ELIXIR is an inter-governmental organisation which builds on existing data resources and services within Europe. It follows a ‘Hub and Nodes‘ model, with a single Hub located alongside EMBL-EBI in Hinxton, Cambridge, UK and a growing number of Nodes located at centres of excellence throughout Europe. Governments and ministries of countries are members of the ELIXIR consortium, and the scientific community in each member country develops their national Node.
ELIXIR Slovenia (ELIXIR-SI) is a Slovenian node of ELIXIR coordinated by Faculty of Medicine in the name of University of Ljubljana. Besides other members of University of Ljubljana (Biotechnical Faculty, Faculty of Computer and Information Science and Veterinary Faculty), ELIXIR-SI members are Slovenian research organizations who signed the National Node Consortium Agreement.
- national infrastructure for obtaining high-density data with high-throughput laboratory technologies (genomic technologies),
- a central national data node for life sciences and
- center for education and training in life sciences (usage of bioinformatic tools, analysis and services).
The upgrade is funded by European Regional Development Fund and the Ministry of Science, Education and Sports and is expected to be finished in mid 2021.
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Head of ELIXIR-SI node (HoN): Brane Leskošek
Technical Coordinator: Marko Vidak
Agricultural Institute of Slovenia (KIS)
The Academic and Research Network of Slovenia (ARNES) is a public institute that provides network services to research, educational and cultural organizations, and enables them to establish connections and cooperation with each other and with related organizations abroad.
As a member of GEANT, Arnes maintains national e-infrastructure for research&educational community, offering its cloud resources and services including computational and storage resources, videoconferencing and collaboration tools.
Arnes also co-ordinates Slovenian consortium for HPC, distributed high-throughput computing and open science data (SLING), and manages national authentication and authorization federation ArnesAAI (member of EduGAIN) to help users from R&E access services and resources.
National Institute of Biology (NIB)
National Institute of Biology (NIB, est. 1960) is the largest independent Public Research Institution for Life Sciences in Slovenia. NIB’s diverse research undertakings revolve around solutions to environmental, agricultural, food and human health issues. Its primary activity has been and continues to be basic, developmental and applicative research in the fields of biotechnology, biophysics, biomedicine, bioinformatics and systems biology.
At NIB, ELIXIR and ELIXIR-SI activities are coordinated by the Department of Biotechnology and Systems Biology, with a strong focus on plant related bioinformatics and systems biology and is the co-leader of the Plant Science Community within ELIXIR.
Members of the Department have developed several tools and approaches to extract biological information from complex omics datasets. Starting with functionally describing gene products using functional ontologies (GoMapMan), an approach of experimental data set integration with prior knowledge networks was developed (DiNAR). Combined with network analysis the developed tools were successfully used for identification of important regulatory hubs in plant immunity, but their general nature allow use in different fields of plant biology and beyond. An extension of these analyses was the collaboration with the Department of Knowledge Technologies (IJS, Slovenia) in Biomine Explorer construction.
At the level of analysis of raw/primary data we developed tools for simplification of qPCR data analysis and organisation (quantGenious), pipelines for RNA-Seq data analytics and R-based solutions for differential gene expression analyses, plant-specific image analysis pipelines in Matlab and a tool for experimental project data organisation aimed at experimental scientists (pISA-tree). We are also involved in development of community standards, in the H2020 project ELIXIR-EXCELERATE consortium we have extended a plant standard for phenotyping (MIAPPE).
Jožef Stefan Institute (IJS)
The Jožef Stefan Institute (IJS) is the leading Slovenian scientific research institute, covering a broad spectrum of basic and applied research in natural sciences, life sciences and engineering.
IJS accumulates and disseminates the knowledge at the frontiers of natural science and technology to the benefit of society at large through the pursuit of education, learning, research, and development of high technology at the highest international levels of excellence.
The relevant department at JSI for ELIXIR is the Department of Knowledge Technologies
National Institute of Chemistry (KI)
University Medical Centre Ljubljana (UKCLJ)
University Medical Centre Ljubljana (UKCLJ) is the largest tertiary health care institution in Slovenia and one of important drivers of biomedical research in the region.
UKCLJ pursues health care, education and research and is committed to providing safe, high quality and standardised patient care.
Clinical Institute of Special Laboratory Diagnostics (CISLD), University Children’s Hospital, UMC Ljubljana
a) Genomics Department
- Unit of molecular genetics
- NGS unit
- Unit of Bioinformatics
b) Cytogenetic Department
- Cell Lab
- Karyotype and FISH analysis unit
d) Clinical Genetics Department
- Administrators of National contact point for rare diseases
- Administrators of Slovenian Rare Disease registry
The University Medical Centre Ljubljana (UMCL)/Department of Rheumatology
UMCL is the largest public medical institution in Slovenia providing diagnostics and therapy, as well as promoting clinical research and education, with the aim of encouraging innovative/applicable knowledge for the benefit of patients. The national research program entitled »Systemic Autoimmune Diseases« (#P3-0314), within the Department of Rheumatology/Laboratory of Immunology, represents a dynamic environment for research of inflammatory rheumatic diseases with multidisciplinary approaches. In the future, our research will be geared toward new technologies, such as single-cell RNA sequencing and spatial positioning, in order to reflect our overall strategy for comprehensive understanding of cell/tissue functional organization and pathophysiology, providing insight into disease mechanisms/processes and novel therapies.
University of Ljubljana (UL)
University of Ljubljana (UL) is the oldest and largest higher education and scientific research institution in Slovenia. It is renowned for its quality social and natural sciences and technical study programmes, structured in accordance with the Bologna Declaration.
UL participating institutions in ELIXIR-SI are:
- ELIXIR-SI centre
National archive of genomic and connected (clinical) data
part of federated EGA
including internal Archive UL MF
- Laboratory for Single cell analyses (LePA) at UL MF
- Central laboratory for high-throughput genomic technologies in Maribor (ELIXIR-SILVR)
- CFGBC IBK
- Laboratory for general molecular biology techniques, mammalian cell culture and bacterial culture work
- Laboratory for high throughput transcriptome and genome analyses
- The CFGBC laboratories are registered for:
- Genetically modified organisms safety level 1 (GMO-1)
- Genetically modified organisms safety level 2 (GMO-2) and Biological safety level 2 (BSL-2) are in the process of certification
- ELIXIR-SI centre
- Biotechnical faculty, Department of Animal Science
- Biotechnical faculty, Department of Biology
- Biotechnical faculty, Department of Food Science
- Biotechnical faculty, Department of Agronomy