Explanipedia

A research data management (RDM) community for ELIXIR Open

Flora D’Anna, Niclas Jareborg, Mijke Jetten, Minna Ahokas, Pinar Alper , et al. · 2024

Research data management (RDM) is central to the implementation of the FAIR (Findable Accessible, Interoperable, Reusable) and Open Science principles. Recognising the importance of RDM, ELIXIR Platforms and Nodes have invested in RDM and …

Systems Biology in ELIXIR: modelling in the spotlight Open

Vítor A. P. Martins dos Santos, Mihail Anton, Barbara Szomolay, Marek Ostaszewski, Ilja C.W. Arts , et al. · 2024

In this white paper, we describe the founding of a new ELIXIR Community - the Systems Biology Community - and its proposed future contributions to both ELIXIR and the broader community of systems biologists in Europe and worldwide. The Com…

Synergising ELIXIR resources for training in systems biology Open

Claire Rioualen, Finn Bacall, Cristina Furlan, Matúš Kalaš, Brane Leskošek , et al. · 2024

Systems biology (SB) is a new ELIXIR community, that aims to utilise the ELIXIR ecosystem, such as the Training eSupport System (TeSS) and bio.tools, a registry of software tools and data resources for life sciences. One of the main initia…

A research data management (RDM) community for ELIXIR Open

Flora D’Anna, Niclas Jareborg, Mijke Jetten, Minna Ahokas, Pinar Alper , et al. · 2024

Research data management (RDM) is central to the implementation of the FAIR (Findable Accessible, Interoperable, Reusable) and Open Science principles. Recognising the importance of RDM, ELIXIR Platforms and Nodes have invested in RDM and …

Recommendations from the COST action CA17116 (SPRINT) for the standardization of perinatal derivative preparation and in vitro testing Open

Aleksandar Janev, Asmita Banerjee, Adelheid Weidinger, Jure Dimec, Brane Leskošek , et al. · 2023

Many preclinical studies have shown that birth-associated tissues, cells and their secreted factors, otherwise known as perinatal derivatives (PnD), possess various biological properties that make them suitable therapeutic candidates for t…

Building Research Data Management (RDM) Expertise and Training Resources in ELIXIR Nodes Open

Celia van Gelder, Alexia Cardona, Brane Leskošek, Patricia M. Palagi · 2023

Research data Management (RDM) is central to the implementation of the FAIR (Findable Accessible, Interoperable, Reusable) and Open Science principles. Recognising the importance of RDM, the ELIXIR-CONVERGE project was launched in 2020 and…

ELIXIR-CONVERGE D2.4 2nd Report on delivered data management and stewardship courses Open

Brane Leskošek, Alexia Cardona, Celia van Gelder, Patricia M. Palagi · 2023

This deliverable reports on the delivered data management (DM) and data stewardship (DS) training events across ELIXIR Nodes in the period from January 1, 2022 to June 30, 2023 as well as cumulative report of DM and DS training events from…

ELIXIR-CONVERGE D2.5 Report on the outreach activities and training activities produced Open

Patricia M. Palagi, Alexia Cardona, Celia van Gelder, Brane Leskošek · 2023

The scope of deliverable D2.5, part of ELIXIR-CONVERGE WP2 Task 2.4, is to provide an overview of the data management and stewardship related training and outreach activities that have been undertaken during the ELIXIR-CONVERGE project. EL…

ELIXIR-CONVERGE D4.3 Review of effectiveness of the Node Impact Assessment Toolkit Open

Corinne Martin, Kim De Ruyck, Ana Portugal Melo, C. T. Stansberg, Eva Alloza , et al. · 2023

An Impact Toolkit was created to support performance and impact evaluation in ELIXIR. The intended audience of this Toolkit is operators, developers and managers wishing to demonstrate and communicate the performance, impact, and ultimatel…

ELIXIR-CONVERGE D2.2 Report on the ready-to-use training materials for usage and rolling-out in Task 2.3 Open

Celia van Gelder, Brane Leskošek, Alexia Cardona, Patricia M. Palagi · 2023

Research data Management (RDM, also used interchangeably with Data Management/Data Stewardship, abbreviated as DM/DS) is central to the implementation of the FAIR (Findable Accessible, Interoperable, Reusable) and Open Science principles. …

ELIXIR-CONVERGE D5.3 Report on the dedicated training and capacity building activities Open

Brane Leskošek, Vanita Haurheeram, Federico Bianchini, Pinar Alper, Laura Portell-Silva , et al. · 2023

One of the objectives of WP5 was to identify the needs in terms of capacity building, in the context of the 6 use cases, and to develop strategy(ies) in collaboration with WP2 to address these needs. This was achieved in three steps: Creat…

Systems Biology in ELIXIR: modelling in the spotlight Open

Vítor A. P. Martins dos Santos, Mihail Anton, Barbara Szomolay, Marek Ostaszewski, Ilja C.W. Arts , et al. · 2022

In this white paper, we describe the founding of a new ELIXIR Community - the Systems Biology Community - and its proposed future contributions to both ELIXIR and the broader community of systems biologists in Europe and worldwide. The Com…

TiO2 Nanoparticles and Their Effects on Eukaryotic Cells: A Double-Edged Sword Open

Jan Gojznikar, Bogdan Zdravković, Marko Vidak, Brane Leskošek, Polonca Ferk · 2022

Nanoparticulate TiO2 (TiO2 NPs) is a widely used material, whose potential toxicity towards eukaryotic cells has been addressed by multiple studies. TiO2 NPs are considered toxic due to their production of reactive oxygen species (ROS), wh…

The future of food and nutrition in ELIXIR Open

Bachir Balech, Lorraine Brennan, Enrique Carrillo de Santa Pau, Duccio Cavalieri, Susan L. Coort , et al. · 2022

Non-communicable diseases are on the rise and are often related to food choices; nutrition affects infectious diseases too. Therefore, there is growing interest in research on public and personal health, as related to food, nutrition behav…

Community-driven ELIXIR activities in single-cell omics Open

Paulo Czarnewski, Ahmed Mahfouz, Raffaele Calogero, Patricia M. Palagi, Laura Portell-Silva , et al. · 2022

Single-cell omics (SCO) has revolutionized the way and the level of resolution by which life science research is conducted, not only impacting our understanding of fundamental cell biology but also providing novel solutions in cutting-edge…

ELIXIR-CONVERGE: D2.3 - 1st Report on delivered data management and stewardship courses Open

Brane Leskošek, Alexia Cardona, Celia van Gelder, Patricia M. Palagi, WP members · 2022

The scope of this deliverable is to report on the delivered training events across ELIXIR Nodes related to Data Management (DM) and Data Stewardship (DS). The delivered training events include both reruns of existing Node courses (that add…

The Carniolan Honeybee from Slovenia—A Complete and Annotated Mitochondrial Genome with Comparisons to Closely Related Apis mellifera Subspecies Open

Ajda Moškrič, Andraž Marinč, Polonca Ferk, Brane Leskošek, Mai‐Britt Mosbech , et al. · 2022

The complete mitochondrial genome of the Carniolan honeybee (Apis mellifera carnica) from Slovenia, a homeland of this subspecies, was acquired in two contigs from WGS data and annotated. The newly obtained mitochondrial genome is a circul…

Single Cell RNA Sequencing in Autoimmune Inflammatory Rheumatic Diseases: Current Applications, Challenges and a Step Toward Precision Medicine Open

Tadeja Kuret, Snežna Sodin‐Šemrl, Brane Leskošek, Polonca Ferk · 2022

Single cell RNA sequencing (scRNA-seq) represents a new large scale and high throughput technique allowing analysis of the whole transcriptome at the resolution of an individual cell. It has emerged as an imperative method in life science …

ELIXIR-SI tools & services Open

Urban Bren, Marko Cotman, Tomislav Dolenc, Sašo Džeroski, Polonca Ferk , et al. · 2022

Pulse pressure in patients with arterial hypertension in Slovenia Open

Marjetka Pal, Marjan Pajntar, Brane Leskošek, J. Drinovec, Polonca Ferk · 2021

Purpose: The aim of our study was to evaluate age- and gender-dependent pulse pressure (PP), systolic blood pressure (SBP), and diastolic blood pressure (DBP) distributions as well as their interconnected relationships in a large patient s…

ELIXIR-CONVERGE D2.1 Report on the identified training needs and a timeline for training courses Open

Alexia Cardona, Celia van Gelder, Patricia M. Palagi, Brane Leskošek · 2021

The scope of this deliverable is to report on the identified Data Management (DM) training needs across ELIXIR Nodes and present the initial plans and activities of ELIXIR-CONVERGE WP2 to address these needs. This report thus provides an o…

ELIXIR‐EXCELERATE: establishing Europe's data infrastructure for the life science research of the future Open

Jennifer Harrow, John M. Hancock, Niklas Blomberg, Niklas Blomberg, Søren Brunak , et al. · 2021

The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research Open

David Salgado, Irina M. Armean, Michael Baudis, Sergi Beltrán, Salvador Capella‐Gutierrez , et al. · 2020

Copy number variations (CNVs) are major causative contributors both in the genesis of genetic diseases and human neoplasias. While “High-Throughput” sequencing technologies are increasingly becoming the primary choice for genomic screening…

A framework to assess the quality and impact of bioinformatics training across ELIXIR Open

Kim Gurwitz, Prakash Singh Gaur, Louisa J. Bellis, Lee Larcombe, Eva Alloza , et al. · 2020

ELIXIR is a pan-European intergovernmental organisation for life science that aims to coordinate bioinformatics resources in a single infrastructure across Europe; bioinformatics training is central to its strategy, which aims to develop a…

<i>ELIXIR Training Platform Task 2: </i>Gap analysis, training materials development and training delivery Open

Fotis Psomopoulos, Celia van Gelder, Pascal Kahlem, Brane Leskošek, Jessica M. Lindvall · 2020

Training and Skills development: Resources from the ELIXIR’s Training Platform Open

Pascal Kahlem, Annalisa Milano, Brane Leskošek, Marko Vidak, Jure Dimec , et al. · 2020

Training Needs across ELIXIR in Management and Operations Open

Pascal Kahlem, Juan Arenas, Brane Leskošek, Corinne Martin, Sarah Morgan , et al. · 2020

Author Correction: Leveraging European infrastructures to access 1 million human genomes by 2022 Open

Gary Saunders, Michael Baudis, Regina Becker, Sergi Beltrán, Christophe Béroud , et al. · 2019

Leveraging European infrastructures to access 1 million human genomes by 2022 Open

Gary Saunders, Michael Baudis, Regina Becker, Sergi Beltrán, Christophe Béroud , et al. · 2019

The bio.tools registry of software tools and data resources for the life sciences Open

Jon Ison, Hans Ienasescu, Piotr Jaroslaw Chmura, Emil Rydza, Hervé Ménager , et al. · 2019

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