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:
- Thanasis Vergoulis, Scientific Associate at ATHENA RC: Facilitating fair researcher assessment with BIP! Scholar
- Christos Ouzounis, Professor of Bioinformatics-AUTH/Director of Research-CERTH: Impact of bioinformatics tools in the literature and the importance of normalization
- Video recording
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.
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