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Weekly news 16.12.2019

The last Gallantries Project face-to-face meeting took place at INAB | CERTH, Thessaloniki, Greece 9-10 December. During this meeting the R and RStudio lessons within Galaxy were refactored, along with a pop-up course on making volcano plots in R. Helena Rache put out a blog-post on this, and materials were shared by the Galaxy twitter channel.

ELIXIR-CZ have created a very engaging animated video all about ELIXIR and the Czech Node. Features FAIR data and ELIXIR AAI. Well worth a watch! 

ELIXIR Finland has published a new article about ELIXIR Compute Platform for life and health sciences. Read to find out about how the Compute Platform has helped research across multiple ELIXIR Communities. 

The Dutch Techcentre for Life Sciences (DTL) have released their 2019 highlights newsletter. Read on to find out about their activities with ELIXIR and beyond. 

FAIRplus Innovation and SME Forum: Implementing FAIR data principles in industrial life science research
29 January 2020 | Hinxton, Cambridge, UK

Innovation and SME Forum: Data Driven Innovation in the Agritech Sector
24 -25 March 2020 | Lyon, France

Weekly news 09.12.2019

The Finnish IT Centre for Science (CSC) have published a new video: 'How do I authorise access to my sensitive data?'. Explaining the process of making your data open, the data access committee and authorisation tool. 

recent article published in Science on how GDPR affects international biomedical research features comments from members of the Spanish National Bioinformatics Institute (INB) including Deputy Head of Node for ELIXIR Spain Salvador Capella. 

The European Open Science Cloud (EOSC) Life project recently released their second newsletter. You can sign up here to find out about their news and events. 

Best practices in research data management and stewardship 27 - 28 January 2020 | Esch-sur-Alzette, Luxembourg

Data visualisation for biology: A practical workshop on design, techniques and tools 16 - 20 March 2020 | Hinxton, Cambridge, UK


Weekly news 02.12.2019

Galaxy have loaded fully consented genome sequences from 10 individuals from the Personal Genomes Project (PGP) along with transcriptomic and methylomic data in collaboration with PGP to facilitate training within the platform. These data are open and available to be looked at within Galaxy and please feedback to if you require specific analysis on this data.

The ELIXIR Tools Platform published a paper "Towards FAIR principles for research software". The paper analyses how FAIR principles can be applied to software, as opposed to data. It also explores whether existing FAIR principles can be applied directly to software, or where they need to be adapted or reinterpreted. This publication coincides with the launch of website, which provides recommendations on ways to improve the quality and reproducibility of software.

The programme of SIB training courses for 2020 is now online. Over 20 courses are already planned, and lots more are yet to come!  The topics covered span areas such as NGS and other omics data analysis, single-cell, statistics, programming, machine learning, and several SIB resources.




Weekly news 25.11.2019

The ELIXIR TeSS portal has a variety of interesting events and courses organised by the ELIXIR Nodes.

ELIXIR events

Webinar: Nextflow: Introduction and practical demonstration
TODAY 25 November 2019 | 11:00 CET | Webinar

Online: Training Platform "Ask us anything"
27 November 2019 | Teleconference

ELIXIR Innovation and SME Forum: Data management in the life sciences - a driver for innovation
27 - 28 November 2019 | Milan, Italy

Introduction to statistics (in R) 
20 - 23 January 2020 | Lausanne, Switzerland

FAIRplus Innovation and SME Forum: Implementing FAIR data principles in industrial life science research
29 January 2020 | Hinxton, Cambridge, UK

CORBEL - Data visualisation in Biology (DEADLINE for applications 29 November)
16 - 20 March 2020 | Hinxton, Cambridge, UK

gProfiler is now running on Galaxy at and

gProfiler (  is a toolset for functional enrichment analysis and conversions of gene lists that is now available also at Galaxy platform. Galaxy is meant for supporting data intensive research in a convenient manner through building and using custom workflows.

Biological data analysis often deals with lists of genes arising from various studies. The gProfiler toolset is widely used for finding biological categories enriched in gene lists, conversions between gene identifiers and mappings to their orthologs. The mission of gProfiler is to provide a reliable service based on up-to-date high quality data in a convenient manner across many evidence types, identifier spaces and organisms.

gProfiler relies on data retrieved from Ensembl database and fungi, plants or metazoa specific versions of Ensembl Genomes, and parasite specific data from WormBase ParaSite. In addition to Gene Ontology, supported data sources include KEGG, Reactome, WikiPathways, TRANSFAC, miRTarBase, Human Protein Atlas, CORUM and HP.

gProfiler supports close to 500 organisms and accepts hundreds of identifier types.

gProfiler has been supporting developers by offering a standardized access through public APIs. The usage of APIs was simplified by wrapping them into Python and R packages. The latter, `gprofiler2` (which was published as a Conda Forge package named `r-gprofiler2`), was wrapped to be used as a set of Galaxy tools:

  • gProfiler GOSt performs functional enrichment analysis, also known as over-representation analysis (ORA) or gene set enrichment analysis, on input gene list; in addition to the detailed tabular results, it can also create a Plotly graph with the Manhattan plot very similar to the one shown by the web tool.
  • gProfiler Convert enables to convert between various gene, protein, microarray probe and numerous other types of namespaces
  • gProfiler Orth translates gene identifiers between organisms
  • gProfiler SNPense maps SNP rs-codes to gene names, chromosomal coordinates and variant effects
  • gProfiler Random fetches a (not actually random) list of gene identifiers; useful for testing purposes.

gProfiler Galaxy toolset was admitted to the Galaxy Tools IUC. It is distributed via the ToolShed and can be installed as a bundle with the gProfiler tool suite repository.

gProfiler is part of the ELIXIR infrastructure. It belongs to the portfolio of ELIXIR Recommended Interoperability Resources.

gProfiler is developed and maintained in Estonia, at the University of Tartu, Institute of Computer Science, BIIT research group. It is an ELIXIR Estonia service.

Our latest publication of the g:Profiler tool - Uku Raudvere, Liis Kolberg, Ivan Kuzmin, Tambet Arak, Priit Adler, Hedi Peterson, Jaak Vilo: g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update) Nucleic Acids Research 2019; doi:10.1093/nar/gkz369 

Weekly news 21.10.2019

The slides and recording of the presentation on the ELIXIR Beacon & Beacon Network as a service are now available on the ELIXIR website.

ELIXIR Innovation and SME forum highlights from 'Distributed data analysis - the (health) data train' in Utrecht are available in the industry news release.

DNAstack have launched Clinical Evidence Beacons, extending from the GA4GH approved Beacon standard, as detailed in their latest news release.

We're pleased to announce the publication of the Intrinsically Disordered Protein (IDP) community's white paper in the ELIXIR F1000 channel. 

FAIDARE, the Plant Data Lookup service, is now fully operational both with Phenotyping and Genotyping data! Five data repositories from EBI, INRA, VIB, CIRAD and iBET are connected to this service, and others from Europe and beyond will be available soon.

BrAPI, the plant Breeding API, has a new publication out in Bioinformatics: BrAPI-an application programming interface for plant breeding applications.

We are delighted to announce a Memorandum of Understanding between FAIRsharing and DataCite to identify a set of criteria for the recommendation of research data repositories for the benefit of the broader research community. This project will be used to improve the recommendations that FAIRsharing provides to journal publisher and funder policy makers. 

Are you attending ICSB in Japan this year? De.NBI are hosting a full day satellite workshop on 31 October - "COMBINE & de.NBI Tutorial: Modelling and simulation tools in systems biology" with an impressive speaker lineup and agenda that still has a few spots remaining for free registration. 

EMBL-EBI have launched a new sister resource to the GWAS catalog for Polygenic scores - the PGS Catalog. As a new resource, they are seeking input into how to develop the resource to meet user needs. Please fill in and share their survey. You can find out more from this twitter thread.

ELIXIR Innovation and SME Forum: Data management in the life sciences - a driver for innovation
27 - 28 November 2019 | Milan, Italy

EMBO practical course: Integrative modelling of biomolecular interactions
10 - 15 May 2020 | Izmir, Turkey

Weekly news 14.10.2019

Take a look at our news release, ELIXIR as a global actor in bioinformatics training, to find out about how the ELIXIR Training Platform is supporting training across the world. 

Can you can help drive the open source software community and make a positive contribution by taking part in Hacktoberfest 2019? Anyone and everyone is welcome to participate!

The final report of the project Towards a community-endorsed data steward profession for life science research, funded by ZonMw, DTL/ELIXIR-NL, UMC Groningen, Radboud University and UMC Utrecht is out now. Full details on the project can be found on the Zenodo website.

ELIXIR Finland have published a new case study on using AI for health risk assessments, with a specific focus on cardiovascular disease, presenting work by Andrea Ganna at FIMM.

EJP-RD Workshop and Hackathon: Molecular pathways for rare diseases - (FAIR) data analysis
26 - 29 November 2019 | Maastricht, Netherlands

ELIXIR Innovation and SME Forum: Data management in the life sciences - a driver for innovation
27 - 28 November 2019 | Milan, Italy

Gentle hands-on introduction to Python programming
9 - 10 January 2019 | Leuven, Belgium

Helis Academy - FAIR Data Stewardship course by DTL in Utrecht Nov 2019

From 4-6th November, 2019, we will give another round of the Helis Academy - FAIR Data Stewardship course:  

FAIR Data Stewardship – digital data scholarship for life scientists

The target audience is life scientists – from industry and academia – and graduate students in the Life Sciences who wish to improve their digital scholarship on data handling. Some basic experience with programming and scripting languages like python, perl, R, matlab, etc. are an advantage, but not needed. The course is also relevant for Data Stewards who are supporting the life science researchers.

The course will introduce the trainees to important concepts of data stewardship. We start with a general introduction covering the data life cycle, the FAIR principles and a definition of data stewardship and data stewards.

The course will introduce the trainees to important concepts of data stewardship. We start with a general introduction covering the data life cycle, the FAIR principles and a definition of data stewardship and data stewards.

We will pass the stages of the data life cycle in more detail in the training modules of this 3 day course.

  • Day 1: Why use a data management plan and what for? On day one trainees will investigate data management plans, which types are there and how they should be used. 
  • Day 2: Mastering the data chaos during the research phase. On day two the course highlights how to work with data during the research phase, explaining how to create well formatted data which helps in the second module of day two to make data interoperable already during the active research phase.
  • Day 3: Boost your visibility and get cited for your data! On day three trainees will have an in-depth at persistent identifiers, different use cases and types of identifiers. Finally we are closing the data life cycle by making data fit for sharing, archiving and publishing. The training is organised by DTLand delivered as a joint effort by DTL partners.


You can find all the information, including the full programme and registration possibilities here: This course is part of the Data Analysis and Stewardship theme of Helis Academy and is organised by DTL and DTL collaborators. Info about other courses in the theme of Data Analysis and Stewardship can be found on the Helis Academy website and on the Helis Academy page on the DTL website.


Weekly news 23.09.2019

The Partnership for Advanced Computing in Europe (PRACE) have launched their 20th call for Proposals for Project Access. The call enables people to apply for access to high powered computer (Tier-0) systems. This year the applications are also open to Industry. Deadline 29 October 2019. 

The Data Platform have released a new paper in our F1000 channel "Understanding life sciences data curation practices via user research".   

ELIXIR Innovation and SME Forum: Distributed data analysis - the {health} data train 10 - 11 October 2019 | Utrecht, Netherlands


Weekly news 16.09.2019

ELIXIR Estonia together with Estonian Scientific Computing Infrastructure (ETAIS) has the first GDPR seminar today (16th of September). Futher information is available at 

We are pleased to announce three new ELIXIR Communities:

  • 3D-BioInfo
  • Intrinsically Disordered Proteins
  • Microbial Biotechnology

Please read our latest news release to find out more about the aims of these Communities and who is involved. 

The Pistoia Alliance FAIR/Ontologies Mapping (OM) project 'Communities of Interest' opens the first of its monthly webinar series with “Progress towards commercial FAIR data product and services” by Ted Slater this coming Thursday 19th September 2019 15:00 - 16:00 BST, join the meeting here.

Abstract: Elsevier is a global information analytics business that helps institutions and professionals advance healthcare and open science to improve performance for the benefit of humanity. In this webinar, we will discuss how Elsevier is increasingly leveraging the FAIR Guiding Principles to improve its products and services to better serve the scientific community. Ted is one of the authors on the seminal 2016 FAIR guiding principles paper. He has worked extensively within pharma R & D and more recently for providers of data analytics. 

Fotis Psomopoulos (ELIXIR-GR) has been selected to be an Research Data Alliance (RDA) Europe Ambassador for Bioinformatics. Part of his activities in this role will be to act as the formal RDA liaison for the ELIXIR Training Platform, with an additional focus on early career researchers at the intersection of Life Sciences and RDA.

ELIXIR Finland have recently published a new user case study on Targeted treatment for venous diseases with vascular system modelling, which details a collaboration with academics in Belgium as well as a Finnish start up microfluidics company, FinnAdvance. 

The National University of Ireland (NUI) Galway have been awarded €13 million for a new centre for Graduate Research Training in Genomics data science. The funding was awarded from the Science Foundation Ireland to train 115 PhD students over the next seven years. The centre is led by Prof. Cathal Seoighe, who is ELIXIR’s Training Coordinator for Ireland.