18,521 Works

ELIXIR-EXCELERATE

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.

METAkube – META-pipe over Kubernetes

Mayeul Marcadella, Alexander Agafonov, Igor Molchanov, Espen Robertsen & Nils-Peder Willassen
META-pipe is a specialized pipeline for assembly, annotation and analysis of marine metagenomic samples. Provided as a service to the ELIXIR community, it is an invaluable resource for metagenomics of the marine domain.
A new kubernetes-based implementation, coined METAkube, let us explore modern frameworks for big data and heterogenous scientific pipelines.

CORBEL: Harmonising access to Europe's biomedical research infrastructures

Christiane Hauk, Sonja Hansen, Frauke Leitner & Friederike Schmidt-Tremmel
A H2020 cluster project uniting 13 European biological and medical research infrastructures (BMS RIs), bringing together 37 partners offering cutting-edge technologies, biological samples and expertise to researchers.

EOSC-Life: Providing an open collaborative space for digital biology in Europe

Niklas Blomberg & Friederike Schmidt-Tremmel
A H2020 cluster project uniting 13 European life science research infrastructures (LS RIs), bringing together 46 + 17 partners to create an open collaborative digital space for life science in the European Open Science Cloud.

Viewing and sharing molecular dynamics simulations on the web using the MDsrv

Johanna K. S. Tiemann, Ramon Guixà-González, Alexander S. Rose & Peter W. Hildebrand
Molecular dynamics (MD) simulations are these days a well-established and widely used technique to investigate time-resolved motions of macromolecules such as G protein-coupled receptors (GPCR). Sharing of the resulting coordinate trajectories for visualization is complicated by their size, the requirement of having special software set-up and the knowledge of the software usage. However, in light of increasingly interdisciplinary research and remote collaborations, it is desirable to make sharing of MD trajectories easier to facilitate discussions...

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...

The role of OmpF and OmpC porins on the translocation of fluoroquinolones and their metallocomplexes across the outer membrane of E. coli

Raúl G. Saraiva, Matthew P. McCusker, Séamus Fanning, Paula Gameiro & Maria J. Feio
Background: OmpF and OmpC, the major outer membrane porins in E. coli, are believed to play a major role in the internalization of fluoroquinolones. Moreover, the quick development of bacterial resistance to these drugs has led to the need for their constant reinvention, with metalloantibiotics arising as a possible solution.

Methods: A battery of 8 E. coli BL21(DE3) mutants lacking OmpF, OmpC and/or OmpA was extensively characterized by PCR, RT-PCR and Western blotting. MIC values of...

ELIXIR-UK

Aidan Budd, Nicola Soranzo, Catherine Hunter & ELIXIR-UK Management Committee
ELIXIR-UK participates in activities across ELIXIR including: Providing two of the three ELIXIR portals (FAIRsharing for community standards, and TeSS for life science training courses and materials - both are ELIXIR-UK Node Services) Co-leading training and interoperability platforms Providing one of the four ELIXIR Core Data Resources (CATH) that is not EMBL-EBI based We are a distributed node involving collaboration between 15 different UK research institutions.

The Node contributes 15 Node Resources to the ELIXIR...

A PostgreSQL-based RDF/SPARQL engine not only for small-molecule data

Jakub Galgonek
One of the ELIXIR tasks is to make the published life-science data FAIR, which is often solved by using Semantic Web technologies. These technologies include the RDF framework for representing data, and the SPARQL language for querying these data. Although there are several RDF/SPARQL engines that can be freely used, none of them was fully suitable for our purpose of implementing a large database of small molecules in terms of performance, reliability and extensibility. To...

FAIR training working group

Caterina Barillari, Bérénice Batut, Melissa Burke, Victoria Dominguez Del Angel, Leyla Garcia, Kim Gurwitz, Mateusz Kuzak, Peter McQuilton, Patricia Palagi, Fotis Psomopoulos, Paivi Rauste, Gabriella Rustici & Allegra Via
FAIR Training Working Group has been first informally formed after the “How to make training FAIR” workshop held at the All Hands in Berlin in 2018. During the workshop, it has become clear that there are two different but interdependent topics (1) availability and findability of training materials about FAIR Data Stewardship, (2) making training resources FAIR. Within the WG two Task Forces has been initialised. Task Force 1 (TF1) has started with research into...

Federating human data using neXtProt SPARQL

Monique Zahn, Pierre André Michel, Alain Gateau, Amos Bairoch & Lydie Lane
The neXtProt platform (www nextprot org), developed at the SIB Swiss Institute of Bioinformatics the Swiss ELIXIR node, is a one stop shop for human proteins. neXtProt proposes solutions to explore, select and reuse available genomic, transcriptomic, mass spectrometry and antibody based proteomic data. The neXtProt team manually curates data from the literature (post translational modifications, variant phenotypes, protein protein interactions, etc and combines it with high quality omics data generated by systems biology projects...

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