New links added to the COVID-19 News section

There are new links in the COVID-19 News section of the ELIXIR-SI home page. We have added links to the epidemics forecast models provided by data experts from University of Ljubljana, Faculty of Medicine (core institution of ELIXIR Slovenia). The pages with the forecasts are in Slovene only. There is also a link to an online lecture about COVID-19 immunity, reinfection, testing, therapy and vaccination (in Slovene). The lecture took place on December 7 with the participation of some of the leading COVID experts in the country. Another link leads to the Slovenian section of the European Covid Data Portal (in English).

ELIXIR Slovenia team co-authored a paper about the ELIXIR Human Copy Number Variations Community

ELIXIR Slovenia actively participates in the ELIXIR Human Copy Number Variations (hCNV) community. We have recently co-authored a paper that outlines our work programme and has been published in the F1000Research journal. The paper defines seven strategic objectives of the hCNV community: pipelines for CNV detection, definition of reference datasets, data exchange formats, use of Beacon and Phenopackets to find similarities between cases, creation of new tools, FAIRification, and dissemination activities.

Copy Number Variations represent the most common type of genetic mutations associated with human diseases. However, the identification and interpretation of CNVs is still a major challenge. The seven strategic objectives described in the F1000 paper represent the means to address this challenge. The hCNV community has already been working on these objectives in the framework of the first Implementation Study, which kicked-off in June 2019.

Besides these objectives, the paper outlines interactions and links with other ELIXIR Communities and Platforms (e.g. with the Data Platform and the Interoperability Platform). The ELIXIR Data Platform will support the creation of deposition databases for CNV data and the Interoperability Platform will support the development of recommendations for CNV reporting formats.

PerMedCoE: new center of excellence for European Personalised Medicine

Coordinated by the Barcelona Supercomputing Center (BSC) and funded by the European Commission, this recently launched HPC Centre of Excellence (CoE) will optimise codes for cell-level simulations in HPC/Exascale and bridge the gap between organ and molecular simulations, thus contributing to the European Personalised Medicine Roadmap.

University of Ljubljana, Faculty of Medicine (the lead institution of ELIXIR Slovenia) is among the 12 world-class academic and industry partners from across Europe that are participating in this CoE. Please visit the PerMedCoE website to learn more about the project.

Success for Beyond 1 Million Genome Stakeholders Virtual Meeting

The Beyond 1 Million Genome Stakeholders Meeting was successfully held online on Wednesday, 21 October 2020, with more than 220 participants. The core aims of the 1 Million Genome Stakeholder Coordination Framework initiative are to connect national genomic data infrastructures, harmonize the ethical and legal framework for sharing sensitive data, and co-ordinate the implementation of genomic technologies in national and European health-care systems.

The European Commission is working on an European Health Data governance framework, the European Parliament is allocating healthcare funding, and there is a growing conviction among Europe’s policymakers that people must be at the centre of any healthcare improvement strategy.

The ambition of the European Commission is a transition to a healthy planet and a new digital world. European citizens expect access to health care and protection against epidemics. However, many chances for improvement are still waiting to be taken up, especially in the field of personalized healthcare. Secure and authorized cross-border access to genomic data would improve patient outcomes, ensure sustainability of healthcare, enable the diagnosis and treatment of cancer at a much earlier stage, advance the understanding of genetic factors that cause common diseases, and strengthen the effectiveness of disease prevention by improving the screening accuracy.

ELIXIR organizes a hackathon on Machine Learning and BioStatistics

Dear colleagues,

the first part of a two-day ELIXIR international hackathon on Machine Learning and BioStatistics will take place on Monday, October 12, 9:00 to 17:00 CEST. Due to the COVID-19 pandemics the event will be held completely online. The second part of the hackathon took place on November 2, 2020 (9:00 – 17:00 CET).

The hackathon topic has been chosen with regard to the results of an ELIXIR survey from 2019. The survey identified training needs across ELIXIR Nodes, and Machine Learning and BioStatistics was one of the topics with the biggest identified gaps in course availability and training material quality. That is why ELIXIR now organizes a hackathon to prepare materials for practical training in this field. The materials will be designed following the policies and guidelines of the ELIXIR Training Platform.

The first part of the hackathon (12/10/2020) will be focused on drafting a framework for practical training materials, including defining training goals, expected outcomes, and participants’ profile. The second part (mid-November) will have the purpose of finalizing the materials and designing exercises for hands-on training. materials authored during the hackathon will be publicly available through GitHub, under a CC-BY license, to be reused both within and outside ELIXIR.

All interested persons with knowledge of Machine Learning and BioStatistics are invited to join our effort at the hackathon. If you are interested in participating, please fill in the registration form by Friday, October 9, 2020. After this deadline all participants will receive links to the video conference system that will be used for the hackathon. We also ask you to spread the news about the hackathon through your networks.

For any questions and/or clarifications, please reach out to the main organizer of the hackathon Fotis Psomopoulos (INAB|CERTH, ELIXIR Greece) –

With kind regards,

ELIXIR Slovenia Team

Izobraževanje za delo na sekvenatorju Nanopore GridION

Spoštovani člani vozlišča ELIXIR Slovenija!

Vabimo vas na izobraževanje za delo na sekvenatorju Nanopore GridION, ki je del infrastrukture ELIXIR-SI. Oprema je dobavljena v okviru kohezijskega projekta ELIXIR-SI RI-SI-2.

Prva dva dneva (5. 10. in 7. 10.) sta dopoldan namenjena teoretični predstavitvi tehnologije Nanopore za aplikacije RNA in DNA, tretji dan (9. 10.) pa analizi podatkov. Teoretični del bo v celoti dostopen vsem zainteresiranim preko aplikacije ZOOM.

Praktični del bo izveden 5. 10. in 7. 10. popoldan na Medicinski fakulteti UL, v prostorih CFGBC IBK, Zaloška 4. Obsegal bo testna sekvenciranja RNA pod video nadzorom strokovnjakov Nanopore. Organiziran bo za omejeno število udeležencev, poleg skrbnikov opreme predvsem za raziskovalce z izkušnjami s tehnologijo Nanopore.

Podroben program in povezava sta navedena spodaj.

Vljudno vabljeni!

Več informacij najdete v vabilu.

ELIXIR Microbial Community has new tools for Galaxy analysis

ELIXIR Microbial Community leads the effort to develop tools for analysis and design of microbial processes. Tools developed by the Community are now available in a Galaxy toolshed for Synthetic Biology and Metabolic Engineering. The Community is also preparing a new implementation study on how to integrate FAIR (Findable, Accessible, Interoperable, Reusable) data sets into meaningful mathematical models.

ScienceEurope and OECD have published a report on optimising the use of national research infrastructures

ScienceEurope and the Organisation for Economic Co-operation and Development (OECD) have published a joint report on how to improve national research infrastructures. The report is focused on the state of infrastructure in 12 OECD member states: Australia, Canada, France, Germany, Hungary, Japan, South Korea, the Netherlands, Norway, Switzerland, UK and USA. The report can be accessed at this link .