News and announcements

ELIXIR Estonia is part of the new ELIXIR-CONVERGE project

ELIXIR-CONVERGE — a new project to streamline data management practices

From accelerating to converging

After the completion of the successful ELIXIR-EXCELERATE project, which provided  ELIXIR with solid foundations, today ELIXIR kicks off a new project to support the provision of data management across Europe.

ELIXIR-CONVERGE, a €5 million three-year H2020 project, will bring together experts from all 23 ELIXIR Nodes, representing 29 research institutes and 22 countries across Europe to work collaboratively on some of the major challenges in data access, provisioning and distribution. The development of a data management toolkit will sit at the core of the project, providing researchers with a strategy to manage their data to international standards. 

The toolkit will be tested across multiple domains and data types against ‘Demonstrator Projects’ that cover:

  • Plant genotype and phenotype
  • Epitranscriptomics
  • Marine metagenomics
  • Human genomics
  • Toxicology
  • Bimolecular simulation

ELIXIR CONVERGE map

Niklas Blomberg, Director of ELIXIR and Coordinator of ELIXIR-CONVERGE, said: “Many ELIXIR Nodes already provide local support and expertise with data management to national research projects and life scientists in that country. With the ELIXIR-CONVERGE project, we want to ensure that this data management provision is as developed as possible within each country and as connected as it can be across countries too. While data generation is a local process, often the expertise for the management of that dataset sits in another country, or the resource where the data will be deposited is in a different country. So there is a strong need to move beyond national data management support, we need to connect them across countries. ELIXIR-CONVERGE will allow us to construct that system across Europe”.

Further information

Dive into the ELIXIR-CONVERGE project to find out more about its key objectives, outputs and structure.

gProfiler is now running on Galaxy at https://usegalaxy.eu and https://galaxy.hpc.ut.ee/.

gProfiler (https://biit.cs.ut.ee/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 14.09.2020

COVID-19 Viral Beacon

A beacon in the ocean of SARS-CoV-2 data

The COVID-1 Viral Beacon is an ELIXIR Spain platform that allows researchers to browse SARS-CoV-2 variability at the genome, amino acid, structural and motif level
Bioinformaticians from the Center for Genomic Regulation (CRG) have built this time-saving tool with an extremely friendly interface. 

More information at https://elixir-europe.org/news/beacon-ocean-sars-cov-2-data 

 

Online X-omics festival "The future is now!"

28 September 2020 | 9:30 - 14:00 (CEST)

If you are a researcher working in -omics (genomics, proteomics, metabolomics) and / or deal with data analysis, integration & stewardship join the online X-omics festival. Read more on the event website.

Unix Shell Advanced Training courses on March 17th and 20th - POSTPONED TO UNFORESEEN FUTURE

WE HAVE POSTPONED THE COURSES TO UNFORESEEN FUTURE.

Advanced computing power is hidden away in clouds/cluster/supercomputers that you do not have click and point access. As a general rule these high performance computer resources use Linux operating systems and are accessible only by a shell terminal.

This course is aimed to streamline your skills in Linux and terminal environment. We will teach you how to make your life easier by creating maintainable and flexible bash scripts for your commonly used workflows or SLURM jobs.

Objectives:

  • Learn how to iterate operations over many input files with bash loops and conditions.
  • Learn how to combine complicated command line based workflows into maintainable bash scripts.
  • Add additional useful utility functions and tools to your toolbox.

Expected prior knowledge:
Experience in using the basic commands covered in the Basics course (e.g. cd, ls, mkdir, mv, cp, head, cat, find, less, pwd).

Requirements:
Lecture venue is computer class with linux computers. In case you bring your own Windows laptop, please make sure to install Putty application (https://www.putty.org/) beforehand.

Materials:
https://elixirestonia.github.io/2020-03-17-tartu/

Registration:
Application is open at https://forms.gle/pzWrKDNcxpStEADk8

Time:
March 17, 2020
10:15–14:00

March 20, 2020
10:15–14:00

 

Venue:
Auditorium 2005 (the Linux classroom)
UT Delta Centre
Narva mnt 18
51009 Tartu
Estonia

Unix Shell Basics training course March 3rd

Advanced computing power is hidden away in clouds/cluster/supercomputers that you do not have click and point access. As a general rule these high performance computer resources use Linux operating systems and are accessible only by a shell terminal.

This course is aimed to provide basic survival skills in Linux and terminal environment. We will teach you how to access files and folders, move around and hopefully shake off the fear of getting stuck somewhere along the way.

Objectives:

  • Obtain basic knowledge on dealing with files using command line (Linux or Mac)
  • Learn how to use search over several text files, combine files, extract certain knowledge.
  • Master tips and tricks for effective command line hacks that would save a lot of time.

Requirements:
Lecture venue is computer class with linux computers. In case you bring your own Windows laptop, please make sure to install Putty application (https://www.putty.org/) beforehand.

Materials:
https://elixirestonia.github.io/2020-03-03-tartu/

Registration:
The course is full!

Time:
March 3, 2020
10:15–14:00

Venue:
Auditorium 2005 (the Linux classroom)
UT Delta Centre
Narva mnt 18
51009 Tartu
Estonia

NB! Two weeks later we will run an Unix Shell Advanced course for people who have already basic knowledge.

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