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2021

ONLINE seminar: Research Code Review by Open Science Coffee

On September 1st (2021), 10-11am CEST, Open Science Coffee will be holding an online seminar "Research Code Review". 

More researchers are writing code to process, analyse and visualise their data. For reproducible and robust research, it is increasingly important that this code is reviewed. Join this inaugural Open Science Coffee to learn more and discuss best practices, challenges and opportunities in reviewing research code. 

Register before seminar in here: https://tudelft.zoom.us/meeting/register/tJwtcOypqzwpHNZPRVlObq8dK_DIGy0yWLrs 
More information: https://osc-delft.github.io/events 

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g:Profiler latest article reached 1000 citations!

The g:Profiler team from ELIXIR Estonia is celebrating. The latest update article of our g:Profiler enrichment analysis and gene list conversion toolkit published in NAR on July 2nd, 2019 reached 1000 citations on July 27th 2021. We are truly happy that we have had a chance to help so many reasearchers across the world in carrying out their research. 

g:Profiler https://biit.cs.ut.ee/gprofiler/ most popular tools are GOSt for enrichment analysis and g:Convert for translating between different gene/protein/transcript/probe identifiers. Both of these tools receive millions of queries per year. We also have g:Orth that enables translating identifiers between species and g:SNPense that annotates provides for SNP RS-ids chromosomal coordinates and predicted variant effect for SNPs that lie in protein coding genes.

g:Profiler relies heavily on ENSEMBL and ENSEMBL Genomes databases and we follow their data relase cycle. This ensures that our users have always the latest data at their service. g:Profiler includes data for 714 different species and for the largest organisms we support more than 200 different identifier types. We have kept all data releases since summer 2011 and these are available from https://biit.cs.ut.ee/gprofiler/page/archives

We also support custom datasets for researchers whose organisms are not supported by ENSEMBL or ENSEMBL Genomes or Wormbase Parasite or who want to do enrichment analysis using their own knowledgebase that goes beyond the Gene Ontology, KEGG, Reactome, Wikipathays, Transfac, miRTarBase, Human Phenome Ontology, Human Protein Atlas, CORUM that are already included in g:Profiler.

We are welcome user requests and development ideas either out our website or directly to our biit.support@ut.ee email. Your feedback helps us to keep improving and providing the best service for the life science community!

 

 

 

 

 

 

 

How to manage your data well? - Helis Academy can teach you how

What is data management? How to do it well? How to write a data management plan? If you have these questions, then Helis Academy can help you out. They provide a variety of courses and seminars about data management and data stewardship. 

On 17th and 18th of June, they will host a 2-day event, introducing their academy and Data Analysis and Data Stewardship (https://helisacademy.com/en/data-analysis-stewardship)  project with one of its aims to increase the industry readiness in Health and LifeSciences by developing training programmes in line with the knowledge and skills that are required in the industry. Helis is organizing 2 half-day events, filled with informative, interactive sessions:

Day 1: Symposium (17 June 2021)  9.30-13.00 CEST, Online You’ll learn more about the Helis project, the cross-border collaboration programme, how careers in life sciences are stimulated and the Helis domains during keynotes and interactive parallel sessions.  More info: https://helisacademy.com/en/closing-event/symposium

Day 2: Virtual company visits (18 June 2021) 8.30-13 CEST Curious to learn more about the life sciences sector in the Netherlands and Flanders? Join the virtual company visits on 18 June to find out more about the diverse job opportunities and career paths that the life sciences domains offer.  More info: https://helisacademy.com/en/closing-event/student-programme

The data analysis and stewardship pillar of Helis  is organized by DTL/ ELIXIR-NL, VIB/ELIXIR-Belgium, Maastricht University and Eindhoven University of Techonology (TU/e). 

Take part in a Data Management Practices survey

We are inviting all Estonian research community members to take part in a survey about the current data management practices in Estonia.

 

EDIT: The survey will remain open until 10th of October, 2021. 

The survey will remain open until at least the end of July (July 31st, 2021) 10th of October 2021 and should take approximately 30 minutes to fill out. We will randomly pick a couple of lucky people who have participated in the survey to win a goodie bag from us. The survey can be found here: https://survey.ut.ee/index.php/752887?lang=en 

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Helis FAIR Data Stewardship course materials available

Presentations from the Helis FAIR Data Stewardship course

For those who missed the 6 day Helis FAIR Data stewardship course, the organisers have made the presentations available via Zenodo.

You can find the relevant links from the original course programme https://www.aanmelder.nl/fair-data-stewardship-2021/part_program

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CINECA FAIR events - ELSI seminar and hackathon, April 2021

Ethics/ELSI considerations - From FAIR to fair data sharing on April 15th, ONLINE

The CINECA "How FAIR are you" webinar series last webinar by Dr Melanie Goisauf, from BBMRI-ERIC

The FAIR principles – standing for Findability, Accessibility, Interoperability, and Reusability – have become the guiding principles for the wider sharing of research data in the life sciences. While FAIR provides guidance for the management of data as well as tools and workflows, the institutional conditions and organizational challenges associated with data sharing need to be taken into account to ensure responsible and fair data practices. This requires considering the context of legal requirements, for instance the principle of fairness and transparency in GDPR, expectations of research participants/data subjects, societal aspects and the “ethics work” that is an integral part of data flows, as well as fairness, equity and benefit sharing within transnational collaborations, which is of utmost importance. This webinar will, from the perspective of ethical, legal and societal implications (ELSI), discuss this broader context of responsible and fair data sharing associated with FAIR.

More info at https://www.cineca-project.eu/news-events-all/ethics/elsi-considerations

“How FAIR are you” Hackathon on April 28-29, ONLINE

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

This hackathon will be an online event and will run over 2 days for 4 hours each day. The participants will be grouped into 3 streams: cohort metadata, software tools and training materials. Each stream will discuss current practices and recommendations for moving towards a practical application of FAIR principles and will explore the FAIRness of participants’ resources using assessment tools. Additional CINECA staff will be on hand for questions.

More info at https://www.cineca-project.eu/news-events-all/how-fair-are-you-hackathon

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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.

 

 

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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

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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.