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 

Estonia Joined the Nordic e-Infrastructure Collaboration Initiative

On February 11th Estonia joined the Nordic e-Infrastructure Collaboration NeIC by signing the collaboration agreement at the Delta Centre in Tartu. This agreement gives Estonian research infrastructures the possibility to maintain and enhance their competitiveness and do more international cooperation.

The agreement was signed by Arne Flåøyen, Director for NordForsk, an institution  that facilitates and provides funding for cooperation on research across the Nordic region, and Andres Koppel, the chairman of the board of the Estonian Research Council.

More information is available at 

https://www.etag.ee/en/estonia-joined-the-nordic-e-infrastructure-collaboration-initiative/

https://neic.no/news/2020/01/09/estonia-joins-neic/

 

 

Weekly news 17.02.2020

ELIXIR Guest Webinar: Text mining of disease-gene networks 

19 February 2020 | Online | 14:00 GMT/15:00 CET

Most of what we know about human diseases and genes/proteins involved in them is buried in the biomedical literature. Text mining is thus a key tool for creating databases with structured data on disease-gene associations and the underlying gene networks.

In this webinar, Lars Juhl Jensen from the Novo Nordisk Foundation Center for Protein Research at the University of Copenhagen, Denmark, will describe a highly efficiently text-mining pipeline, which allows his team to systematically mine such information from very large corpora of full-text articles as well as abstracts. The presentation will also cover how this information is made available through interoperable, web-based databases, including the DISEASES database and the STRING database (an ELIXIR Core Data Resource). Finally, Lars will show how the Cytoscape stringApp brings together these databases, allowing users to easily retrieve, analyze, and visualize gene networks for diseases or other topics of interest.

Lars Juhl Jensen is a professor at the Novo Nordisk Foundation Center for Protein Research at the University of Copenhagen in Denmark. His research group develops state-of-the-art tools for generation and analysis of molecular interaction networks from proteomics data and text mining. The tools are freely available to the scientific community.

More: jensenlab.org


paper on TeSS was recently accepted and published by Oxford University Press to review the training platform's features, workflows and future prospects.

 

ELIXIR events

3-Day Course Single-cell Transcriptomics
1-3 April 2020 | University of Lausanne, Switzerland 

Software Carpentry Course 
30-31 March 2020 | Cologne, Germany

Innovation and SME Forum: Data-Driven Innovation in the Agritech Sector
24 -25 March 2020 | Lyon, France

ELIXIR Bioinformatics Industry Forum 
28 April 2020 | London, UK

Bioinformatics Research and Education Workshop (BREW)

The Institute of Computer Science at the University of Tartu is organising this year's Bioinformatics Research and Education Workshop

The workshop will take place at Delta centre during May 21-22, 2020

BREW is a workshop for PhD students in bioinformatics, which aims to give an introduction to scientific conferences, including submission, peer review and presentation of scientific papers. All participants must submit a paper and take part in reviewing papers from other participants in order to attend the workshop. After the review deadline, students have a chance to make alterations to their paper and deliver a final version. All participants will present their paper at the conference-style meeting.

BREW is open for students and supervisors from the PhD programs in Bioinformatics and Computational Biology in participating universities. For particular details, please contact the organizers via email.

The workshop is free of charge, and will include lunch, snacks and a social evening. Accomodation is paid for by the local organizing committee. More details are available on the corresponding page.

Registration by March 1, 2020

More info at https://brew2020.cs.ut.ee/index.php

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