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ELIXIR Belgium

Newsletter October 2020
National coordination COVID-19 Data Portal
The European Commission and the EBI have launched the European COVID-19 Data Portal to link generated data and make it available for research. Although the focus is on virus data, linking of clinical data is also a high priority (taking privacy legislation into account of course).
 
ELIXIR Belgium is involved in the coordination at the national level. To assist in this data sharing effort, a national coordination team is formed and efforts are undertaken to identify where COVID-19 related data is generated in Belgium. Next to this small and agile coordination team, an advisory board is composed to capture a broad group of relevant disciplines. This group is open for additional members. Feel free to contact us for more information.
 
ENA upload tool for COVID-19 viral sequence data
Some background

The most commonly used repository to submit viral sequence data is GISAID. Today, there are 1.127 coronavirus sequences available in GISAID from Belgium. This repository collects only consensus sequence data and has restrictions on data reuse. As such, raw coronavirus sequence data remains largely unavailable and reuse of assemblies is limited.

The European COVID-19 platform and ELIXIR promote the European Nucleotide Archive (ENA) as a solution to provide access to both raw data and assemblies. ENA is an open platform providing a comprehensive record of the world’s nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation.
Facilitate upload to ENA

The coronavirus sequence data from Belgium has not found its way to ENA yet. Submitting data to deposition databases requires a learning curve and can therefore be time consuming at the first submission. To facilitate submission of viral sequence data to ENA, our team has developed an ENA upload tool. Further documentation and improving of the user friendliness of the tool is ongoing.

If you are interested to share COVID-19 data through ENA, do reach out to us to explore how we can assist.
Custom Galaxy training for DiSSCo researchers
In the framework of the “Connecting ESFRIs in Flanders project’ supported by the Flemish government, we organized a custom Galaxy training for scientists from DiSSCo (the research infrastructure on scientific collections). The Belgian Galaxy instance, useGalaxy.be - hosted at VSC - enables researchers to perform reproducible analysis of their data.

Next to the 1-day course illustrating how to use the Galaxy platform for variant discovery, phylogenetic analysis tools were made available in Galaxy. Researchers from the Botanic Garden Meise and the Research Institute Nature and Forest (INBO) attended this training. If you, your lab or your institute have the need for a specific Galaxy training, let us know.
 
Did you know
During the summer, the Intrinsically Disordered Protein Community conducted an open selection process to elect the two new co-leads of the Community: Damiano Piovesan (ELIXIR-IT) and Wim Vranken (ELIXIR-BE). They are joining Zsuzsanna Dosztanyi (ELIXIR-HU) to make up the Community’s leadership team.
Sequence and Structure Data Visualisation Survey
If you are interested in visualizing biological sequence and/or structure data, and want to give your opinion on what you are using and what is missing in current tools, you can give your input until the end of October. Take the survey

Your responses will help identify common visualization practices for displaying structural and functional annotations and determine any gaps that could form the basis of future work in the community. This survey is part of an ELIXIR 3D-Bioinfo community study in which Wim Vranken (VUB) is involved in.
 
Upcoming events
See the ELIXIR TeSS portal for all events organized by ELIXIR Nodes.


Seminar: Compelling data visualization with D3 (info)
Organized by the Belgium Research Software Engineers association
14 October 2020, online
 
ReproHack - A hackathon on reproducible data analysis (info)
Organized by ELIXIR Belgium and the VIB Bioinformatics Core
20 October 2020, online

Containers and Workflow Pipelines for reproducible and automated data analysis (info)
Organized by ELIXIR Belgium and the Centre for Genomic Regulation (CRG) of Barcelona
26-27 October 2020, online
 
Seminar: The role of software development in reproducible research (info)
Organized by the Belgium Research Software Engineers association
5 November 2020, online

Research Data Management in Life Sciences (info)
Organized by Ghent University and ELIXIR Belgium
9-10 November 2020, online

BioHackathon Europe 2020 (info)
9 -13 November 2020, online
 
Gentle hands-on introduction to Python programming (info)
Organized by ELIXIR Belgium and the VIB Bioinformatics Core
16, 23, 30 November 2020, online

International FAIR Convergence Symposium (info)
Organized by CODATA and GFISCO
30 November - 4 December 2020, online

Research Software Developers Day (info)
Organized by the VIB Bioinformatics Core and ELIXIR Belgium
3 December 2020, online
 
Label-free Proteomics data analysis in Galaxy (info)
Organized by the VIB Bioinformatics Core and ELIXIR Belgium
3-4 December 2020, online

Introduction to Git and Github (info)
Organized by ELIXIR Belgium
10 December 2020, online
@ELIXIRnodeBE @ELIXIRnodeBE
www.elixir-belgium.org www.elixir-belgium.org
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