Community-driven ELIXIR activities in single-cell omics

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 medical research. The rapid development of single-cell technologies has been accompanied by the active development of data analysis methods, resulting in a plethora of new analysis tools and strategies every year. Such a rapid development of SCO methods and tools poses several challenges in standardization, benchmarking, computational resources and training. These challenges are in line with the activities of ELIXIR, the European coordinated infrastructure for life science data. Here, we describe the current landscape of and the main challenges in SCO data, and propose the creation of the ELIXIR SCO Community, to coordinate the efforts in order to best serve SCO researchers in Europe and beyond. The Community will build on top of national experiences and pave the way towards integrated long-term solutions for SCO research. Keywor

Training bioinformaticians in High Performance Computing

In the last decade, bioinformatics has become an indispensable branch of modern science research, experiencing an explosion in financial support, developed applications and data collection. The growth of the datasets that are emerging from research laboratories, industry, the health sector, etc., are increasingly raising the levels of demand in computing power and storage. Processing biological data, in the large scales of these datasets, often requires the use of High Performance Computing (HPC) resources, especially when dealing with certain types of omics data, such as genomic and metagenomic data. Such computational resources not only require substantial investments, but they also involve high maintenance costs. More importantly, in order to keep good returns from the investments, specific training needs to be put in place to ensure that wasting is minimized. Furthermore, given that bioinformatics is a highly interdisciplinary field where several other domains intersect (such as biology, chemistry, physics and computer science), researchers from these areas also require bioinformatics-specific training in HPC, in order to fully take advantage of supercomputing centers. In this document, we describe our experience in training researchers from several different disciplines in HPC, as applied to bioinformatics under the framework of the leading European bioinformatics platform ELIXIR, and analyze both the content and outcomes of the course

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

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 circular closed loop of 16,447 bp. It comprises 37 genes (13 protein coding genes, 22 tRNA genes, and 2 rRNA genes) and an AT-rich control region. The order of the tRNA genes resembles the order characteristic of A. mellifera. The mitogenomic sequence of A. m. carnica from Slovenia contains 44 uniquely coded sites in comparison to the closely related subspecies A. m. ligustica and to A. m. carnica from Austria. Furthermore, 24 differences were recognised in comparison between A. m. carnica and A. m. ligustica subspecies. Among them, there are three SNPs that affect translation in the nd2, nd4, and cox2 genes, respectively. The phylogenetic placement of A. m. carnica from Slovenia within C lineage deviates from the expected position and changes the perspective on relationship between C and O lineages. The results of this study represent a valuable addition to the information available in the phylogenomic studies of A. mellifera-a pollinator species of worldwide importance. Such genomic information is essential for this local subspecies' conservation and preservation as well as its breeding and selection

Defining a lingua franca for the ELIXIR/GOBLET e-learning ecosystem

Today, the term e-learning is widely used in a variety of contexts. Many of us are familiar with concepts like Massive Open Online Courses (MOOCs), such as those provided by Coursera, Udacity, edX or MIT OpenCourseWare; Content- or Learning-Management Systems (CMSs, LMSs), like Moodle or Blackboard; Virtual Learning Environments (VLEs), like EMBER; problem and tutorial portals, such as Rosalind and Train online; repositories for uploading and hosting Educational Resources (ERs), such as that provided by GOBLET; ER aggregators that harvest and disseminate training information, such as TeSS; and so on. Resources like these are seamlessly discussed under the umbrella term ‘e-learning’; however, they are heterogeneous and do not mean the same thing from user, developer, trainer or content-provider perspectives. Confusion can therefore arise if those using the term generically have not grasped each other’s specific meanings. In the context of ELIXIR, this situation came to the fore in preparations for the EXCELERATE project, whose training programme (WP11) includes an explicit e-learning subtask (11.1.3) as part of the commitment to build an ELIXIR training infrastructure. The ultimate deliverable of the subtask is to develop an ELIXIR e-learning policy and deploy e-learning platform(s) at the ELIXIR level. But what does an ‘e-learning platform for ELIXIR’ mean? Is it an instance of a MOOC platform, a customised LMS, a bespoke VLE, an ER repository, an aggregator, or something else? Clarification of this question was important, because each of the possible answers has very different implementation and resource requirements. To try to address this question, and to facilitate communication both within ELIXIR, and between the ELIXIR and GOBLET trainer communities, an initial workshop – Defining an e-learning lingua franca – was held in Ljubljana (SI), 15-17 September 2015. At one level, the aim was to develop an overview of some of the e-learning approaches and applications developed or used by representatives from ELIXIR, GOBLET and other organisations – participants were therefore asked briefly to describe the systems they’d developed, to allow them, and their respective strengths and weaknesses, to be compared. At another level, the aim of the workshop was to try to converge on a common e-learning ‘language’, to help the ELIXIR and GOBLET trainer communities to communicate more coherently. To broaden the picture and gain a wider understanding of the challenges, a follow-up event was held during the GOBLET Annual General Meeting in Cape Town (ZA), 18-20 November 2015. Here, the outcomes of the first meeting were further discussed and refined. Gaining a clearer view of the current e-learning landscape, and consensus on what we collectively mean by e-learning, were the necessary first steps towards formulating appropriate e-learning strategies for ELIXIR and GOBLET, and suggesting solutions that can feasibly be implemented. In the event, the issues were more deep-rooted than we expected, and many additional discussions were needed. This paper reflects the results of those discussions and of the deliberations of the workshop participants

A multiscale model of the electrohysterogram the BioModUE-PTL project

The electrohysterogram (EHG) is a promising means of monitoring pregnancy and of detecting a risk of preterm labor. To improve our understanding of the EHG as well as its relationship with the physiologic phenomena involved in uterine contractility, we plan to model these phenomena in terms of generation and propagation of uterine electrical activity. This activity can be realistically modeled by representing the principal ionic dynamics at the cell level, the propagation of electrical activity at the tissue level and then the way it is reflected on the skin surface through the intervening tissue. We present in this paper the different steps leading to the development and validation of a biophysics based multiscale model of the EHG, going from the cell to the electrical signal measured on the abdomen

Ten steps to get started in Genome Assembly and Annotation

As a part of the ELIXIR-EXCELERATE efforts in capacity building, we present here 10 steps to facilitate researchers getting started in genome assembly and genome annotation. The guidelines given are broadly applicable, intended to be stable over time, and cover all aspects from start to finish of a general assembly and annotation project. Intrinsic properties of genomes are discussed, as is the importance of using high quality DNA. Different sequencing technologies and generally applicable workflows for genome assembly are also detailed. We cover structural and functional annotation and encourage readers to also annotate transposable elements, something that is often omitted from annotation workflows. The importance of data management is stressed, and we give advice on where to submit data and how to make your results Findable, Accessible, Interoperable, and Reusable (FAIR).ELIXIR-EXCELERATE is funded by the European Commission within the Research Infrastructures Programme of Horizon 2020 [676559]

Leveraging European infrastructures to access 1 million human genomes by 2022

Human genomics is undergoing a step change from being a predominantly research-driven activity to one driven through health care as many countries in Europe now have nascent precision medicine programmes. To maximize the value of the genomic data generated, these data will need to be shared between institutions and across countries. In recognition of this challenge, 21 European countries recently signed a declaration to transnationally share data on at least 1 million human genomes by 2022. In this Roadmap, we identify the challenges of data sharing across borders and demonstrate that European research infrastructures are well-positioned to support the rapid implementation of widespread genomic data access

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

Bioinformaticians and biologists rely increasingly upon workflows for the flexible utilization of the many life science tools that are needed to optimally convert data into knowledge. We outline a pan-European enterprise to provide a catalogue () of tools and databases that can be used in these workflows. bio.tools not only lists where to find resources, but also provides a wide variety of practical information

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

Bioinformaticians and biologists rely increasingly upon workflows for the flexible utilization of the many life science tools that are needed to optimally convert data into knowledge. We outline a pan-European enterprise to provide a catalogue (https://bio.tools) of tools and databases that can be used in these workflows. bio.tools not only lists where to find resources, but also provides a wide variety of practical information

Leveraging European infrastructures to access 1 million human genomes by 2022 (vol 20, pg 693, 2019)

An amendment to this paper has been published and can be accessed via a link at the top of the paper.status: publishe