7,226 Works

EC projects with ELIXIR Hub involvement

Hannah Hurst
A summary of European Commission H2020 and Innovative Medicines Initiative (IMI) projects with ELIXIR Hub involvement.

These projects have received funding from the European Union’s Horizon 2020 research and innovation programme.

ELIXIR tools platform: software best practices

Mateusz Kuzak, Jennifer Harrow, Allegra Via & Fotis Psomopoulos
ELIXIR is an intergovernmental organization that brings together life science resources across Europe. These resources include databases, software tools, training materials, cloud storage, and supercomputers. One of the goals of ELIXIR is to coordinate these resources so that they form a single infrastructure. This infrastructure makes it easier for scientists to find and share data, exchange expertise, and agree on best practices. ELIXIR's activities are divided into the following five areas Data, Tools, Interoperability, Compute...

Proof-of-concept implementation of human genomics variant calling pipeline using BioContainers and Galaxy

Giacomo Tartari, Salvador Capella Gutierrez, Castrense Savojardo, Pier Luigi Martelli & Rita Casadio
We present a proof-of-concept workflow from Laurie et al 2016, based on BioContainers and Galaxy. It includes one aligner, one BAM processor and one variant caller.
More specifically: Burrows Wheeler Aligner (BWA) is used to map NGS reads on the reference genome, the samtools and bcftools packages to process the BAM files and call variants, respectively. The tools, installed from the main Galaxy toolshed, were configured manually with Biocontainers images.

Containerized workflows provides a prominent advantage: the...

Setting up a Galaxy platform in a HPC infrastructure for genomics implementation into diagnosis routines for a health reference center

Miguel Juliá, Sara Monzón Fernández, Luis Chapado, Angel Zaballos & Isabel Cuesta
The Health Institute Carlos III (ISCIII) is the main Public Research Entity funding, managing and carrying out biomedical research in Spain. From its Bioinformatics Unit (BU-ISCIII), we give support to a great variety of research groups with different needs and expertise, and also external researchers from universities and public hospitals and their associated research centers. In order to provide a unified and user friendly platform to execute standard genomics analysis, use our in-house tools and...

Life cycle decisions in Mycobacteriophage MPhalcon

Alec Griffith, Raveena Mann, Riley Spurling, Andrew Lund, Krisanavane Reddi, Jordan Moberg Parker & Amanda Freise
Bacteriophages are the most abundant organism in the biosphere and are influential in soil ecosystems, affecting many biogeochemical cycles. Through horizontal gene transfer, temperate bacteriophages, which replicate via lytic or lysogenic life cycles, exchange genomic information with hosts. This affects bacteria-phage coevolution, genetic diversity, and microbial community structure. This study explored the conditions and parameters that influence lytic-lysogenic life cycle decisions of temperate mycobacteriophages, such as incubation at increasing temperatures and exposure to ultraviolet radiation,...

WES-ELIXIR: A Language-Agnostic Execution Service for Bioinformatics Workflows

Foivos Gypas, Jaroslaw Surkont, Kevin Sayers, ELIXIR Switzerland, ELIXIR Finland, ELIXIR Hub, ELIXIR Germany, ELIXIR Italy, Torsten Schwede, Mihaela Zavolan & Alexander Kanitz
The availability of software solutions enabling the reuse and rapid application of computational workflows is essential for handling the dramatically accumulating volumes of genomics and imaging data in biomedical research and the healthcare sector. Specifically, scientists and healthcare professionals need easy and secure access to public and controlled data, as well as distributed interoperable platforms on which they can be analyzed. To facilitate this process, international organizations such as ELIXIR and the Global Alliance for...

Tool prediction in Galaxy workflows using deep learning

Anup Kumar & Björn Grüning
Galaxy workflows are scientific data processing pipelines for performing and reproducing data analyses. The workflows are complex and difficult to create from a suite of 2,000+ tools available in Galaxy, especially for new Galaxy users. In order to make creating workflows easier, faster and less error-prone, a recommendation system was developed to predict the following tools. The predictive system analyses the complete set of workflows available on Galaxy’s European server using a deep learning approach...

Applying FAIR to InterMine

Daniela Butano, Justin Clark-Casey, Sergio Contrino, Josh Heimbach, Rachel Lyne, Julie Sullivan, Yo Yehudi & Gos Micklem
InterMine is a platform to integrate and access life sciences data, providing a user-friendly web interface and RESTful web services. Whilst InterMine comes with a core data model for common biological entities and loaders for popular data sources and file types, different deployments can extend these components to publish any type of data.
InterMine currently includes some FAIR principles such as search and structured query functionalities, web services, cross-references to other InterMine instances and resources, but,...

Elixir-SE – the Swedish node

Bengt Persson, Mikael Borg, Henrik Lantz, Niclas Jareborg, Jonas Hagberg, Jessica Lindvall, Fredrik Levander, Jessica Lindberg, Kalle Von Feilitzen, Per Oksvold, Johan Viklund, Pontus Freyhult, Malin Ahlberg, Andreas Kähäri, Martin Norling, Nanjiang Shu, Jon Ander Novella, Dimitrios Bampalikis, Yvonne Kallberg, Jacques Dainat, Mahesh Binzer-Panchal, Lucile Soler, Åsa Björklund, Olga Dethlefsen, Roy Francis … & Kim Kultima
NBIS (National Bioinformatics Infrastructure Sweden), forming the SciLifeLab Bioinformatics platform, provides excellence in bioinformatics support to researchers in Sweden, enabling world-class life science by offering support, infrastructure and advanced training. NBIS constitutes the Swedish node in Elixir. NBIS is a distributed infrastructure formed as a consortium of major Swedish universities with ~80 staff placed at all sites.

Sweden has been active since the start of Elixir, contributing with the Elixir Core Data Resource Human Protein Atlas...

Predicting gene expression from histone modifications and chronological age by RNA-Seq data using Galaxy machine learning tools

Alireza Khanteymoori & Anup Kumar
Machine learning algorithms are available in Galaxy as tools. These are wrapped around the scikit-learn machine learning package. Using these machine learning tools, we demonstrate how gene expression can be predicted using histone modification signals and how RNA-Seq data can be used to predict chronological age.

Assessing CNN and RNN models to classify scientific literature into UniProt entry categories

Julien Knafou, Douglas Teodoro, Cecilia Arighi & Patrick Ruch
In the UniProt Knowledgebase (UniProtKB), publications providing evidence for a specific protein annotation are organized across different categories such as function, interaction and expression. The current document categorization approach relies on the information provided by the original source. To provide a more effective way of categorizing computationally mapped bibliography in UniProt, we developed an automatic classification method using the evidence available in the collection.

The main challenge to classify publications at the protein accession level...


Juan Arenas & Hannah Hirst
Presentation of the ELIXIR-EXCELERATE project, its structure, objectives and achievements. Presented at the ELIXIR All Hands meeting 2019 in Lisbon, Portugal.

FAIRplus project

Serena Scollen & Hannah Hurst
Presentation of the objectives and activities of the FAIRplus project at the ELIXIR All Hands meeting 2019 in Lisbon, Portugal.

The de.NBI / ELIXIR-DE Training Network

Daniel Wibberg
The 'German Network for Bioinformatics Infrastructure' (de.NBI) provides bioinformatics services and training to users in life sciences research, industry and biomedicine. Training activities of de.NBI are focused on supporting and training end users. Life science researchers will thus be enabled to exploit their data more effectively by applying tools, standards and compute services provided by de.NBI. To effectively coordinate training courses of the consortium, de.NBI has established the Special Interest Group 3 (SIG3 - Training...

Data stewardship wizard

Robert Pergl, Marek Suchánek, Jan Slifka, Vojtěch Knaisl, Rob Hooft & Mateusz Kuzak
The development of the Data Stewardship Wizard is a project that is ongoing since 2016.The Wizard gets more and more attention in life sciences as well as other domains where scientists need to efficiently work with data as a key element of their projects. In the last year, we released a new generation of the Wizard with brand new features and increased usability. This development has largely been done as part of the ELIXIR Implementation...

EOSC Life: Creating EOSC for the life sciences

Niklas Blomberg
Presentation of the cluster project EOSC Life at the ELIXIR All Hands meeting 2019 in Lisbon, Portugal.


Serena Scollen
Presentation of the FAIRplus project at the ELIXIR All Hands meeting 2019 in Lisbon, Portugal. The FAIRplus project aims to develop tools and guidelines for making life science data FAIR (Findable, Accessible, Interoperable, Reusable).

Future EC funding landscape

Andrew Smith
Presentation about the upcoming funding opportunities for ELIXIR and research infrastructures in general from the European Union research funding programmes. Presented at the ELIXIR All Hands meeting 2019 in Lisbon, Portugal.

Integration​ ​and​ ​standardisation​ ​of​ ​intrinsically​ ​disordered​ ​protein​ ​data

Alan Bridge, Norman Davey, Zsuzsanna Dosztanyi, Rob Finn, Maria Martin, Sandra Orchard, Silvio Tosatto & Sameer Velankar
Presentation of the ELIXIR Implementation Study 'Integration and standardization of intrinsically disordered protein data' at the ELIXIR All Hands meeting 2019 in Lisbon, Portugal.

Extending open proteomics data analysis pipelines in the cloud

Juan Antonio Vizcaíno
Presentation of the ELIXIR Implementation Study 'Extending open proteomics data analysis pipelines in the cloud' at the ELIXIR All Hands meeting 2019 in Lisbon, Portugal.

Integrating reference taxonomic databases for metabarcoding and metagenomics identification

Jeena Rajan
Presentation of the ELIXIR Implementation study 'Integrating reference taxonomic databases for metabarcoding and metagenomics identification' at the ELIXIR All Hands meeting 2019 in Lisbon, Portugal.

Data Validation

Mélanie Courtot & Frederik Coppens
Presentation of the ELIXIR Implementation Study 'Data Validation' at the ELIXIR All Hands meeting 2019 in Lisbon, Portugal

FAIRCDR: An Elixir Implementation Study to examine the FAIRness of the ELIXIR Core Data Resources

Michel Dumontier
Presentation of the ELIXIR Implementation study FAIRness of the current ELIXIR Core resources at the ELIXIR All Hands meeting 2019 in Lisbon, Portugal.

ELIXIR Contextual Data Clearinghouse

Jeena Rajan
Presentation of the ELIXIR Implementation Study 'Establishment of an ELIXIR Contextual Data Clearinghouse' at the ELIXIR All Hands meeting 2019 in Lisbon, Portugal.

Registration Year

  • 2015
  • 2016
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  • 2018
  • 2019

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