In 2013, ELIXIR initiated the implementation phase of an infrastructure for biological information. This is achieved by linking the bio-industry organisations of ELIXIR’s member countries to the services provided by EMBL-EBI (European Molecular Biology Laboratory).
ELIXIR is made up of Life Science Centres of Excellence located across Europe. These so-called ELIXIR nodes are connected via high-speed communications links to the hub, or the European Bioinformatics Institute (EMBL-EBI), located in Hinxton, UK.
ELIXIR data sources include, for example, sequence data, nucleotide transcript data, data on protein expression and information on the structure and function of drug-like small molecules. Data generated through metabolomics is also obtained. Metabolomics is a method used for the comprehensive study of small-molecule metabolites and their structure, function and synergistic effects in the cells, tissues, blood and secretions of the body.
ELIXIR nodes share and store data and provide computing resources, software and tools for member organisations. ELIXIR headquarters creates the data registers and defines standards for the data. It also establishes a decentralised computing infrastructure for biomedical data in Europe.
ELIXIR provides the research community with training, advising how data can be efficiently utilised and how to create standards for data. The objectives include, for example, that Finland will provide the data in its biobanks internationally. The access rights to the materials will remain in Finland. An access right to sensitive material may be applied for through REMS (Resource Entitlement Management System).
Biomedical research requires access to large volumes of biological data. The Finnish ELIXIR node supports the utilisation of “big data” by means of information technology. One example of this is the use of the genetic data from the Finnish population, digitised by the National Institute for Health and Welfare and the Institute for Molecular Medicine Finland, in medical science.
In recent years, biomedical research has become data and computing intensive. Data analysis requires more and more sophisticated software and combinations thereof. Research teams have created their own analysis methods to meet the growing need, but computing resources and methods seem unable to keep pace with this development. Researchers also need resources to store data and access to reference data in order to make reasonable comparisons with the latest knowledge. The use of reference materials may also require personal access rights. The best way to respond to the challenge is to use cloud services with the reference data available. The Finnish node designs these services in cooperation with biomedical organisations.
The Finnish ELIXIR node CSC provides secure, scalable national computing resources for Finnish researchers through a cloud-based interface. The cloud service of CSC can be connected directly to the research organisation’s own internal network. After the data network configuration, the IT specialists of the local research organisation may choose to manage virtual computing and storage resources and to install the desired operating system and required software. The researchers will not be able to distinguish whether they are using the capacity of their own institute in the research project or if their processes are run using the capacity provided by CSC’s data centre. The network connection between CSC and the research organisation can be established via a MPLS connection or light path over the Funet communications network. For example, the connection between CSC, the Meilahti Campus and the Institute for Molecular Medicine Finland is a 10 Gb light path that enables the quick analysis and utilisation of genetic data obtained from biobanks.
The scientific focus is medical bioinformatics. ELIXIR builds biobank services and diagnostic tools. The National Institute for Health and Welfare and the Institute for Molecular Medicine Finland digitise the data collections and registers that can be accessed via the Finnish bbmri.fi (Biobanking and Biomolecular Resources Research Infrastructure).
Biomedical organisations can make use of the services of the national ELIXIR node through a cloud-based service. The organisation can connect its own devices (such as microscopes) over the network to the virtual machines of CSC’s cloud service. In addition to computing capacity, storage space is also available. CSC experts collaborate with the IT support staff of biomedical organisations to provide a seamless and functional view of the service to end users. Through the Finnish ELIXIR node, the end user can access many services, including the international biomedical data resources provided by ELIXIR.
ELIXIR Finland offers medical and bioinformatics research tools developed in Finland and Europe. All the tools can be found here: http://bio.tools
ELIXIR implemented five pilot projects testing cloud services. CSC is participating in two pilots: the first one examines continuous, massive data archive transfer and the second the simplification of the granting of access rights to EGA (European Genome-Phenotype Archive) data. SIB (Swiss Institute of Bioinformatics) tests the usability of virtual devices in cloud between the data reserves of EMBL-EBI and various nodes.
Together, EMBL-EBI and CRG (Centre for Genomic Regulation) of Spain are examining the ways in which a new node could share the workload of building the EGA data reserves in future. The Swedish SciLifeLab is investigating how the Human Proteome Atlas database can be linked to other protein databases.
The utilisation of data requires knowledge of analysis methods. ELIXIR offers training opportunities across Europe. The Finnish ELIXIR node CSC organises a wide range of courses in bioinformatics, providing guidance in the use of software and cloud-based services. CSC experts advise researchers on the use and development of computing methods and related software and provide assistance with IT problems.
Trainers of the international ELIXIR network visit the different nodes and organise training events. ELIXIR’s training portal TeSS (https://tess.elixir-europe.org/) lists bioinformatics courses arranged in Europe and can also be used to search for links to the training materials of previously held courses.