Weekly Brief, 24 October 2022

This week's highlights

ECCB2022 | ELIXIR SME Forum in Sitges

As the partner organiser of ECCB2022, ELIXIR had a dedicated track, a workshop and an exhibition booth at the conference to showcase activities and services.
In collaboration with the Spanish ELIXIR Node, ELIXIR hosted the Innovation and SME Forum after ECCB2022.

Read the news

Follow updates on the European Health Data Space - EHDS HealthDat@EU Pilot

EHDS 2 pilot is now on Twitter and the full website will be coming soon.
Follow the projects Twitter account (@ehds2pilot) and subscribe to EHDS2 newsletter

Recommended reads

Assessing the Impact of SARS-CoV-2 Lineages and Mutations on Patient Survival

An ELIXIR-CONVERGE paper

More than two years into the COVID-19 pandemic, SARS-CoV-2 still remains a global public health problem. Successive waves of infection have produced new SARS-CoV-2 variants with new mutations for which the impact on COVID-19 severity and patient survival is uncertain. A significant association of B.1.1.7, the alpha lineage, with patient mortality was found upon adjustment by all the covariates known to affect COVID-19 prognosis. Moreover, survival analysis of mutations in the SARS-CoV-2 genome revealed 27 of them were significantly associated with higher mortality of patients. This study illustrates how a combination of genomic and clinical data can provide solid evidence for the impact of viral lineage on patient survival.


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Hidden neural networks for transmembrane protein topology prediction

An ELIXIR-GR paper

Hidden Markov Models (HMMs) are amongst the most successful methods for predicting protein features in biological sequence analysis. However, there are biological problems where the Markovian assumption is not sufficient since the sequence context can provide useful information for prediction purposes. Several extensions of HMMs have appeared in the literature in order to overcome their limitations. The authors apply a hybrid method that combines HMMs and Neural Networks, termed Hidden Neural Networks (HNNs), for biological sequence analysis in a straightforward manner. The HNNs show performance gains compared to standard HMMs and the respective predictors outperform the top-scoring methods in the field.

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Updates from Nodes

Registration for the 1st BioHackathon Germany is open

12-16 December 2022 | Wittenberg, Germany
Registration deadline: 20 November 2022

de.NBI | ELIXIR-DE is holding the 1st BioHackathon Germany in December, there are 11 projects involved.

More information and registration

BioData.pt | ELIXIR-Portugal All Hands

BioData.pt | ELIXIR-PT held its All Hands on 28-30 September 2022. The meeting consisted of the assessment of BioData.pt | ELIXIR-PT by its external scientific advisory board and a technical meeting dedicated to an overview of the infrastructures services and resources and intensive discussions of the challenges and goals of BioData.pt | ELIXIR-PT.

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Updates from Platforms

Training Data Stewards for life sciences

BioData.pt | ELIXIR-PT, in collaboration with several other organisations, namely ELIXIR-NL and ELIXIR-SE has designed a program to train Data Stewards for life sciences. If you already know the basics about DM/DS and want to advance to the intermediate level, pre-register by contacting communityeventsmanager [at] biodata.pt.

More information

Updates from Communities

News updates on the Galaxy Community

• Outcomes of the European Galaxy Days

  On 3-7 October 2022, more than 130 registrants from around the world participate in the European Galaxy Days.
  
  Read the news

• Galaxy as a cross-EOSC platform

  The Galaxy community has been working on another scientific collaboration agreement between the European Open Science Cloud (EOSC) projects, EOSC-Pillar and EOSC-Life.
  
  Read the news

• Research Data Management in Galaxy

  Galaxy has developed a data management strategy for reproducing and reusing data and analysis.
  
  Read more

Invitation to join the ELIXIR Single Cell Omics Community F2F/hybrid Meeting

5 & 6 December 2022 | Hybrid - Stockholm, Sweden
Registration deadline: 14 November (F2F) | 4 December (virtual)

This hybrid meeting is the first F2F for members of the ELIXIR Single Cell Omics Community. It will address general Community updates, short presentations and an outlook on activities and actions from the Community Implementation Study, starting in January 2023.

Find out more and register now

Updates from Other Initiatives

Registration open: National-level experiences of pathogen-related data sharing in pandemic times and beyond

25 November 2022 | Virtual

The aim of this meeting is to exchange national experiences on data sharing during the COVID-19 pandemic and learn about ongoing projects in relation to COVID-19 and other pathogen data sharing/genomic surveillance.

More information and registration

BY-COVID workshop: BEACON - How to make sensitive data discoverable

2-3 November 2022 | Virtual
Registration deadline: 31 October 2022

The EGA team is organising a training workshop on BEACON - How to make sensitive data discoverable. The training workshop consists of two sessions, one on each day:

• Session 1: Understanding Beacon and Mapping of By-COVID human data onto Beacon model
• Session 2: Deployment of Beacon on your dataset

More information and registration

Registration open for EOSC Symposium 2022

14-17 November 2022 | Prague, Czech Republic
Registration deadline: 2 November 2022

In EOSC Symposium 2022, there will be over 60 sessions covering topics related to EOSC implementation as well as EOSC-related projects and initiatives. The EOSC Future project will have a prominent place on the agenda.

More information and registration

Upcoming ELIXIR events & webinars

ELIXIR Training Courses & Webinars

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

ELIXIR Events and Conferences

BioHackathon Europe

7-11 November 2022 | Paris, France

Job vacancies

All vacancies are also published on the ELIXIR website (also including those from industry). If you need our help communicating your new open positions, you can submit a job advertisement and it will automatically appear on our newsletters. Go to our vacancy page to submit a job
 

Cancer Genomics Research Assistant

IRB Barcelona

Technical Coordinator

SIB Swiss Institute of Bioinformatics

Web developers

CRG

Senior scientist (m/f/d) - SILVA taxonomy curation

DSMZ

Senior scientist (m/f/d) - SILVA metadata curation

DSMZ