News and announcements

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

Weekly news 19.08.2019

Supporting innovation in bioinformatics. How ELIXIR connects public bioinformatics infrastructure with industry report is available at https://f1000research.com/documents/8-1136

The EC has opened a call for expression of interest in joining an eHealth stakeholder group to provide high-level advice and expertise. It may be of interest to those groups in ELIXIR working at the interface of human research data and eHealth. 

A new "The bio.tools registry of software tools and data resources for the life sciences​" on the bio.tools registry was released last week in Genome Biology. Read on to find out about the successes of the project, and about their future plans.  ELIXIR Estonia members Ahto Salumets and Hedi Peterson are among the authors.

Upcoming ELIXIR events

Statistical tests and statistical learning for omics data 
11 - 12 September 2019 | University of Luxembourg, Luxembourg 

Current advances in text mining 
25 - 26 September 2019 | University of Luxembourg, Luxembourg 

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

Algorithms for Genomics
14 - 18 October 2019 | Delft, Netherlands

Final OpenRiskNet Workshop: Creating powerful workflows combining data and software services demonstrated on risk assessment case studies [Industry workshop]
23 - 24 October 2019 | Amsterdam, Netherlands

Constraint based modelling 
25 - 29 November 2019 | Leiden, Netherlands

Modelling and optimisation for bioinformatics and systems biology 
9 - 13 December 2019 | Wageningen, Netherlands 

EMBO Practical Course: Integrated multi-omic analysis of microbial communities 
16 - 23 March 2020 | Luxembourg City, Luxembourg 

 

 

Andmekaitse (GDPR) teemalised seminarid loodusteadlastele Tartus, September 2019

Information in English below.
 
Eesti Teadusarvutuste Infrastruktuur (ETAIS) ja Eesti loodusteaduste taristu (ELIXIR) korraldavad septembris kaks andmekaitse valdkonna seminari.
 
Esmalt loodusteadlastele suunatult laiemat ülevaadet andev seminar TÜ andmekaitse spetsialisti Terje Mäesalu poolt.  Seminaris käsitletakse  kogu  GDPR ja andmekaitse raamistikku, loogikat, põhimõtteid ja seda, kust konkreetse teema täpsustamiseks nõu ja tuge saab Tartu Ülikoolis. Täpsemad detailid allpool. Seminar toimub 16. septembril  kell 13:00-17:00  
 
Nädal hiljem, teine seminar genoomika, biomeditsiini ja biopankade spetsiifikaga seonduvast Euroopa andmekaitse ja teaduskoostöö  hea tava kokkulepetest. Seminari viib läbi EU andmekaitse õiguse ja andmebankade vallas kogenud juristi Irene Schündler Berliinist (esineja täpsustus allpool). Seminar on plaanitud ettekandena vahelduvalt kaasakiskuva päevakohase aruteluga. Kaasame auditooriumisse ka kohalikud andmekaitse spetsialistid, kes on tõstatatud küsimusi ka Eesti seadusandluse vaatevinklist valmis kommenteerima. Seminar toimub 23. septembril ajavahemikus 13.00-17.00.
 
Mõlemad seminarid toimuvad Omicumis , Riia 23b, ruumis 105. 
 
Registreeruda saab https://forms.gle/sNhXKsajW4rsFbCC8. Terje Mäesalu seminari saab registreeruda 12. septembri lõunani (kl 11.59). Irene Schlünderi seminari saab registreeruda 19. septembri lõunani (kl 11.59). Registreeru varakult ja vastutustundlikult!

Terje Mäesalu seminari täpsemad teemad:

Seminar on planeeritud kahes osasa pikema turgutava kohvipausiga. Pigem seminar arutelu kui monoloogi vormis.  See on ühtlasi õige koht tuua lauale oma kõhklused ja seni vastuseta jäänud  andmekaitset puudutavad küsimused.

Käsitletavad teemad:

  • Mis on isikuandmed ja millised on õigused nende töötlemiseks
  • Isikuandmed ja isikuandmete töötlemise põhimõtted
  • Vastutava ja volitatud töötleja staatus ning kohustused
  • Nõusolek isikuandmete töötlemiseks 
  • Ürituste korraldamine ja isikuandmete töötlemine
  • Pildistamine ja filmimine 
  • Lõimitud ja vaikimisi andmekaitse
  • Isikuandmete edastamine EL sees ja kolmandatele riikidele ning organisatsioonidele
  • Andmesubjekti õigused ja kohustused, sh „õigus olla unustatud“
  • Isikuandmete töötlemine muul eesmärgil kui see, milleks andmed algselt koguti
  • Mõjuhinnangust
  • Isikuandmetega seotud rikkumised ja trahvid

Irene Schlünderi tutvustuseks:

"Irene Schlünder is a lawyer and expert in EU data protection law and database governance as well as IP rights and works for TMF e.V., Berlin. TMF is a member-based non-profit organisation, which brings together the German academic community in biomedical and healthcare research in various topic groups, one focus is data protection law. TMF represents the community with regard to the relevant authorities and the legislator as well as on the international level and is a permanent partner of The German Health Ministry in developing strategies for eHealth and big data applications in healthcare. Irene is a senior consultant and responsible for the international activities. She was involved in EHR4CR (co-author of the IMI Code of Conduct) as well as BioMedBridges and CORBEL. She recently led WP4 of DO-IT, the CSA for the IMI BD4BO Programme, which focused on the development of an Informed Consent Template for clinical trials including secondary use of the data for  future research. She is closely collaborating with BBMRI-Eric as a member of the Common Service ELSI and belongs to the core drafting group of the BBMRI lead initiative for a “Code of Conduct for health research” under the GDPR.”

Estonian Scientific Compute Infrastructure (ETAIS) together with Estonian Life Science Infrastructure (ELIXIR) are organising two data protection (GDPR compliance) seminars for life scientists in September.

  • The first seminar will be held in Estonian and will cover general overview of GDPR and data protection framework, logics and principles and resources for assisatnce at  University of Tartu. The seminar will be held on September 16th, 13.00-17.00 at Riia 23b-105, Tartu.
     
  • The second seminar will be held in English and will be more specific about data protection intricacies for genomics, biomedical research and biobanking. The seminar will be held by an experienced laywer Irene Schündler. She has extensive experience in EU data protection laws and database governance (see more below). The seminar is planned to be interactive and we expect active participation from the audience and everybody is welcome to share the ups and dows of their past experience with drafting collaboration contracts. The seminar will take place on September 23rd, 13.00-17.00 at Riia 23b-105, Tartu.

 
Registration is open at https://forms.gle/sNhXKsajW4rsFbCC8. The first seminar by Terje Mäesalu accepts registrations till noon of 12th of September. Registration to the second seminar by Irene Schlünder remains open till noon of 19th September. Register early!

More information about Irene Schündler:

"Irene Schlünder is a lawyer and expert in EU data protection law and database governance as well as IP rights and works for TMF e.V., Berlin. TMF is a member-based non-profit organisation, which brings together the German academic community in biomedical and healthcare research in various topic groups, one focus is data protection law. TMF represents the community with regard to the relevant authorities and the legislator as well as on the international level and is a permanent partner of The German Health Ministry in developing strategies for eHealth and big data applications in healthcare. Irene is a senior consultant and responsible for the international activities. She was involved in EHR4CR (co-author of the IMI Code of Conduct) as well as BioMedBridges and CORBEL. She recently led WP4 of DO-IT, the CSA for the IMI BD4BO Programme, which focused on the development of an Informed Consent Template for clinical trials including secondary use of the data for  future research. She is closely collaborating with BBMRI-Eric as a member of the Common Service ELSI and belongs to the core drafting group of the BBMRI lead initiative for a “Code of Conduct for health research” under the GDPR.”

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