.
The future pan-European compute infrastructure should therefore:
Enhance the capacity of the existing compute infrastructure to meet demands that evolve from the data deluge;
Maintain integration despite distribution, with access to central databases such that the collective expanding capacity across the continent is utilised optimally.
In the past, biological data resources were used by a relatively small community of ‘bioinformatics aware’ researchers, but as access to data becomes increasingly central to biomedical research, this user base is growing and diversifying to include, for example clinicians, experimentalists in the pharmaceutical industry, plant breeders and environmental scientists. It is anticipated that the increase in demand for online bioinformatics services by new users will be accompanied by an increase in demand for training for the use of such services, and this has been borne out by increasing demand for places at training courses organised by EMBL-EBI.
The European training infrastructure is not adequate to accommodate this anticipated increase.
Failure to build adequate capacity to meet training needs will create a bottleneck that will impede the optimum use of life science data.
The future pan-European training infrastructure should therefore:
- Empower European researchers to make effective use of the data by making bioinformatics user training accessible to the rapidly growing and diversifying user community;
- Achieve appropriate coordination of the currently fragmented training infrastructures such that the collective expanding capacity across the continent is utilised optimally;
- Integrate training with the development and diversification of data resources and
- Enable the development of new training programmes, especially in new accession states, and their integration with existing initiatives.
The data resources that will be provided through ELIXIR will be used in many different ways and in numerous combinations using a huge number of different analytical software tools written by investigators all over the world. Typical analyses can use dozens of tools linked together into data processing pipelines. A key role for ELIXIR is to provide an infrastructure to support maximum efficiency and effectiveness in the deployment and use of these tools. During the course of the Preparatory Phase four distinct capabilities necessary for the ELIXIR Infrastructure for tool integration were identified.
- Tool discovery: It is essential that potential users of ELIXIR can find the most appropriate tool as quickly as possible and that the tools are available for download and deployment;
- Ease-of-use: Tools should be usable by as wide a range of users as possible without the need for specialised knowledge or IT skills;
Standards are of vital importance to the success of ELIXIR and it is inevitable that ELIXIR will be heavily involved in the development, implementation and deployment of standards. To ensure that this happens in a coordinated manner, ELIXIR will need to create a European-wide infrastructure for standards. During the course of the preparatory phase we identified the following areas where this will be necessary:
- Programmatic access: standardisation of the technology to be used to build connections to databases and tools;
- Nomenclatures: harmonisation of names and symbols of biological entities;
- Controlled vocabularies and ontologies: harmonisation of the terminologies used to describe database content;
- Reporting requirements: standardisation of the minimal information content to be reported for a given domain and the format used for submission to databases and journals, to guide deposition and facilitate exchange of the information.
The ELIXIR Hub
The ELIXIR Hub will host the ELIXIR Executive Management and Secretariat, who will report to the ELIXIR Board for delivery of ELIXIR. The Executive Management will initially comprise ELIXIR Director supported by a small secretariat with administrative, financial and legal expertise. They will be responsible for: coordinating and leading the infrastructure; ensuring that its service provision is of the highest quality; liaising with ELIXIR Member States; implementing collaborative agreements with the ELXIR Nodes; arranging meetings of the ELIXIR Board and the Scientific Advisory Board; planning and securing ELIXIR’s financial sustainability, including applications for pan-European funding; and representing Europe in global bioinformatics initiatives.
The ELIXIR Hub will include components of EMBL-EBI services that will be funded by ELIXIR. The most significant of these is the delivery of the ELIXIR core data resources to European life scientists with very high levels of availability and robustness through the European Data Centre in London. EMBL-EBI will manage the European Data Centre, ensuring maximum accessibility to data for the benefit of ELIXIR. This includes 24/7 delivery with archiving and replication to ensure no loss of data and continuity of service during failures. EMBL-EBI will continue with its current activities in data collection, curation and database production. ELIXIR will complement these activities in the European Data centre by focusing on data delivery and also coordination of data nodes and integration around Europe.
The ELIXIR Hub will provide oversight of biological data throughout Europe, by creating data registries and coordinating data standards. Both of these require involvement of relevant domain specialists, often in a global context, to ensure adoption by the scientific community. The Hub will help to coordinate these activities across Europe. The major focus at EMBL-EBI is currently on biomolecular data and this will remain the core activity for the Hub, but as new data types emerge, ELIXIR will need to consider its role and evolve according to community needs.
The distributed network of data resources envisaged, with ELIXIR Nodes acting as data centres linked together by the ELIXIR Hub is an ambitious goal and will rely on state-of-the-art technical developments and alignment of standards and annotations. The ELIXIR Hub will seek to enable the best compute infrastructure for life scientists throughout Europe. As data sets grow in size, the need to co-locate data and compute will increase. Therefore, it is inevitable that the large data Nodes will also become large compute Nodes and vice versa. ELIXIR will seek to establish the best solutions and ensure good interconnectivity, building where possible on the e-infrastructures already developed in Europe.
The ELIXIR Hub will also spearhead interactions with the other ESFRI BMS infrastructures, enabling ELIXIR members to work with these infrastructures and helping to coordinate the e-infrastructure for data that they will require. ELIXIR already provides such an infrastructure for some aspects of BMS data, such as for structural data through the PDBe (INSTRUCT) or omics related data for translational research (EATRIS) and biobanks (BBMRI). Building bridges between the different types of data, such as clinical trials and biobank data, will be essential for future research and for addressing the Grand Challenges. ELIXIR, together with the other 12 BMS Infrastructures, is currently exploring possibilities for interoperability and abstraction of data between the infrastructures.
The ELIXIR Hub will also play a role in coordinating the provision of training activities for ELIXIR users across Europe. The need for training to ensure optimal usage of the data and associated tools is paramount. Experts based at the Hub and Nodes, working closely with the data and tool developers, will provide training. This will be delivered either electronically or through face-to-face courses held throughout Europe. The ELIXIR Hub will help to ensure the provision of appropriate training both by providing support for and coordination of suitable trainers in the Nodes, and by supplying an infrastructure for the management of training materials, so that they can be used and re-used by all of ELIXIR’s trainers.
The ELIXIR Nodes
The ELIXIR Hub will connect with ELIXIR Nodes at existing centres of excellence in the ELIXIR Member States. Each Node will take responsibility for providing a defined set of scientific and technical activities that are in line with the strategic priorities of the host country but are accessible to researchers throughout Europe. Contributions could, for example, comprise biomolecular data resources, bio-compute facilities, software tools, standards or bioinformatics training.
There are a number of criteria that will apply to all ELIXIR Nodes:
- Nodes will be located in a Member State of ELIXIR;
- Nodes will be, or will be represented by, a legal entity that is able to enter into formal agreement with the ELIXIR Hub regarding such matters as service level agreements;
- Nodes will need to have the capability to provide one or more, internationally competitive services at the European level. An institute that only provides services at a National level would not normally be considered for inclusion in ELIXIR. Bearing in mind the stringency of this criterion, it is anticipated that most Node applications will be from pre-existing institutes with a significant history of robust service provision. Nevertheless, ELIXIR will welcome applications from new and innovative Nodes whose management can demonstrate that they can meet this requirement;
- Nodes will need to be able to demonstrate sustainability of funding. This is a very important criterion because of the importance of ELIXIR services to the European research community.
ELIXIR Nodes that perform similar functions will work closely together and form ELIXIR service networks. For example, Nodes that provide data resources will collaborate to form a data network; Nodes that provide training will collaborate and form a training network, etc.
ELIXIR Nodes will provide some or all of the following services:
Data resources- Nodes may provide data services similar to those provided by the Hub. These may be core data resources that are better located near a facility that has high levels of appropriate domain expertise, or they may be specialist data resources that are only needed by a small part of the community but are nonetheless of exceptional scientific importance. In the future, as the amount of data grows, some of the heavily used services might need to be duplicated for performance or load-balancing reasons.
Compute provision - Nodes based at major computer centres will provide large-scale computational resources for the more demanding services.
Training- Nodes that have the appropriate training expertise and facilities will provide: training throughout Europe on data resources provided by the node; application expertise; and use cases based on the node’s specialty; and/or eLearning expertise and infrastructure. It is likely that many Nodes will be involved in providing training, specialising in their particular area of expertise and combining forces to deliver a comprehensive suite of training tools and courses.
Tools Infrastructure- A robust infrastructure that supports best practice in tool deployment and use is a key component of ELIXIR. Tool Infrastructure Nodes will need to provide capability for users that supports tool discovery and benchmarking, and/or capability for developers that promotes ease-of-use and interoperability in software development. There is some overlap between this and the kinds of capability that will be provided by Standards Nodes. It is thus likely that there will be at some combined Standards and Tools infrastructure Nodes.
Standards Infrastructure - A Node offering standards infrastructure should provide capability to address standardisation activities in one or more of the following: programmatic access to databases and tools; biological and medical nomenclature; controlled vocabularies and ontologies; and/or reporting requirements for data deposition and exchange.
Steps taken towards construction
In April 2010 ELIXIR made a request to receive input from institutions interested in hosting one of its "nodes". In total 54 suggestions were received from 23 countries. The suggestions covered a wide range of different models, including National Nodes or networks offering a broad portfolio of services, data providers, compute service providers, tool integration platforms and training providers, varying greatly in size and complexity and the domains of expertise offered, including medicine, pharmaceutical research, agri-food and environmental science.
As a follow up to this request for suggestions, an ‘ELIXIR Funding Agencies Planning Meeting’ was held in October 2010 to begin discussions regarding the construction of ELIXIR. This meeting provided the opportunity for the PIs submitting node suggestions and representatives from funding agencies to review the landscape of potential ELIXIR Nodes and to provide input regarding the process for the construction of ELIXIR. In total representatives from 36 potential nodes attended and 11 countries funders were represented following this meeting, a decision was taken by the ELIXIR Steering Committee that a ‘light’ non- binding Memorandum of Understanding (MoU) for ELIXIR would first be established between interested parties, in order to set up an interim structure for ELIXIR, in advance of a more binding International Consortium Agreement being developed.
Subsequently, ELIXIR’s preparatory phase Steering Committee approved the MoU and a Business Case for ELIXIR in late 2010; and in March 2011 both of these documents were sent to governments in ESFRI Member States for their consideration. Following a consultation period, the final version of the MoU was approved by EMBL Council in July 2011 and the MoU issued for signing. The MoU, came into effect once five countries and EMBL had signed it, and would be limited in duration to 24 months, during this time, any other country interested in participating could join by signing the MoU and to date fifteen counties (Czech Republic, Denmark, Estonia, Finland, Greece, Israel, Italy, Norway, Netherlands, Portugal, Slovenia, Spain, Sweden, Switzerland, UK) plus EMBL have signed the MoU. The goal of this’ interim phase’ would be to negotiate a Consortium Agreement for the establishment of ELIXIR, that will be issued to ELIXIR Member States and EMBL for signing as soon as it is ready, with signing expected to take place summer 2013.
Those countries that have signed the MoU were invited to appoint Scientific and Administrative representation on the Interim ELIXIR Board which would drive ELIXIR into its construction phase; and in October 2011 the ELIXIR Preparatory phase Steering Committee was superseded by the Interim ELIXIR Board consisting of the appointed representatives of the signatories to the ELIXIR MoU, tasked with negotiating the Consortium Agreement for ELIXIR. In addition, countries interested in ELIXIR but not yet ready to sign the MoU (including Belgium, Croatia, France, Germany, Lithuania, Luxembourg, Poland, Romania, Russia and Turkey) were invited to send representatives to join the Interim Board meetings as observers.
Following the signing of the MoU in Summer 2011, the Interim ELIXIR Board held its first meeting in London on 7th and 8th of November 2011 ; at which, rules of procedure for the Interim ELIXIR Board were established, a procedure for setting up a Scientific Advisory Board for ELIXIR was approved and the groundwork for the negotiations of the ELIXIR Consortium Agreement (ECA) began, with the establishment of a ECA working group and in November 2011 a decision was taken regarding ELIXIR becoming an EMBL special project, which would provide a legal structure for ELIXIR.
The ELIXIR legal structure
During the preparatory phase project, a large number of possible legal models were evaluated for ELIXIR using expert legal advice from internationally operating law firms. One of the main questions addressed was whether ELIXIR should be set up as a new organisation or by using an existing organisation. The recommendation was to establish ELIXIR, at least initially, under the umbrella of EMBL as an EMBL special project with the option to set up an independent new legal entity, possibly as a European Research Infrastructure Consortium (ERIC), later.
By establishing ELIXIR using the mechanism of an “EMBL Special Project” ELIXIR will thereby be able to profit from EMBL’s established privileges and legal personality to make ELIXIR operational at the earliest opportunity and all ESFRI Member States will be eligible to become members of ELIXIR. It will also be possible for additional collaborative agreements, for example with industry and charitable funding bodies, to be established by ELIXIR.
The details of the “Special Project” and in particular how ELIXIR will be established, the role of EMBL-EBI within ELIXIR, as well as the rights and duties arising from ELIXIR’s role to support other ELIXIR Member States; and EMBL-EBI’s rights and obligations with regards to the ELIXIR Hub have been defined in the ECA.
Under the mechanism of an “EMBL Special Project”, ELIXIR’s budget and activities will be ring-fenced from EMBL with separate accounts, auditing, clear reporting lines and standalone communication activities to ensure visibility. EMBL Council will oversee EMBL’s participation in ELIXIR but will not oversee ELIXIR itself. ELIXIR will have its own governing body, the ELIXIR Board and the ELIXIR Hub and Nodes will all have separate legal identities.
Collaborative agreements between the Hub and each Node will deal with the relationship between EMBL, representing the ELIXIR Hub, and the ELIXIR Nodes. For legal reasons the agreements will have to be concluded between EMBL representing the ELIXIR hub and the organizations that are hosting the ELIXIR nodes. These agreements will define their mutual responsibilities and obligations within ELIXIR. These could, for example, include the goals; duration; administrative issues; monitoring and reviews; representation and reporting structures; and mechanisms for termination. The ELIXIR Hub will not have a collaborative agreement with EMBL-EBI because legally it is part of EMBL-EBI and it is impossible to have an agreement with oneself; EMBL-EBI’s rights and obligations – including the tasks of the ELIXIR Hub – will be defined in the ECA, which is the only agreement that deals with the ELIXIR members’ rights and obligations.
The ELIXIR Hub will be responsible for the overall technical coordination of ELIXIR activities and the ELIXIR Nodes will be responsible for ensuring that they comply with applicable local, national and international laws, regulations and guidelines (including health and safety, data protection, good scientific and clinical practice).
The ELIXIR Funding Strategy
The ELIXIR budget will consist of two different categories. The ELIXIR member states will provide funding for the ELIXIR Hub, and national funding streams for the ELIXIR Nodes.
The figure showing the ELIXIR Funding Strategy attached shows the streams of funding that will go into the Hub and the Nodes and the potential to leverage this funding to jointly apply for additional funds from other sources, including European Framework programme funds.
The capital construction costs for the Hub include the cost of the European Data Centre, based in London to cope with the data deluge, the IT equipment within it, and the technical hub for the coordination of ELIXIR at Hinxton, have essentially already been met.
In 2009 the UK government made its first substantial commitment to the ELIXIR Project with a 10 million GBP investment being awarded to the EBI, by the Biotechnology and Biological Sciences Research Council (BBSRC ) this funding was used to purchase a five-year lease for the European Data Centre and computing equipment for it, which permitted a dramatic increase in the institute’s data storage and handling capacity and was the first step in developing the existing data resources and IT infrastructure of EMBL-EBI towards its planned role as the central hub for ELIXIR.
In 2010 EBI in collaboration with the UK research councils submitted an application for an additional £75M from the UKs Large Facilities Capital Fund (LFCF) to further increase data storage capacity for extension of the European Data Centre lease, as well as for enhancing and upgrading the storage and compute equipment over the next ten years, which would contribute to the sustained production and delivery of the core data resources from EMBL-EBI; and also for the building of a technical hub with the capacity to house ELIXIR staff; additional training and meeting room facilities to be used by ELIXIR, and a purpose built Industry and Innovation suite. Following the approval of a scientific case in support of the application and the development of a detailed business plan, in February 2011 it was announced funds from the LFCF had been earmarked for ELIXIR and in December 2011 the funds were approved, subsequently construction of a new technical hub building to house ELIXIR Hub staff began in June 2012. It is expected the building will be ready for occupancy in autumn 2013. Additionally, the investment has also been used to purchase additional off-site data storage capacity at the London Data Centre. The Wellcome Trust, has been supportive in providing the land needed for the new building and with the combined investment from the UK of close to €100 million, it is expected that the full construction costs of the ELIXIR Hub have now been met through this award.
The ELIXIR Member States will pay the operational costs of the Hub include staff costs, IT networking, electricity costs and consumables. It is expected that the total staff would increase gradually from approximately 14 staff in 2013 to approximately 35 staff in 2018 and that the total budget of the ELIXIR Hub will rise to over 5 million Euros per annum by 2018, with a total cost from 2013 to 2018 of approximately 19 million Euros.
In the interim phase the Interim ELIXIR Board agreed that, before the ECA is signed, annual operating budgets for the Hub would be approved and implemented, which would allow the appointment of an ELIXIR Director, a small team of administrative support staff and technical staff to begin the technical construction of ELIXIR.
In 2012 ELIXIR Member States approved an interim operating budget for the ELIXIR Hub of €557,523 for 2012 and €1,369,993 for 2013. Much if the 2012 budget was used to support five Pilot Projects acting as test beds for the integration of the Nodes, with work beginning on these projects 1 October 2012 and for the recruitment of the ELIXIR Director, Niklas Blomberg (Sweden) who was selected in December 2012 following a lengthy recruitment process.
The 2013 budget will allow for the further continuation of the technical work to integrate the Hub and Nodes and will cover the salary costs of the ELIXIR Director, a small secretariat to support him, and a technical team to begin the work of integrating services.
Once the ELIXIR Consortium Agreement is signed a full five-year budget for the ELIXIR Hub will come into force, and discussion around this are taking place in tandem to the on-going development of the ECA. During 2013 the newly appointed ELIXIR Director will work with the interim ELIXIR board and representatives from the prospective ELIXIR nodes to develop a scientific programme for ELIXIR and the five- year budget for the ELXIR Hub for the period 2014-2018, ready to be presented for approval at what is hoped will be the first meeting of the full ELIXIR Board, consisting of the representatives of members states that have signed the ECA with ELIXIR in November 2013. A first draft will be presented to the interim board for comment in April 2013.
ELIXIR Nodes will need to be funded at the national level by government agencies, charities and other funders. ELIXIR Nodes are expected to apply for their own funding in coordination with ELIXIR, and proof of sustainable funding will be required for a Node to become part of ELIXIR, and the exact costs of the ELIXIR Nodes will be determined by the Node coordinators, their host institutions and national and other funding organisations.
The cost of the construction of a Node will depend on many factors and local circumstances. Member states hosting the ELIXIR Nodes will work out the details depending on their local budget requirements. The actual cost will depend on what type of infrastructure is already available at the host organisation and what would have to be added to establish a Node; whether existing facilities can be used or whether new ones have to be constructed and on local prices; and where provision of pan-European services requires expanding existing facilities in the ELIXIR Member States, funding may have to be raised from local and other sources, including EU Structural Funds.
The costs of the operation will also depend on the Nodes’ function and size and may range from several hundred thousand Euros per year up to 10 million Euros per year for a very large Node with large numbers of staff and high IT costs, for example for a compute-intensive Node. ELIXIR will only function if coordination between the Hub and the Nodes is ensured, which will require staff both at both ends. The Nodes will vary in size from a few scientists to 25 or more staff, responsible for maintaining and running the infrastructure at each centre. IT equipment will also have to be upgraded every 3-5 years representing a recurring capital investment with the amount depending on the size of the compute facilities and local prices.
Several countries have already committed funds to prepare for the construction of ELIXIR nodes, including Finland (€6.85 M), Sweden (€1.7 M), Denmark (€5 M) and Spain (€1.7 M).In addition, ELIXIR is being included on the roadmap in an increasing number of countries.
Capital construction costs will include the costs of staff accommodation (mainly incurred at the start of construction), plus the larger and arguably more important computing component. The costs for the storage and compute for ELIXIR are large; and IT equipment will need to be regularly renewed, requiring an annual capital budget and will have to grow as the data increases and demand expands. The infrastructure will therefore need an initial upfront capital investment for construction and IT costs, plus a yearly computing budget to allow regular replacement and upgrading.
ELIXIR will be constructed gradually starting with the Hub and a few Nodes and adding more Nodes over time; and it is anticipated that the hub will be fully operational after five years.
Based on the fourteen Node applications received so far (from Czech Republic, Denmark, Estonia, Finland, Italy, Netherlands, Norway, Portugal, Slovenia, Spain, Sweden, Switzerland, UK and EMBL-EBI; not including applications from France, Israel and Greece which are currently undergoing preparation) the ELIXIR Nodes are expected to have operating costs of 88 Mio € per year by 2015, with the expectation that the number of Nodes will grow steadily, with up to 25 Nodes expected to be established at the end of the first five year period (as new countries join ELIXIR)
In line with this, it is expected the operating budget of the ELIXIR Hub would need to grow from 1.4M€ in 2013 to over 5M€ in 2018, and it is expected that the hub will grow from approximately 13 staff dedicated to ELIXIR in 2013 to upwards of 30 in 2018.
Funding from the European Union Framework Programme will be sought to support some aspects of the operation of ELIXIR in addition to its core activities. ELIXIR will jointly apply to the European Union, and other international funders, for additional funding for projects that involve building e-infrastructure, enhancing user access, training, collaborations with industry (for example, through the Innovative Medicines Initiative) and building bridges between ELIXIR and the BMS research infrastructures.
The ELIXIR Governance Model
ELIXIRs governance model takes into consideration ELIXIR’s scientific and technical structure. The ELIXIR Board will oversee ELIXIR’s activities. The ELIXIR Member States and EMBL will appoint the ELIXIR Board. The ELIXIR Board will appoint the ELIXIR Executive Management and the Scientific Advisory Board (SAB) that will advise the ELIXIR Board and Executive Management in scientific matters, including the selection of ELIXIR Nodes, and regularly review of scientific and technical aspects of the ELIXIR Hub and Nodes.
The ELIXIR Board
The ELIXIR Board will be composed the scientific and administrative representatives from each ELIXIR Member State. Each country will have one vote and members will have due authority to deliberate, negotiate and decide issues relating to budget and to ELIXIR’s strategic programme, as well as establishing and monitoring rules and procedures, including those for the selection of ELIXIR Nodes. They will be expected to report back to their own Member States, and draw on advice from the SAB.
As the most senior body of ELIXIR, the ELIXIR Board will give high-level oversight, and approval of devolved ELIXIR strategy and budget (including managing additional bilateral agreements). It will oversee management of risks and liabilities of ELIXIR, and resolve disputes and disagreements.
The ELIXIR Board will provide Member States with voting rights in order to:
- Agree and monitor the strategic plan;
- Adopt budget;
- Commission and receive operational reports;
- Approve agreements;
- Appoint (and dismiss) the Executive Management;
- Agree new Nodes and terminate nodes that are no longer serving ELIXIR’s purpose;
- Appoint members of the Scientific Advisory Board;
- A more detailed list of tasks and responsibilities will be defined in the International Consortium Agreement and the ELIXIR Statutes.
The ELIXIR Board may also decide to admit observers, from prospective member states and from charities and industry.
The ELIXIR Director
The ELIXIR Director, assisted by the Secretariat Staff, will be responsible for:
- Day-to-day operational (management, financial and administrative) activities such as:
- Operational responsibility for delivery of strategy and services;
- Coordination of ELIXIR Nodes and Hub
- Supporting ELIXIR standing committees;
- Maintaining accounts, auditing etc.;
- Coordination of ELIXIR publicity and communications.
- Management and administration of ELIXIR in accordance with the decisions of the ELIXIR Board;
- Convening meetings of technical representatives from the Nodes as required;
- Presenting the annual report to the ELIXIR Board;
- Preparing the strategic programme
- Submitting the annual budget estimates.
- Appointment and termination of employment would be in accordance with EMBL staff rules and regulations.
The ELIXIR Scientific Advisory Board (SAB)
For ELIXIR to understand and assess its position and role within the wider international body of research activity, it must be able to draw coherently on the independent views and knowledge of the wider research community. Membership of the SAB will be made up of distinguished international experts including academics not associated with ELIXIR Nodes, representatives of other internationally renowned organisations operating outside of Europe, and representatives of researchers in the commercial sector. This group will be appointed by the ELIXIR Board, following the proposal of candidates by the ELIXIR Executive Management.
The SAB shall provide independent consideration and advice to the ELIXIR Board and ELIXIR Executive Management on scientific issues in order to:
- Review applications for new Nodes and make recommendations to the ELIXIR Board;
- Ensure scientific and technical excellence and relevance (including independent quality assurance);
- Identify and recommend emerging challenges and opportunities, both within and beyond ELIXIR activities (including specific periodic reviews);
- Carry out periodic scientific reviews of elements of both the ELIXIR Hub and the Nodes, and functional activities (i.e. training, data storage etc.).
- The SAB will meet regularly and report directly to the ELIXIR Board, and will act independently of EMBL.
Approval of the ECA and the process for establishing the ELIXIR Nodes
Although, the final decision on which Nodes become part of ELIXIR will be taken once the ECA is established, in order to start moving forward with construction of ELIXIR, in April 2012 the Interim Board appointed a Scientific Advisory Board for ELIXIR. Over summer 2012 a process for the establishment of the ELIXIR nodes and an application template was developed by a working group consisting of representatives from the Interim Board; and in August 2012 a call was made for signatories to the MoU to submit ELIXIR Node applications, with review of initial applications for ELIXIR Nodes by the ELIXIR SAB taking place in December 2012.
At the third Interim Board meeting held in London 22nd – 23rd October 2012 a draft ECA was presented to the Interim Board for discussion and following this meeting the draft ECA was circulated to legal representatives for final comment. The final draft will be put to the Interim Board for approval at the fourth interim ELIXIR Board meeting scheduled for April 2013 and it is anticipated that the ECA will be issued for signing in summer 2013 following approval by EMBL council. In the meantime, following favourable review by the ELIXIR SAB and ELIXIR Board, principles for associated collaboration agreements will be developed, and negotiation of bilateral collaborative agreements will begin with the institutions operating initial Nodes. The interim phase of ELIXIR will end with the signing of the ECA by five countries plus EMBL, that will establish ELIXIR’s permanent structure. Additional countries will be able to sign the ECA and establish Nodes as needed in the future. Once the ECA is established the admission of new Member States to ELIXIR will be a rolling process that allows any country to join if the ELIXIR Member States unanimously agree.
Feedback from the ELIXIR SAB
In their report following the first SAB meeting in December 2012, the SAB commended the ELIXIR participants on the tremendous efforts to date in organizing ELIXIR and from each member node in putting together their applications. They advised that they strongly endorsed the creation of shared global bioinformatics infrastructure, which will greatly enable research and industry in biomedicine, agriculture, biology, biotechnology, environmental and other life sciences. The size and complexity of data in these domains, and the associated software and computing requirements, are daunting and quite distinct from many other ESFRI projects. There have been prior attempts to develop distributed e-infrastructures for life sciences, but none have been successful. ELIXIR’s model, combined with advances in technology and the explosion of big data, makes this effort particularly timely and likely to succeed in the proposed step-by-step fashion. They anticipate that ELIXIR will greatly accelerate progress of scientific research by removing barriers to entry, introducing standardization and interoperability and flexible computing, and reducing duplication of effort.
They noted that there was a lot of heterogeneity in the offered resources and associated funding, as expected due to the diversity of the country size and respective resources and maturity of the bioinformatics communities, but they wished to emphasize that this should be seen as a major strength of ELIXIR that smaller countries or nodes will be positively impacted by their participation in ELIXIR, and that they would encourage them to fully take advantage of the resources coming from other ELIXIR nodes. It was also noted that while some nodes clearly identified roles within the ELIXIR framework, others seemed to be less detailed as to how they would best interact within ELIXIR. Also, many of the nodes proposed are distributed across multiple sites, and this leads to large staff/output ratios. They added that again, this is to be expected, and is a natural consequence of trying to unify a distributed community of bioinformatics researchers. However in these cases, it is very important that projects be clearly prioritized to better develop ELIXIR resources across the sites.
The SAB also wanted to emphasize the importance of developing good metrics for measuring the effectiveness of ELIXIR resources and efforts, as these will allow both the initial assessment of importance of resources and evaluation of their success. They felt that many of the applications in the first round would have had even stronger cases had they emphasized the often quite sizeable existing user bases and they would like to encourage increased involvement of users and industry in each ELIXIR node.
They also commented that there is potential redundancy and synergy between the nodes, offering opportunities for focusing and coordinating the efforts, and they would particularly recommend greater coordination between groups offering software tools for handling next-generation sequencing data, and also that such groups should look at existing tools and already funded networks and initiatives (e.g. such as the protein interaction databases have already done with iMEX). For next-gen sequencing, they should look at the SeqAhead EU COSTaction.
They were particularly challenged to value and assess the impact of the computing resources proposed by a number of nodes and suggested the nodes provide more explicit guidance as to how these resources can be used by researchers outside the host institution, including issues of data transfer. Also the parallel development of cloud computing resources by multiple nodes offer a great opportunity for synergy, and they strongly encouraged the multiple groups developing such resources to work together to ensure common standards.
It was noted that many nodes proposed training components; and the SAB would recommend that nodes attempt to coordinate training across countries and establish common standards. Nodes should mainly focus on training users and training to develop infrastructure; and they recommended that the trainers train at (or come from) other nodes when possible. It is important that there be some ELIXIR node (or hub) that provides training for each major aspect of ELIXIR. The training should align well with the capabilities and goals of the overall project.
For those nodes proposing to study specific genomes, the SAB expect the nodes to focus efforts on added value, such as annotation, and not on reinventing genome browsers and visualization methods. They added that they strongly endorse all genome sequence data and annotations be additionally deposited in standard repositories. In particular, the nodes would be expected to comply and enable others to comply with the expectations of the Toronto statement on prepublication data release. Multiple nodes may be working on related genomes (e.g. woody plants) and should coordinate efforts.
As a general statement, the SAB added that they saw a pressing need for the hub and node directors to come together to agree on the main resources/tools that ELIXIR will focus on initially, work out a common blueprint for the first phase of ELIXIR, and agree which node(s) should take responsibility for which of the main “work packages”. They strongly endorsed the pilot projects which are already in place between nodes, and encouraged more such projects.
The SAB also made it clear that they strongly believed that the hub should have more than an administrative role. While acknowledging the legal and political elements that led to the proposed structure, the SAB notes that from a purely scientific perspective, it would make sense that the EBI service node and hub be integrated into a single structure, especially given the central role of many of the EBI services for ELIXIR and their high utility for all of the other nodes. While there is a real need to keep funding streams separate, we encourage the stakeholders to find ways to ensure that the scientific goals are served optimally.
The ELIXIR Nodes will now have time to revise their proposals in time for presentation to the ELIXIR Board in November. During this time it is expected that those interested in establishing ELIXIR Nodes will continue to discuss with their relevant funders how to resource activities at their Node, for central operations (at the Hub), and finally to apply for resources through appropriate national funding mechanisms. Discussions will also begin regarding how the nodes will work together, and work will start on the drafting of collaboration agreements. Decisions will also be taken regarding the extension the existing pilot actions and establishing of further pilot actions in 2013.
Feasibility of the proposed solution
It is believed the proposed legal and organisational solution is feasible for this infrastructure for the following reasons:
- Experience in international collaborative projects. National centres of excellence as well as EMBL-EBI are organisations with many years of experience in coordinating and participating in international scientific collaborative projects. This experience at the scientific level, as well as the administrative and operational levels, will be applied in successfully setting up and efficiently operating ELIXIR by making use of existing resources at the Hub and the Nodes and spreading investments at international and national levels.
- Service continuity. ELIXIR will be seamlessly built on existing data resources and services. Its construction will not affect the level of current service provision but will deal effectively with the challenges that a distributed infrastructure requires.
- Timeliness. Both the ELIXIR Hub and candidate national Nodes have the means to collaborate effectively on the technical and scientific coordination issues that ELIXIR will require. This will have a positive effect on the timely delivery of the ELIXIR construction phase, with a direct and beneficial impact on restraining budgets and mitigating associated risks.
- Scalability. The proposed model for ELIXIR is scalable in many dimensions. New ELIXIR Nodes can be added as the infrastructure grows into the future, as well as additional services, data resources and tools. New technologies will be better evaluated and assimilated by the participating parties, thus guaranteeing cost-effective implementation and migration solutions across the infrastructure.
ELIXIR offers essential services to the scientific community in the life sciences. These need to be expanded and maintained to make best use of previous and future large investments into research. These services cost only a fraction of the initial investment in generating the data, some of which is unique and could never be regenerated.
European countries have struggled to develop a mechanism that would allow the main biological data resources to be provided in a sustainable manner. EMBL-EBI has been financed by the 20 EMBL Member States, which have been very supportive in increasing the EMBL budget to enable the EMBL-EBI to respond to the data deluge and maintain Europe’s competitive position in this area. It has also been necessary to raise additional funds for EMBL-EBI to manage the data, with major contributions from the European Union, the US National Institutes of Health, the Wellcome Trust and the UK Research Councils.
ELIXIR provides the opportunity to develop a longer-term plan. It will enable the load to be distributed across multiple sites in Europe by setting up a distributed research infrastructure linking EMBL-EBI with other centres of excellence in biological data provision in the ESFRI Member States.
A pan-European bioinformatics infrastructure will deliver the backbone for new discoveries that address and meet the Grand Challenges and, in doing so, will:
- Spur economic development and innovation, and thus create new, knowledge intensive, highly skilled jobs;
- Generate opportunities to increase Europe’s knowledge-based industry and competitiveness, by supporting the success of innovative small-to-medium biotech enterprises; Attract world-leading scientists to Europe (increase “brain gain”) and retain key expertise (stem “brain drain”);
- Increase the application of new innovations in the biotechnology and pharmaceutical industries, as well as in agriculture and environmental protection;
- Safeguard the investment that nations have already made in funding biological research by ensuring that data are safely kept, and openly accessed by everyone.
ELIXIR, as a pan-European bioinformatics infrastructure principally funded by public funds, will guarantee that open access to biological data is maintained. Speaking with a single voice will strengthen Europe’s influence in such global discussions.
ELIXIR’s Member States will benefit from:
- Enhanced exploitation of data being produced from their investments in biomedical research, especially genomics and other high-throughput technologies;
- Optimisation of the value of data by rapid and timely translation into other sectors such as clinical, agricultural and environment research;
- Enhanced competitiveness through European coordination;
- Enhanced bioinformatics capabilities and expertise within their funded communities;
- Access to expertise and advice beyond national boundaries to structure their own national infrastructure for biological information.
Only ELIXIR Member States can establish ELIXIR Nodes in their country. Therefore, only ELIXIR Member States can play an active role in the construction and operation of a world-leading research infrastructure for biological data.
Individual ELIXIR Member States will benefit enormously from the shared expertise in bioinformatics service provision that currently exists within the various organisations involved in ELIXIR. ELIXIR will bring together some of Europe’s leading bioinformatics providers and through collaborating closely with these, staff within Nodes will be able to learn new skills and adopt the state of the art quicker.
Participating in ELIXIR has the added benefit for many Member States of helping to reduce fragmentation nationally by bringing together several resources and service providers into one dedicated ELIXIR resource. This national pooling of excellence has already been seen through the first round of ELIXIR Node Applications, where the majority of Nodes constitute consortia of national institutes. In many countries, such national coordination would not have happened were it not for ELIXIR and it will continue to provide a long-term collective framework to ensure better cooperation both within and between countries.
For a number of countries, participation in ELIXIR will serve to support capacity building in the sphere of bioinformatics. In countries with limited budget for science, or where existing bioinformatics resources have a more limited international use, participation in ELIXIR will enable participating organisations to improve their expertise in bioinformatics through the adoption of best practice techniques and the application of the latest methodologies in use within the discipline. ELIXIR’s independent Scientific Advisory Board (SAB) will also support this process through the provision of valuable advice and suggestions in relation to deploying world-leading bioinformatics services. Staff trained to handle and exploit the biodata are keenly sought in industry and will help to develop local companies in this area of science.
ELIXIR Member States are able to contribute to the shaping of the direction of ELIXIR, both in its implementation stage and as it progresses to full operation over the coming years. In real terms this means that countries can ensure that their own national priorities in terms of bioinformatics can be prioritised and responded to through the larger ELIXIR consortium. In practical terms, this will mean contributing to decisions regarding the ELIXIR budget, ELIXIR’s scientific and technical direction and operational matters.
ELIXIR will help to preserve the national investments already made in generating life sciences data through research. The data storage and retrieval capabilities of ELIXIR will significantly increase research efficiency, resulting in cost reductions through reduced replication of experimentation. Countries which choose to act alone in the management of life sciences data risk not being able to take advantage of the efficiencies which derive from working collectively within the framework of a large e-infrastructure.
In an increasingly global world, Europe’s economic prosperity lies in the knowledge economy; growth can only come from the strength of Europe’s highly skilled workforce and its ability to attract top talent. The hosting of ELIXIR Nodes will help to lay the foundation for, and strengthen, the knowledge-based bio-economy throughout ELIXIR Member States. By funding the construction and operation of ELIXIR Nodes, Member States are making sound long-term investments in their local workforce, putting steps in place to help retain the best talent.
New commercial ventures and spin-outs will emerge from ELIXIR Nodes, creating new jobs and supporting the local economy. Over time, a positive filtering effect will see well-trained and highly-skilled staff employed within ELIXIR Nodes taking their skills and knowledge into other areas of the local labour force. This phenomenon is already witnessed in areas such as Cambridge, where there is a positively healthy rotation of staff between leading bioinformatics organisations in the region.
Through their participation in the distributed infrastructure of ELIXIR, the Nodes themselves will benefit from an enhancement in the quality of the research they undertake in their respective national institutes.
Databases are generally more valuable when they contain high-quality data in large volume as this scale enables more robust results to be derived. The world’s most widely used bioinformatics resources are frequently the result of international collaboration where data follows a standard and is shared by many partners. In such collaborations, the data are distributed globally and partners work on building a relevant cultural and local interface for their users.
Through ELIXIR, current and future bioinformatics resources developed in ELIXIR Member States will become more widely used internationally and, through better integration with other ELIXIR services, will ultimately become more powerful resources, than if they were developed and operated in isolation.
Given the importance of ELIXIR to life sciences, and the political investment Member States have made in implementing ESFRI Research Infrastructures, it is expected that the European Commission may wish to use a specific budget within the Horizon 2020 programme to supplement existing Member State investments in these infrastructures. Only ELIXIR Member States will be able to jointly access this funding under the name of ELIXIR.
ELIXIR Member States will benefit from a stronger collective voice, as witnessed through successful joint lobbying efforts, on behalf of the group of ESFRI Biomedical Science Research Infrastructures, with EU Institutions, with the aim of highlighting the importance of such infrastructures under Horizon 2020.
ELIXIR will place Europe - and each of its Member States - at the heart of bioinformatics globally. Individual bioinformatics providers will have a stronger collective voice through ELIXIR than they would should they operate individually including on issues such as personalised medicine, Open Access and the development of data management policies and systems. Additionally, Research Infrastructures are a key component of European Research Area (ERA) policy and participation in ELIXIR ensures that Members are active drivers in implementing the European Research Area.
Support for other ESFRI BMS Infrastructures
Research in the life sciences has changed markedly during the last few years. Traditionally, scientific progress was made by individual research groups, which focused on specific problems (classical reductionist hypothesis-driven research). Nowadays, more holistic approaches (discovery-driven research) that rely on large distributed teams with common access to extensive infrastructure are becoming increasingly important.
Obtaining deeper insight into the role of genes and their products in the context of the complexity of living systems, or understanding the genetic and environmental factors impacting on human health, require interdisciplinary approaches involving a broad spectrum of demanding technologies and resources.
To overcome these challenges, biomedical scientists are now adopting large-scale collaborative approaches, involving scientists from various fields within and outside the biological and medical sciences (BMS) community. Even within the BMS community there is a need to promote greater cross-fertilisation between sub-disciplines. The current fragmentation of scientific communities in Europe is a major obstacle to this, and single institutions or even national networks are often unable to address this need.
Apart from ELIXIR, the ESFRI process has identified a number of other BMS research infrastructures, which are developing in parallel with ELIXIR. These include mouse clinics, structural biology laboratories, biobanks and support for clinical trials. These infrastructures either produce or use data that lie within ELIXIR’s remit. Therefore, close co-operation and coordination with these infrastructures to ensure seamless deposition, access and integration of their data is essential.
ELIXIR is therefore aiming to:
- Establish and promote good co-operation between the BMS infrastructures, helping to create an e-infrastructure that allows transfer of data and easy, yet secure access to data for all Europe’s life scientists;
- Provide the proper framework for registration of resources, as well as access to and integration of high-end technologies and expertise, required to address key scientific questions.
Throughout the project ELIXIR management have attended the stakeholder meetings of the other ESFRI BMS projects and also e-infrastructures, to present ELIXIR and discuss how ELIXIR could interact and support their infrastructures. ELIXIR is the coordinating partner of the EC funded project BioMedBridges which will construct the e-infrastructure to allow interoperability between data and services in the biological, medical, translational and clinical domains. Additionally, many of the proposed ELIXIR Nodes already have links with these projects and will be actively looking to build upon these links in order to define the scope of these commitments and ensure that ELIXIR will be able to deliver on them.
Interaction with Industry
Very few ESFRI research infrastructures will have as high levels of industry usage as ELIXIR. Intellectual Property (IPR) generated by users in using ELIXIR services will be the users to exploit. Users from industry will range from SMEs to large multinationals and the sectors covered include pharmaceuticals, biotechnology, healthcare, through to food and agriculture. These industries are major employers, generating wealth and supporting Europe’s transformation to a knowledge-based economy.
In addition to having a high expected consumption of data from industry, ELIXIR will also develop a forward looking programme for comprehensive engagement with industry at all levels. This programme, which will be developed exclusively by ELIXIR Member States, will enable industry to derive support, expertise and training. Industry is already a partner in some of the emerging ELIXIR Nodes, which demonstrates clearly one of the commercial benefits that can be derived from hosting Nodes.
The private sector currently represents approximately 20% of public usage of data resources (based on EBI statistics), and will of course continue to have open access to all the data where appropriate. Industry has participated in ELIXIR and in developing the ELIXIR Business Case. However, closer collaboration would be of benefit to all. Currently, the bioindustries are facing exactly the same data challenges as academia. They see some major risks in their current way of interacting with publicly funded data providers. These include budget and manpower challenges, duplication of effort, difficulty integrating private and public data and lack of necessary standards. They also see the added value of ELIXIR in terms of reduced costs and duplication of effort, higher scalability, access to common data and interface standards and much better public–private data integration. Their key requirements from ELIXIR are a service-oriented delivery organisation, unrestricted resource distribution, agreed levels of service, secure access to protect IP and common standards.
Industry-specific services may include:
- Industry-sponsored customised training
- Industry-sponsored customised development of data resources or tools
- Pre-competitive projects
- Industry-sponsored development of relevant standards
- Private industry servers deployed in and supported by the ELIXIR Data Centre
- Industrial provision of cloud-based server access to copies of public data.
These interactions should involve not only large companies in the life science sector (including pharmaeutical, consumer goods, healthcare, agriculture and biotechnology companies) but also SMEs, which will require a different model of engagement.
Many commercial organisations are poorly equipped to deal with the challenges caused by the data deluge using internal resources alone; this is true both for large companies and for small-to-medium enterprises (SMEs).
In addition, the data deluge has arrived at a time when information system budgets are static or shrinking, with reduced internal infrastructure and manpower. Consequently, few industrial organisations can now afford to work alone, and many are re-evaluating the need for pre-competitive IP generated internally. An increasingly collaborative landscape is emerging, with a range of pre-competitive alliances being formed in specialised sectors. There is a strong business requirement to organise and integrate public and proprietary internal data. Clear and unambiguous data and meta-data standards are necessary and these must be adopted across industry. Thus, there is an unequivocal need for industry to work with the academic community to develop and apply these standards universally. This can only benefit both parties and will be a real boon to the increasingly prevalent public–private research partnerships within Europe. The benefits to European industrial organisations of such a service-oriented infrastructure are likely to be numerous. The opportunity to reduce duplication of internal effort will make European life science companies more competitive through significant cost reductions. The benefit of integrating external public data with internal data in an efficient way should greatly reduce the probability of overlooking significant facts in the interpretation of internal data. The improved insight into these data will lead to more informed decision making at critical points in the research/development pipeline. It is also considered that open innovation will be supported by these initiatives. The adoption of widely supported standards will reduce barriers between information sharing and help to facilitate cross company research partnerships.
Many of the institutes which are likely to become part of ELIXIR Nodes are already interacting with industry at a local level and discussions are taking place with IMI and EFPIA as to how ELIXIR can further support industry. The next step will be to take the recommendations of the prep phase report on industry and through consultation with the nodes to develop a framework for future interactions with industry, with work to begin in 2013.
Ongoing dissemination activities
During the course of the preparatory phase project ELIXIR held three stakeholders each attended by upwards of 110 stakeholders from most of the countries in Europe and has consulted directly with the full range of stakeholders through the medium of the WP3 Bioinformatics Communities Committees and two surveys, one of data users and one of data providers. Feedback from these stakeholders has strongly influenced the development of the ELIXIR.
ELIXIR has continuously developed its public relations campaign throughout the project. Articles describing ELIXIR have been published in key journals, DVDs and leaflets distributed and ELIXIR has been presented by the ELIXIR management team and other representatives at various meetings and ELIXIR regularly exhibits, displays posters and distributes literature at conferences.
The www.elixir-europe.org website continues to be maintained for both communications with project members, and to promote the project’s objectives to a wider audience and regularly receives over 65000 hits per month from over 1000 unique visitors; with the website averaging about 80 visits per day. In 2011 ELIXIR was rebranded with a new logo to coincide with the distribution of the ELIXIR Business case and MoU to the member states and to symbolize the moving forward into the next phase of ELIXIR and the ELIXIR website re-launched with tabs containing information for specific groups of ELIXIR stakeholders (replacing the prep-phase project management website which can still be linked to via the new website).
During the course of the project an External Relations Team has been recruited by EBI to help support ELIXIR outreach activities, drafting of documents for the Interim ELIXIR Board; and engagement with member states and other stakeholders.
In January 2012 the first edition of the ELIXIR quarterly e-newsletter ‘Informed’, was sent out to ELIXIR stakeholders. The newsletter provides stakeholders with the latest news and updates in relation to ELIXIR and has a circulation of over 800 stakeholders. Press releases announcing important milestones for ELIXIR are also sent to this mailing list.
It is anticipate that ELIXIR will continue to carry out dissemination activities and stakeholder engagement in the future and external relation support is included in the budget for the ELIXIR Hub to support the ELIXIR secretariat in continuing to carry out these activities in the future.
List of Websites:
Further information can be found on the projects public website: www.elixir-europe.org
Names and e-mail addresses of current members of the Interim ELIXIR Board Members
Dr Jiri Vondresek Institute of Organic Chemistry and Biochemistry AS CR, firstname.lastname@example.org
Mr Jan Burianek Ministry of Education, Youth and Sports,
Prof Søren Brunak
Center for Biological Sequence Analysis, Technical University of Denmark,
Mr. Troels Tvedegaard Rasmussen
Danish Agency for Science, Technology and Innovation
Prof Janet Thornton
EMBL-European Bioinformatics Institute
Prof Iain Mattaj
Dr Silke Schumacher
Prof Jaak Vilo
Institute of Computer Science, University of Tartu
Mr Toivo Räim
Ministry of Education and Research
Dr Tommi Nyrönen
CSC - IT Center for Science Ltd.
Ms Marja-Liisa Niemi
Ministry of Education and Culture
Prof Babis Savakis
BioMedical Sciences Research Centre "Alexander Fleming
General Secretariat for Research and Technology,
Dr Yossi Kalifa
Ministry of Science and technology
Ms Ilana Lowi
Ministry of Science and technology
Prof Anna Tramontano
Department of Physics, Sapienza University of Rome
Dr Emanuele Fidora
Ministry of Education, Universities and Research
Dr Barend Mons
Netherlands Bioinformatics Centre (NBIC)
Dr Jasper Diderich
Dr Ruben Kok
Dr Frans Martens
Prof. Inge Jonassen
Department of Informatics, University of Bergen
Dr Jacob E. Wang
The Research Council of Norway
Prof. Jose Pereira Leal
Instituto Gulbenkian de Ciência
Dr Ricardo Migueis
Fundação para a Ciência e Tecnologia / Foundation for Science and Technology
Prof. Damjana Rozman
Centre for Functional Genomics and Bio-Chips (CFGBC),University of Ljubljana
Dr Albin Krajl
Ministry of Higher Education, Science and Technology
Prof Alfonso Valencia
Centro Nacional de Investigaciones Oncológicas
Dr Cristina Bauluz
Secretariat of State for R+D+I
Dr. Rafael De Andres-Medina
Instituto de Salud Carlos III (ISCIII)
Prof. Bengt Persson
BILS -- Bioinformatics Infrastructure for Life Sciences, Linköping University
Dr Anna Wetterbom replacing Dr Elin Swedenborg until Summer 2013
Swedish Research Council
Prof. Ron Appel
Swiss Institute of Bioinformatics (SIB)
Dr Isabella Beretta
State Secretariat for Education, Research and Innovation SERI
Prof Carole Goble
University of Manchester,
Dr Mark Palmer
MRC Strategy Group, MRC - Medical Research Council
Dr Alf Game (Not officially a member but vice-chair of the Interim Board and Advisor to the UK)
Current members of the ELIXIR Scientific Advisory Board
Prof. Alan Archibald
University of Edinburgh, UK
Dr. Ségolène Aymé
French Medical Research Council (INSERM), France
Dr. Robert Gentleman,
Prof. Gunnar von Heijne
Stockholm University, Sweden
Prof. Edward Marcotte
The University of Texas at Austin, USA
Prof. Heikki Mannila
Aalto University, Finland
Assoc. Prof. Nicola Mulder
UCT Computational Biology Group (NBN), South Africa
Dr. Jérôme Wojcik
Grant agreement ID: 211601
1 November 2007
31 December 2012
€ 5 868 924,92
€ 4 500 000
EUROPEAN MOLECULAR BIOLOGY LABORATORY
Deliverables not available
Grant agreement ID: 211601
1 November 2007
31 December 2012
€ 5 868 924,92
€ 4 500 000
EUROPEAN MOLECULAR BIOLOGY LABORATORY
Grant agreement ID: 211601
1 November 2007
31 December 2012
€ 5 868 924,92
€ 4 500 000
EUROPEAN MOLECULAR BIOLOGY LABORATORY