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  • 1 min read

The ELIXIR Estonia eQTL Catalogue Browser

ELIXIR Estonia has developed a simple query interface (https://elixir.ut.ee/eqtl/) for the eQTL Catalogue database jointly developed by the University of Tartu and the European Bioinformatics Institute. The interactive ELIXIR Estonia eQTL Catalogue Browser enables researchers to quickly check if their genetic variant of interest has an effect on gene expression in any of the 112 cell-type- and tissue-specific datasets from the eQTL Catalogue. More information can be found in the accompanying preprint.

 

 

  • 2 min read

2nd Galaxy-ELIXIR webinar series: Open Data Infrastructures to tackle COVID-19 pandemic. Weekly from Jan 20th to Feb 24th

The Galaxy Community and ELIXIR organise a second webinar series to demonstrate how open software and public research infrastructures can be used in analysing and publishing SARS-CoV2 data.

In a series of six webinar sessions, experts from ELIXIR and the global Galaxy community from the US, Australia and Europe will demonstrate how open access and open science are fundamental for fast and efficient response to public health crises. The series follows on the first Galaxy-ELIXIR webinar series organised in April-May 2020. It will introduce the latest Galaxy tools developed for working with SARS-CoV-2 data and discuss some of the challenges in accessing, analysing and interpreting them.

The kick-off session of the webinar series takes place on 20 January 2021 and will run weekly on Wednesdays 18.00-19.00 EEST.

Session 1: COVID-19 analysis in Galaxy: Lessons learned and introduction to the series
Session 2: Importance of (open) infrastructures in responding to a pandemic
Session 3: Supporting the COVID-19 Data portal: viral data cleaning from human reads and submission to ENA
Session 4: Insights from selection analysis of complete genomes and read-level data
Session 5: Viral Beacon and Galaxy variant workflows
Session 6: DRS, long-read-sequencing, proteomics and more — an update to recent COVID-19 workflow developments

Registration is needed before each seminar and will provide access to the seminar recordings afterwards.
More information at the webinar series webpage https://elixir-europe.org/events/2nd-galaxy-elixir-webinar-series

More information about Galaxy analyses of COVID-19 data: covid19.galaxyproject.org

  • 1 min read

ELIXIR Europe Training Survey

ELIXIR Europe is welcoming researchers to let us know your training needs. The survey results will be used to create and deliver trainings according to the research communities' needs.

The survey (link here) should take no more than 5-10 minutes of your time to complete; questions with an asterisk require a response and it would be immensely helpful if you could spare the time to respond fully to all questions. Participants who share their contact details with us will gain early access to the results and will play a vital role in helping us to optimize the training programme. We value your contribution and look forward to sharing the outcomes with you.

“How FAIR are you” Webinar Series and Hackathon (Jan-Apr 2021) organised by CINECA

The “How FAIR are you” webinar series and hackathon aim at increasing and facilitating the uptake of FAIR approaches into software, training materials and cohort data, to facilitate responsible and ethical data and resource sharing and implementation of federated applications for data analysis.

The hackathon will be a practical online event to investigate gaps in the application of FAIR principles to project outputs and facilitate the implementation of FAIR approaches, where possible. The Hackathon will focus on cohort data, software tools including workflows, algorithms as well as web services, and training materials. The hackathon will be preceded by a “How FAIR are you” webinar series to provide background and introduce theoretical concepts that might be useful during the practical sessions. All participants are encouraged to attend or watch the recordings of the webinar series. 

The webinar topics include:

Introduction to FAIR principles - Open science through FAIR health data networks: dream or reality?  
Making Cohort data FAIR   
FAIR Software tools   
Practically Fair    
How to make training FAIR    
Ethics/ELSI considerations - From FAIR to fair data sharing

More information and registration is available at https://www.cineca-project.eu/news-events-all/how-fair-are-you-webinar-series-and-hackathon.

 

  • 2 min read

ELIXIR Estonia Services Terms of Use

ELIXIR Estonia Services Terms of Use

 

  1. ELIXIR Estonia promotes open science through its mission to provide freely available online bioinformatics software and databases to allow the largest possible community to benefit from these resources. Where we present scientific data generated by others we impose no additional restriction on the use of the contributed data than those provided by the data owner.

  2. ELIXIR Estonia expects appropriate attribution (e.g. in publications, services, or products) for any of its online services in accordance with good scientific practice. 

  3. Any feedback provided to ELIXIR Estonia on its services will be treated as non-confidential unless the individual or organisation providing the feedback states otherwise. 

  4. ELIXIR Estonia is not liable for any loss or damage.

  5. Personal data held by ELIXIR Estonia will only be released in exceptional circumstances when required by law or judicial or regulatory order. ELIXIR Estonia may make information about the total volume of usage of particular software or data available to the public and third-party organisations without details of any individual’s use.

  6. Any questions or comments concerning these Terms of Use can be addressed to:  ELIXIR Estonia, University of Tartu, Institute of Computer Science, Narva mnt 18, Tartu, Estonia; elixir@ut.ee

  7. Users of ELIXIR Estonia online services agree not to attempt to use any ELIXIR Estonia computers, files, or networks apart from through the service interfaces provided.

  8. ELIXIR Estonia’s websites gather information about users solely to improve the usability and usefulness of the site, and not for any commercial purposes. No contact information is collected, except when directly provided by the users themselves, e.g. contact information provided through the contact form or email. Other information collected during the course of your usage of the site, such as pages visited, may be collected in server log files and used for aggregated statistical analysis of traffic patterns.  

  9. ELIXIR Estonia will make all reasonable effort to maintain continuity of these online services and provide adequate warning of any changes or discontinuities. However, ELIXIR Estonia accepts no responsibility for the consequences of any temporary or permanent discontinuity in service.

  10. Activities that may impact the stable operation of our services such as systematic or automated queries and downloads, automated submissions, etc. using other mechanisms than the ones provided by us are prohibited and may result in blocking your access to our services.

  11. If you post or send offensive, inappropriate or objectionable content anywhere on or to our websites or otherwise engage in any disruptive behaviour on any of our services, we may use your personal information from our security logs to stop such behaviour. Where we reasonably believe that you are or may be in breach of any applicable laws we may use your personal information to inform relevant third parties about the content and your behaviour.

  12. Software that can be run from the ELIXIR Estonia webpages may be used by any individual for any purpose unless specific exceptions are stated on the web page.

  13. ELIXIR Estonia does not accept responsibility for the consequences of any breach of the confidentiality of the ELIXIR Estonia site by third parties.

 

GTN Smörgåsbord: A Global Galaxy Course, February 15-19 2021

 

For Estonian scientists the most important facts are:

  • https://galaxy.hpc.ut.ee/ will ensure that all the tools covered during the course will be available afterwards at the local instance
  • If you register to the Global Galaxy Course, please notify the UT Galaxy team (galaxy@hpc.ut.ee) as well, so you would be informed about future Galaxy events and local developments among the first ones.
  • Also, in case you have not used UT Galaxy instance at https://galaxy.hpc.ut.ee before, then please include your UT username (in case you have it) to the email above (galaxy@hpc.ut.ee) so your local Galaxy account can be created.


Galaxy Training event showcasing a wide variety of GTN (Galaxy Training Network) tutorials. This will be an online event, spanning all time zones. All training sessions are pre-recorded, so you can work through them at your own pace, and manage your own time. A large community of GTN trainers will be available via online support to answer all your questions.

The program covers a general introduction to the Galaxy platform, NGS Analysis (DNA-seq and RNA-seq), Proteomics, and also features a Choose your own adventure day on Friday, where we encourage you to explore all the tutorials that the GTN training repository has to offer, and follow those that are of interest to you. The GTN tutorials cover a wide range of scientific topics, from NGS to ecology, climate science, machine learning, visualization, and many more. All the tutorials can be found on the GTN website

When: February 15-19, 2021 (all time zones)
Who: Open for everybody
Cost: Free
Format: Virtual event, all training session are pre-recorded, you can work through these at your own pace, with instructors available online for support
Support: Slack Channel (link will be provided here before the course)
Organized by: The Galaxy Training Network (GTN), CINECA, The Galaxy Project, Australian BioCommons, Erasmus Medical Center, Albert-Ludwigs-Universität Freiburg, Avans Hogeschool, The Gallantries Project, The GalaxyP Team, The ProteoRE Team, INAB-CERTH, EMBL-EBI, Institute of Surgical Pathology - University Medical Center Freiburg.

More info and registration is available at https://shiltemann.github.io/global-galaxy-course/. 

Do not miss the great opportunity!

  • 1 min read

We launched ELIXIR TeSS Club

ELIXIR Training eSupport System TeSS had its kick off meeting on October 23rd.

ELIXIR TeSS club brings together all parties interested in further developing TeSS further.
The group gathered for the first time on 23 October and will take place biweekly on Fridays betwen 10–11 CET.

The next meeting will be on 6 November to discuss the prioritisation of tasks for 2021.

ELIXIR Estonia is one of the Nodes helping to develop TeSS further.

 

 

  • 1 min read

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.