Weekly Brief, 27 June 2022

This week's highlights

New Head of Operations joining ELIXIR in September

Ivana Ilijai Veri, currently the Chief Operations Officer of CESSDA office in Bergen, will be joining ELIXIR as our new Head of Operations starting 1 September. She will overlap with Susanna until the end of the year ensuring a smooth transition.

Recorded event: Show and Tell - ELIXIR Strategic Implementation Study on Impact


In last week's Show and Tell, ELIXIR Greece gave a team presentation on their work in relation to scientific impact. The slides and recording are available online:

Recommended reads

AGAMEMNON: an Accurate metaGenomics And MEtatranscriptoMics quaNtificatiON analysis suite

An ELIXIR-GR paper


This paper introduces AGAMEMNON for the acquisition of microbial abundances from shotgun metagenomics and metatranscriptomic samples, single-microbe sequencing experiments, or sequenced host samples. AGAMEMNON delivers accurate abundances at genus, species, and strain resolution. It incorporates a time and space-efficient indexing scheme for fast pattern matching, enabling indexing and analysis of vast datasets with widely available computational resources. Host-specific modules provide exceptional accuracy for microbial abundance quantification from tissue RNA/DNA sequencing, enabling the expansion of experiments lacking metagenomic/metatranscriptomic analyses. AGAMEMNON provides an R-Shiny application, permitting performance of investigations and visualizations from a graphics interface.


Read more

PLAZA 5.0: extending the scope and power of comparative and functional genomics in plants

An ELIXIR-BE paper

PLAZA is a platform for comparative, evolutionary, and functional plant genomics. It makes a broad set of genomes, data types and analysis tools available to researchers. The PLAZA 5.0 release contains information for 5,882,730 genes, and offers pre-computed gene families and phylogenetic trees for 5,274,684 protein-coding genes. This latest release also comes with a set of new and updated features: a new BED import functionality for the workbench, improved interactive visualizations for functional enrichments and genome-wide mapping of gene sets, and a fully redesigned and extended API. Taken together, this new version offers extended support for plant biologists working on different families within the green plant lineage and provides an efficient and versatile toolbox for plant genomics. All PLAZA releases are accessible from the portal website.

Read more

Updates from Nodes

EMBL-EBI 2021 Highlights Report


The EMBL-EBI 2021 Highlights Report (previously known as Annual Report) is now live on EMBL-EBI website.

Read the report

Bioinformatics for Biobusiness event: Accessing biomedical data for data analysis

6 July 2022 | Manchester, UK


The forum is jointly hosted by EMBL-EBI, MDC and UKRI. It provides an opportunity for delegates from the commercial sector to explore practical solutions for accessing health data.

For more information

ELIXIR Swedish Node Training report


Looking back on the activities in the previous 2 years, the Swedish ELIXIR Node has published a Training Report, deposited on F1000, showcasing the breadth of advanced training activities, connections and engagements.

Read the report

Updates from Platforms

Communities & Platforms - Training gap analysis


We would like your input to help us identify potential gaps in current training in Life Sciences across Europe, and to continue taking measures to fill the gaps identified with appropriate training.

Fill out the survey

Updates from Communities

3D BioInfo Community F2F/hybrid meeting

2-4 November 2022 | EMBL-EBI, UK (hybrid)

Deadline: 31 July 2022


The ELIXIR 3D BioInfo Community is inviting its Community members to participate in and contribute to the 3D BioInfo Community F2F/hybrid meeting (Annual General Assembly). This will be a hybrid meeting with F2F attendance at EMBL-EBI, Hinxton. Funding, including travel, accommodation and (food) expenses is available for a number of selected Community members.

Register and submit an abstract by 31 July 2022

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 3D BioInfo webinars: Impact of AlphaFold on research and development
28 June 2022 | 13:30 - 15:00 BST | Online

 

Summer school on genetic epidemiology

29 June - 2 July 2022 | Davos, Switzerland

Training course on facilitation and moderation skills

7-8 July 2022 | Hague, Netherlands


SIB course Advacned Programming with R
29-31 August 2022 | Lausanne, Switzerland

ELIXIR Events and Conference

ELIXIR Innovation and SME Forum: Data driven innovation in healthcare diagnostics
22 September 2022 | 10:00 to 19:00 CEST | Barcelona, Spain


ELIXIR Bioinformatics Industry Forum: Enabling Ecosystems for Machine Learning in the Life Sciences
11 October 2022 | 10:00 to 16:00 CEST | London, UK

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
 

Software developer

VIB

Scientific Relations Manager (50-60%)

Institut Suisse de Bioinformatique

Bioinformatician / software developer

Masaryk University and FNUSA-ICRC