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The FAIR Principles Lecture (registration closed)

On the 27th of September, 2021 and on 14th of October, 2021, ELIXIR-Estonia will be holding a new data management course: The FAIR Principles. This lecture will be a short overview about the principles and is part of a bigger data management course package. The first course, on 27th of September, will be held in Estonian, and the second course, on 14th of October, will be held in English. 

 

The FAIR Principles Lecture 27th of September, 14:15-17:00 (in ESTONIAN) and 14th of October, 12:15-15:00 (in ENGLISH), Delta #1019

In recent years, more attention is put on what researchers do with the data (and other resources) they produce. Especially in Europe, but also everywhere else. The main idea is that when researchers use taxpayers' money, the taxpayers themselves should also have access to the results, free of charge. This means that the research should be published in open access journals and data should be made publicly available. 

Good data management may help you with that, at least to make the process easier on the whole. If you think “how to manage your data” at the beginning and during the project and know what you plan to do with it at the end of the project, the process at the end will be easier. However, what is “good data management”, is up to debate. The FAIR Principles concentrates on making your data findable, accessible, interoperable and reusable, so this is a good start. And let’s be honest, some of these things you are probably already doing. 

In this course, we will be going over all the FAIR Principles and how they are applied in real life. This way, you will already know what to consider, while writing a grant, filling out your data management plan or doing your research. 

 

Information about the lecture

Dates: 27.09.2021 in Estonian; 14.10.2021 in English

Time: 14:15 - 17:00 / 12:15 - 15:00

Place: Delta, Narva mnt 18, room 1019

Register: registration closed

Registration closes at 23:59 on 25.09.2021/12.10.2021 (for the Estonian/English lecture, respectively) or when it gets full.

Materials (ENG): https://doi.org/10.5281/zenodo.5572352

Materials (EST): https://doi.org/10.5281/zenodo.5533534

FAIR Flyer: https://doi.org/10.5281/zenodo.5769084

 

Learning outcomes: 

  • Understands the importance of a good data management
  • Knows what are the FAIR principles and what they mean
  • Knows how to implement FAIR principles throughout the research project
  • Knows where to get more information about the FAIR Principles

 

Data management courses held in the future (may be up to change): 

  • OpenRefine (October 2021)
  • Excel - how to make your data reusable (November 2021)
  • Data licensing (2022)
  • How to organise your files BYOD workshop (2022)
  • How to write a good metadata and README file (2022)
  • Personal data in data management (2022)
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ELIXIR Hungary published a Multiple Testing Correction web-tool

MultipleTesting.com: A tool for life science researchers for multiple hypothesis testing correction

Scientists from nearly all disciplines face the problem of simultaneously evaluating many hypotheses.To facilitate multiple-testing corrections, ELIXIR Hungary developed a fully automated solution not requiring programming skills or the use of a command line. The registration free online tool is available at www.multipletesting.com and compiles the five most frequently used adjustment tools. 
 

 

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Galaxy community’s SARS-CoV-2 Data Analysis and Monitoring with Galaxy - workshop materials available

The Galaxy community held a SARS-CoV-2 Data Analysis and Monitoring with Galaxy workhop in mid August. The video tutorials and slides are available for self-learners at https://galaxyproject.eu/event/2021-06-21-sars-cov-2-data-analysis-monitoring-training/

The topics that were covered ranged from basic Galaxy introduction to more specific topics such as:

  • Galaxy for SARS-CoV-2 genome surveillance projects
  • Variant calling, reporting, consensus building (with Galaxy GUI)
  • The usegalaxy.eu SARS-CoV-2 bot in action
  • Upload data to ENA
  • Using and Customising ObservableHQ

 

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ELIXIR’s latest report: “Open data: A driving force for innovation in the life sciences”

Open access life science resources such as data and software, are fundamental for breakthrough discoveries, scientific excellence and entrepreneurial endeavours. Seventy-six percent of companies surveyed in our newest report “Open data: a driving force for innovation in the life sciences” state that their product or service would not exist without data on open repositories. 

While the importance of these freely available resources is widely accepted, there are sparse efforts to quantify the benefit, despite the need to demonstrate value to funders and policymakers. This report is an up-to-date quantification on the benefit of open data to industry and innovation, with an extensive survey, testimonials, and analysis of the hotspots of European innovation. 

Find the full report at https://bit.ly/SMEreport_news

 

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