ELIXIR Estonia Collaborations
ELIXIR Estonia is collaborating with several Nodes from the ELIXIR network. Our most active partners have been over the years, EMBL-EBI from UK, CSC from Finland and SIB from Switzerland who have both trained our members, shared their long-term technical and organisatorial expertise and are always open for scientific and technical collaborations. Our colleagues from Germany, de.NBI and Belgium, VIB have provided us tremendous help in setting up the Galaxy services for Estonian researchers and SARS-CoV-2 data analysis.
Since 2016 we are also collaborating with Nordic e-Infrastructure Collaboration (NeIC) to train together researchers in Estonia and Scandinavia. In January 2020 Estonia became an official member of NeIC. Estonian Node in NeIC is Estonian Scienctific Computing Infrastructure (ETAIS).
Support for international collaboration projects for Estonian Core Research Infrastructures
The funding scheme by Estonian Research Council supports participation in collaborative projects initiated by the international ELIXIR research infrastructure. ELIXIR Estonia participates in the cooperation of the Genomic Data Infrastructure (GDI, see below), co-financed by the European Commission (50%) and Estonian Ministry of Social Affairs (25%). Also, ELIXIR Estonia participates in the development of ELIXIR's bioinformatics resource portal, bio.tools, and is the creator and developer of its automatic workflow.
Genomic Data Infrastructure (GDI) will work towards realising the 1+MG initiative’s ambition of creating a data infrastructure to enable secure access to genomics data across Europe. During the four year project 20 countries will build infrastructure to host genomic data and respective metadata. The overall goal is to provide a secure environment for the data and enable researchers and clinicians to query data across countries. ELIXIR Estonia is building the solution for Estonia. The project is co-financed by European Commision, Estonian Ministry of Social Affairs, Research Infrastructure grant by Estonian Research Council and by University of Tartu.
BY-COVID will build and expand upon the successful COVID-19 Data Platform, a resource initiated in the early stages of the pandemic and led by EMBL-EBI. Since its launch, many countries have established their own national data hubs, which ensures that data produced locally can be instantaneously connected and shared with the main COVID-19 Data Portal.
Rather than focus purely on providing technical solutions to the biological data, BY-COVID will work with partners such as the Versatile emerging infectious disease Observatory (VEO) and the Public Health Information Research Infrastructure (PHIRI) to incorporate data from a broader range of disciplines, including public health and social sciences.
The objective of HealthyCloud is to generate a number of guidelines, recommendations and specifications that will enable distributed health research across Europe in the form of a Ready-to-implement Roadmap. This roadmap together with the feedback gathered from a broad range of stakeholders will be the basis to produce the final HealthyCloud Strategic Agenda for the European Health Research and Innovation Cloud (HRIC).
Estonian Core Infrastructure grant for ELIXIR
The aim of the core research infrastructure grants is to ensure the openness of research infrastructures of national importance to public, private and third sector users. Support is provided to cover the additional costs of research infrastructures related to the availability of research infrastructures outside the operator of the core infrastructure and the obligations arising from international cooperation.
ELIXIR-CONVERGE is a project funded by the European Commission to help standardise life science data management across Europe. To achieve this standardisation, the project will develop a data management toolkit (RDMkit) for life scientists.
The toolkit will help ensure more research data is in the public domain, which will give scientists access to more data. This will allow them to discover new insights into the challenges facing society, such as food security and health in old age, and help stimulate innovation in biomedicine and biotechnology.
By connecting ELIXIR Nodes to provide FAIR data management as a service, ELIXIR-CONVERGE will build national capacity and create a blueprint for operating sustainable Nodes in distributed research infrastructures.
The rapid advances in molecular biology techniques such as DNA genotyping and sequencing has enabled ever larger cohorts of human exomes and genomes to be generated, facilitating study of the underlying causes of disease. It is predicted that in the next five years through national scale healthcare initiatives, an increasing number of large cohorts including complex variables such as phenotypes, measurements and medical histories will be generated.
To maximise the impact of this data for researchers, healthcare, industry, patients and funders, we have assembled a set of expert partners in resource delivery who are embedded in the communities which generate, analyse, standardise and share genomic data.
We currently operate the state of the art infrastructures, analyses, knowledge discovery and data discovery platforms and translation to healthcare on which we will build to deliver our vision of a federated solution enabling population scale genomic and biomolecular data accessible across international borders accelerating research and improving the health of individuals resident across continents.
With the growing number of life-science training resources currently available through TeSS, it can often be a struggle to choose which may be the most relevant to learning needs or an appropriate match to existing skills and competency level.
Guidance is therefore needed to help users to identify which competencies they need to acquire, which training resources will allow them to acquire such competencies and which learning path they should follow in order to move from their existing competency level to a higher one.
Therefore, the aims of this implementation study are to: 1) identify competency frameworks that are relevant to the ELIXIR user community, in order to derive a set of core competencies and a curriculum for bioinformatics and data science, 2) map ELIXIR training resources to such competencies and expose this information through TeSS, and 3) build learning paths for selected use cases, and make them available in TeSS, to help guide users in moving from one competency level to another by following such learning paths.
The study is a joint effort of ELIXIR UK (Gabriella Rustici, Terri Attwood, Niall Beard), ELIXIR-NL (Celia Van Gelder), ELIXIR France (Victoria Dominguez del Angel), ELIXIR Luxemburg (Roland Krause), ELIXIR Estonia (Hedi Peterson), ELIXIR Switzerland (Patricia Palagi), EMBL-EBI (Cath Brooksbank, Sarah Morgan), ELIXIR Italy (Allegra Via), ELIXIR Finland (Eija Korpelainen), ELIXIR Belgium (Alexander Botzki).
The study will also interact with ELIXIR Industry (develop learning path(s) that specifically address the needs of industry users), global players in bioinformatics (BioExcel, CORBEL, BD2K, H3ABionet, GOBLET) and data-science (CODATA-RDA, EDISON, Software/Data Carpentry) training, and the Bioschemas project (improve the metadata that are exposed through the Bioschemas specifications for training materials).
01.06.2018 - 31.05.2019
ELIXIR Integration from a User Perspective
The goal of this study is to provide the life-scientist a powerful tool to find and use ELIXIR resources - across the spectrum - based on intuitive graphical diagrams of the most prevalent scientific workflows.
Currently, a scientist can use TeSS to find training events and materials and then, in a separate search, use bio.tools to find relevant tools, and BioSharing to find standards and databases. Linking TeSS and bio.tools to ELIXIR’s computer resources via common workflow diagrams would enable end-users to discover and learn about the prevalent bioinformatics workflows. This study will link TeSS and bio.tools via most prevalent bioinformatics workflows and will lay the foundation to incorporate other ELIXIR platforms in a later stage, thereby providing an even more useful service for the researcher.
Eight ELIXIR nodes are involved in this study: Belgium (Frederik Coppens, lead), UK (Terri Attwood), Estonia (Hedi Peterson), Denmark (Jon Ison), Swiss (Heinz Stockinger), EMBL-EBI (Sarah Morgan), Norway (Matus Kalas), France (Hervé Menager).
01.10.2017 - 30.06.2018
Estonian Life Science Infrastructure for Biological Information
ELIXIR (European Life Science Infrastructure for Biological information) is an ESFRI infrastructure for biological data and bioinformatics research. Its goal is to ensure free usage and continuous development of databases, software, compute resources and user trainings. ELIXIR infrastructure is global, covering a variety of life science data (human and other species DNA, RNA, proteins, sequences, structures, molecules, pathways, publications etc) databases, tools, compute resources, relevant standards and trainings. The distributed structure aims to build common infrastructure based on separate but complementary resources across Europe. This enables to develop and combine more easily needed tools and resources and to ease researchers interpreting their results. ELIXIR coordinates development of best practices and standards across and beyond Europe and helps to implement these across the different countries. Estonia has joined ELIXIR consortium under the name of ELIXIR-Estonia (ELIXIR-EE). ELIXIR-EE allows Estonia to contribute to international bioinformatics infreastrcuture and keep Estonia among the important countries driving the fast moving field. ELIXIR-EE intends to unite individual tools and services developed in Estonia and upgrade them into the core components of the European bioinformatics infrastructure by ensuring common standards, and modern, high-quality services. Together with ELIXIR partners in Europe, core services, technical infrastructure, secure cloud solutions, standards and cooperation interoperability frameworks are developed; communication with global communities of data management will be promoted, training programs will be developed and organized. ELIXIR Estonia’s task is to participate in international collaborations as well as to lay the foundation for providing bioinformatics services in Estonia.
The project is supported through European Structural Funds with 1 284 564 euros.
ELIXIR-EXCELERATE - Fast-track ELIXIR implementation and drive early user exploitation across the life-sciences
The life sciences are undergoing a transformation. Modern experimental tools study the molecules, reactions, and organisation of life in unprecedented detail. The precipitous drop in costs for high-throughput biology has enabled European research laboratories to produce an ever-increasing amount of data. Life scientists are rapidly generating the most complex and heterogeneous datasets that science can currently imagine, with unprecedented volumes of biological data to manage. Data will only generate long-term value if it is Findable, Accessible, Interoperable and Re-usable (FAIR). This requires a scalable infrastructure that connects local, national and European efforts and provides standards, tools and training for data stewardship. Formally established as a legal entity in January 2014, ELIXIR - the European life science Infrastructure for Biological Information - is a distributed organisation comprising national bioinformatics research infrastructures and the European Bioinformatics Institute (EMBL-EBI). This coordinated infrastructure includes data standards, exchange, interoperability, storage, security and training. Recognising the importance of a data foundation for European life sciences, the ESFRI and European Council named ELIXIR as one of Europe’s priority Research Infrastructures. In response ELIXIR have developed ELIXIR-EXCELERATE. The project will fast-track ELIXIR’s early implementation phase by i) coordinate and enhance existing resources into a worldleading data service for academia and industry, ii) grow bioinformatics capacity and competence across Europe, and iii) complete the management processes needed for a large distributed infrastructure. ELIXIR-EXCELERATE will deliver a step-change in the life sciences. It will enable cost-effective and sustainable management and re-use of data for millions of users across the globe and improve the competitiveness of European life science industries through accessible data and robust standards and tools.