News and announcements

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.”

Single cell RNA-seq analysis courses by ELIXIR-FI in Espoo

Please note that registration is now open for the following two single cell RNA-seq data analysis courses, which cover the processing of transcript counts from quality control and filtering to dimensional reduction, clustering, and differential expression analysis. You will also learn how to do integrated analysis of two samples. 

 

18.-19.9.2019 Single cell RNA-seq data analysis using R

In order to participate in this course, you need to have prior experience in using R.

Teachers: Heli Pessa, Bishwa Ghimire, Iivari Kleino

For more information and registration, please see https://www.csc.fi/web/training/-/single-cell-r-2019

 

24.9.2019 Single cell RNA-seq data analysis using Chipster

As the R-based tools are used via the graphical user interface of Chipster, no experience of R is required, and the course is thus suitable for everybody.

Teachers: Maria Lehtivaara and Eija Korpelainen

For more information and registration, please see https://www.csc.fi/web/training/-/single-cell-chipster-2019

 

Note that you can combine these courses with the international Single cell transcriptomics symposium, which takes place in Biomedicum Helsinki 23.9.2019. 

For more information and registration, please see 

https://www.helsinki.fi/en/researchgroups/immunomics/single-cell-course-week/single-cell-transcriptomics-symposium-2019

 

Finally, all the material from the ELIXIR course "Single cell RNA-seq data analysis with R" (27.-29.5.2019) is now available at 

https://www.csc.fi/web/training/-/scrnaseq

The material includes lecture videos, slides, exercises with code, and exercise data.

Tags: 

Weekly news 03.06.2019

There are a few seats available for the one-day Data Steward Knowledge and Skills Workshops – A working meeting with and for the Data Steward Community, June 11 & June 12 2019, Utrecht, the Netherlands.

Registrations are open for a Protein Prediction workshop on 10 September in Brussels, Belgium organised by ELIXIR Belgium with the cooperation of VUB-VIB. More information and registration.

Call for abstracts for the international Advances in Computational Biology conference (Barcelona, 28-29 Nov, 2019) is now open. This unique scientific event will highlight research done by women in systems biology, omics technologies, artificial intelligence and HPC with applications to biology -  all presenters will be women.

ELIXIR France is pleased to announce the upcoming Genopole Summer School: Bioinformatics and Bio-statistical tools in medical genomics. 24-28 June, 2019, Château’form Seine-Port, Paris Region.

Weekly news 20.05.2019

Registration is open for the two ELIXIR-DE courses in Kiel:    
Introduction to genome-wide association studies (GWAS)
Eukaryote genome annotation workshop

Applications open for ELIXIR-SE (NBIS) courses in
Epigenomics data analysis (26 - 30 August, Stockholm, Sweden)
Omics Integration and Systems Biology (9 - 12 September, Stockholm, Sweden)
Python programming with applications to bioinformatics, Uppsala or
Python programming with applications to bioinformatics, Umeå (7 - 11 October, Uppsala and Umeå, Sweden)

ELIXIR-CH is delighted to announce that registrations are open for the next ELIXIR-EXCELERATE Data Carpentry with R (Genomics curriculum) workshop, taking place on 1-2 July 2019 in Zurich. The course will address core concepts on Unix, Data wrangling, Data Analysis and Visualization in R, and it is aimed at researchers with no previous knowledge of the tools - no experience required or expected.

 

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