News and announcements

Helis Academy - FAIR Data Stewardship course by DTL in Utrecht Nov 2019

From 4-6th November, 2019, we will give another round of the Helis Academy - FAIR Data Stewardship course:  

FAIR Data Stewardship – digital data scholarship for life scientists

The target audience is life scientists – from industry and academia – and graduate students in the Life Sciences who wish to improve their digital scholarship on data handling. Some basic experience with programming and scripting languages like python, perl, R, matlab, etc. are an advantage, but not needed. The course is also relevant for Data Stewards who are supporting the life science researchers.

The course will introduce the trainees to important concepts of data stewardship. We start with a general introduction covering the data life cycle, the FAIR principles and a definition of data stewardship and data stewards.

The course will introduce the trainees to important concepts of data stewardship. We start with a general introduction covering the data life cycle, the FAIR principles and a definition of data stewardship and data stewards.

We will pass the stages of the data life cycle in more detail in the training modules of this 3 day course.

  • Day 1: Why use a data management plan and what for? On day one trainees will investigate data management plans, which types are there and how they should be used. 
     
  • Day 2: Mastering the data chaos during the research phase. On day two the course highlights how to work with data during the research phase, explaining how to create well formatted data which helps in the second module of day two to make data interoperable already during the active research phase.
     
  • Day 3: Boost your visibility and get cited for your data! On day three trainees will have an in-depth at persistent identifiers, different use cases and types of identifiers. Finally we are closing the data life cycle by making data fit for sharing, archiving and publishing. The training is organised by DTLand delivered as a joint effort by DTL partners.

 

You can find all the information, including the full programme and registration possibilities here: https://www.aanmelder.nl/data-stewardship-course/part_program. This course is part of the Data Analysis and Stewardship theme of Helis Academy and is organised by DTL and DTL collaborators. Info about other courses in the theme of Data Analysis and Stewardship can be found on the Helis Academy website and on the Helis Academy page on the DTL website.

 

Weekly news 23.09.2019

The Partnership for Advanced Computing in Europe (PRACE) have launched their 20th call for Proposals for Project Access. The call enables people to apply for access to high powered computer (Tier-0) systems. This year the applications are also open to Industry. Deadline 29 October 2019. 

The Data Platform have released a new paper in our F1000 channel "Understanding life sciences data curation practices via user research".   

ELIXIR Innovation and SME Forum: Distributed data analysis - the {health} data train 10 - 11 October 2019 | Utrecht, Netherlands

 

Weekly news 16.09.2019

ELIXIR Estonia together with Estonian Scientific Computing Infrastructure (ETAIS) has the first GDPR seminar today (16th of September). Futher information is available at https://elixir.ut.ee/node/262 

We are pleased to announce three new ELIXIR Communities:

  • 3D-BioInfo
  • Intrinsically Disordered Proteins
  • Microbial Biotechnology

Please read our latest news release to find out more about the aims of these Communities and who is involved. 

The Pistoia Alliance FAIR/Ontologies Mapping (OM) project 'Communities of Interest' opens the first of its monthly webinar series with “Progress towards commercial FAIR data product and services” by Ted Slater this coming Thursday 19th September 2019 15:00 - 16:00 BST, join the meeting here.

Abstract: Elsevier is a global information analytics business that helps institutions and professionals advance healthcare and open science to improve performance for the benefit of humanity. In this webinar, we will discuss how Elsevier is increasingly leveraging the FAIR Guiding Principles to improve its products and services to better serve the scientific community. Ted is one of the authors on the seminal 2016 FAIR guiding principles paper. He has worked extensively within pharma R & D and more recently for providers of data analytics. 

Fotis Psomopoulos (ELIXIR-GR) has been selected to be an Research Data Alliance (RDA) Europe Ambassador for Bioinformatics. Part of his activities in this role will be to act as the formal RDA liaison for the ELIXIR Training Platform, with an additional focus on early career researchers at the intersection of Life Sciences and RDA.

ELIXIR Finland have recently published a new user case study on Targeted treatment for venous diseases with vascular system modelling, which details a collaboration with academics in Belgium as well as a Finnish start up microfluidics company, FinnAdvance. 

The National University of Ireland (NUI) Galway have been awarded €13 million for a new centre for Graduate Research Training in Genomics data science. The funding was awarded from the Science Foundation Ireland to train 115 PhD students over the next seven years. The centre is led by Prof. Cathal Seoighe, who is ELIXIR’s Training Coordinator for Ireland.

Gallantries RNA-seq workshop for beginners: from sequences to visualization using Galaxy and R, October 2019

Gallantries team is organising a workshop in three citys across Europe simultaneously about RNA-seq analysis for beginners.

Main document for the event is available at https://galaxy-carpentries.github.io/gallantries/event/2019-08-27-second.... NB - participants form Tartu need to register through our local registration site at https://forms.gle/MhPNFQVz1yTupLUx6

Below is most relevant information for workshop participants in Tartu.

The Gallantries team is offering its second RNA-seq workshop for beginners on October 7-9th.

This workshop will cover:

  • Galaxy introduction
  • Introduction to High-Throughput Sequencing and Quality Control
  • Reference-based RNA-seq data analysis
  • Basics of R programming
  • Post-processing of RNA-seq data using R and Rstudio

Important notes

The workshop is free of charge and covers:

  • 3 days of training
  • Coffee and tea over the days
  • Lunch

No stipends for travel or accommodation are available.

Desktop computers will be available. You can also bring your own notebook if you prefer . Eduroam is available, ask your institute how to connect.

social dinner will be organised at each site on Tuesday October 8th. This dinner will be at your own cost, but we would love to have a chat with you after the workshop!

Workshop Format

This will be a hybrid training. This means the instructors will teach in front of a camera, and this video feed is live-streamed to multiple locations around the world. Each location will have several other instructors and helpers on site to answer questions and who can take over teaching in case this is needed.

We will use this collaborative document for asking and answering questions during the workshop. This document also contains links to all other materials you will need during the course.

Preparation

The workshop will use the European Galaxy server to perform all data analysis. Please register there ahead of time to streamline the training.

You must go through two Galaxy interactive tours before beginning the training. These interactive tours guide you stepwise through the Galaxy user interface and the history. They will help you to follow the Galaxy introduction, and ensure everyone has a basic understanding of how Galaxy works.

 

Weekly news 02.09.2019

The ELIXIR-CONVERGE application has been funded! We expect the project will start in early 2020, subject to negotiations with the EC. 

The ELIXIR Hub and ELIXIR UK will also be a minor partner in another project called EnhanceEOSC, with the role of helping to integrate ELIXIR registries into the European Open Science Cloud (EOSC) eco-system. 

The ELIXIR-EXCELERATE project was finalised on 31 August 2019. A big thanks to the Work Package leads and everyone involved in the projects. Read our news release highlighting the achievements of the project.

The next ELIXIR webinar will take place this Wed, 4 September at 14:00 (BST) / 15:00 (CEST) and will present the ELIXIR Implementation Study "FAIRness of the current ELIXIR Core Data Resources".

A paper authored by members and leads of the ELIXIR Human Data community and BBMRI-ERIC was published in Nature Reviews Genetics last week. The paper ‘Leveraging European infrastructures to access 1 million human genomes by 2022' explores how European research infrastructures can be leveraged to facilitate transnational access to at least one million human genomes. 

SIB announces the BC2 Basel Computational Biology Conference will take place from 9-11 September in Basel.

Genomics for Biodiversity symposium 
*Registration deadline 5 September*
12 - 13 September 2019 | Barcelona, Spain

ELIXIR Innovation and SME Forum: Distributed data analysis - the {health} data train
10 - 11 October 2019 | Utrecht, Netherlands

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