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2018

ELIXIR Info day 14.12.2018 Tartu

ELIXIR Estonia celebrates 5 years of ELIXIR with a series of events.

The major event is ELIXIR Information Day that takes place on 14th of December 2018 at Hotel Lydia Conference Center in Tartu. The day starts with welcoming coffee at 9am and finishes with drinks session around 4pm.

The event is free of charge for all registered participants.

The info day will give researchers from academia and industry, funders, decision makers and wider public an overview what ELIXIR is how it serves the scientific community.

Presenters include: Dr. Mateusz Kuzak (DTL; ELIXIR-Neatherlands), Dr. Ilkka Lappalainen (CSC; ELIXIR-Finland), Dr. Sarah Morgan (EMBL-EBI), Dr. Ulvi Gerst-Talas (TÜ; ELIXIR-Estonia; ETAIS), Dr. Hedi Peterson (TÜ; ELIXIR-Estonia), Prof. Jaak Vilo (TÜ; ELIXIR-Estonia). Learn more about the presenters here.

The purpose of ELIXIR is to construct and operate a sustainable infrastructure for biological information in Europe to support life science research and its translation to medicine and the environment, the bio-industries and society.

These resources include databases, software tools, training materials, cloud storage and supercomputers.

The goal of ELIXIR is to coordinate these resources so that they form a single high quality infrastructure. This coordinated infrastructure makes it easier for researchers to find and share data, analyse their experiments, exchange knowledge, and agree on best practices.

Estonian ELIXIR Node
The Estonian node focuses on developing and maintaining software tools and databases, linking of bioinformatics and biobanking, and last but not least, training researchers across borders.

ELIXIR Information Day is a day full of opportunities to learn how ELIXIR can be beneficial to researchers' every day task. 

Registration is open - https://goo.gl/forms/0ACHoTb5aSmA9iFZ2 Registration deadline December 9th, 11.59pm

Schedule for the Information Day

09.30 - 10.00 Welcoming coffee
10.00 - 10.30 Prof. Jaak Vilo, ELIXIR Estonia Head of Node - “How ELIXIR helps the life science community”
10.30 - 11.00 Dr. Ilkka Lappalainen, ELIXIR Finland  - “What it takes to handle sensitive human data - Finnish and European experience”
11.00 - 11.30 Coffee and discussions
11.30 - 12.00 Dr. Hedi Peterson, ELIXIR Estonia - “Small but important - Estonian contributions to life science infrastructure”
12.00 - 12.30 Dr. Sarah Morgan, ELIXIR EMBL-EBI - “Improving European life science by providing world class trainings in physical and virtual class rooms”
12.30 - 14.00 Lunch
14.00 - 14.30 Dr. Ulvi Talas, ETAIS and ELIXIR Estonia - “Interaction of infrastructures - making scientific computing easier for life scientists in Estonia”
14.30 - 15.00 Dr. Mateusz Kuzak, ELIXIR-Netherlands "Training life science researchers in foundational coding and data science skills in the Netherlands and ELIXIR.”
15.00 - Closing remarks followed by apéro

The accompanying events include:

  • 1 min read

Weekly news 01.10.2018

Registration is still open for the course on 'Adopting Open Source Software FAIR Practices' at the NETTAB 4OSS Satellite workshoptaking place on 22 October 2018. The goal is to introduce the participants to the training materials developed to teach researchers and developers how to implement 4OSS practices in their research software.

SIB is organising a Symposium on Computational Structural Biology celebrating 25 years of SWISS-MODEL in Basel, Switzerland, on 18 October. Registration is currently open.

Registrations are open for the SIB course on “Introduction to RNA-Seq”, in Basel (Switzerland), on 19-20 November 2018.

Registrations are open for the ELIXIR-Carpentries Instructor Training in Heidelberg, Germany on 8-9 October 2018.

Registrations are open for the ELIXIR-Carpentries Genomics Data Carpentry event in Oeiras, Portugal, 15-16 October 2018.

15-16 October 2018 | Frankfurt, Germany
ELIXIR Innovation and SME Forum on Industrial Biotechnology

Data carpentry workshop

Data Carpentry workshops are mainly meant for researchers with no or very little programming experience who have data they want to analyze. This hands-on workshop teaches basic concepts, skills and tools (including basic programming) for working more effectively with data.

We will cover Data organization in spreadsheets and OpenRefine, Introduction to R, Data analysis and visualization in R. Participants should bring their laptops and plan to participate actively. By the end of the workshop learners should be able to more effectively manage and analyze data and be able to apply the tools and approaches directly to their ongoing research.

Website: https://elixirestonia.github.io/2018-11-19-tartu/

Instructors
- Dmytro Fishman, Assistant of Data Science, Bioinformatics/Machine Learning, University of Tartu

- Liis Kolberg, PhD student, Bioinformatics/Statistics, Institute of Computer Science, University of Tartu

- Priit Adler, Research Fellow of Bioinformatics, Bioinformatics, Institute of Computer Science, University of Tartu
 

Registration and participation is free of charge

  • 1 min read

Weekly news 17.09.2018

Greece is now full ELIXIR member, following the signature of the ELIXIR Consortium Agreement by Professor Kostas Fotakis, Alternate Minister of Research and Innovation.

The ESFRI roadmap for 2018 was launched this week in Vienna. ELIXIR continues on the roadmap as an ‘ESFRI landmark’. Several new projects have been added, including two in the Health and Food domain - METRO-FOOD and IBISBA - and one in the field of biodiversity - DISSCO - all of which could have some potential touching points with ELIXIR

The ELIXIR Webinars are back after the summer break! This Wednesday, the webinar will present the eLearning Platform developed and managed by ELIXIR Slovenia. 19 September 2018, 15:00 CEST.

ELIXIR Germany (de.NBI) is organising Tool-Training for Proteomics - a one day course where the Proteomics tools namely “PIA - Protein Inference Algorithms”, “PAA - Protein Array Analyzer” and "CalibraCurve" will be introduced.

Registrations are open for the SIB course on “Bioinformatics of long read sequencing”, in Zurich (Switzerland), on 8-9 November 2018.

 

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Weekly news 10.09.2018

Registration is open for the ELIXIR-Carpentries Instructor Training, to take place at EMBL Heidelberg, Germany, on 8-9 October 2018.


Registration is also open for the ELIXIR-EXCELERATE Train the Trainer event in Stockholm, Sweden, on 9-11 October 2018. The event is a collaboration between ELIXIR Sweden and ELIXIR Italy.


Four Open Source Software recommendations #4OSS. We welcome comments, testimonials, examples, resources to this repository of 4OSS lessons. You can share the link to this repository for others to be aware of this work in progress and then reuse it!

ELIXIR Nodes and partners in Finland, Italy, Switzerland and the UK are running a survey aimed at users of ELIXIR tools and resources for human genomic variation. The survey is open until 30 September and is open to all.

Registrations are open for the SIB course on “First Steps with R in Life Sciences”, in Lausanne, Switzerland, on 6-7 November 2018.

Tabloid Proteome is a database of protein association network generated using publically available mass spectrometry based experiments in PRIDE. ELIXIR Belgium is organising training course about ProteomeXchange, PRIDE, MassIVE and Tabloid Proteome in Ghent on 10 October 2018.

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Weekly news 03.09.2018

The European Galaxy Days will be held on 19 and 20 November 2018 in Freiburg, Germany. The event will discuss the status of the Galaxy project, new developments, interfaces to other systems, extensions and best practice in reproducible research. Registration is now open, space is limited. 

Read the latest newsletter published by Tryggve, a collaboration of Nordic ELIXIR Nodes to manage and process sensitive biomedical data

ELIXIR Belgium is organising a training course Public proteomics data reprocessing and the Tabloid Proteome on 10 October in Gent. Registration is open!

Registrations are open for the SIB course on Protein Bioinformatics: Sequence-Structure-Function in Basel on 14-16 November 2018.

ELIXIR France and AVIESAN organise a workshop on Challenges and Perspectives in Integrative BioInformatics, in Paris on 17 September 17

 

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Weekly news 28.08.2018

Registration is open for Metabolomics Data Processing and Data Analysis, an online SPOC (Small Private Online Course) running from 8 October until 2 November 2018. This course will explore the tools and approaches used to process and analyse metabolomics data, investigate the challenges typically encountered and provide solutions to overcome them. Organised by the University of Birmingham (ELIXIR UK).

Registration is open for the ELIXIR Netherlands Galaxy Course Bioinformatics for Translational Medicine using Galaxy: see it, do it, teach it!, 17-19 October 2018 in Amsterdam.

Registrations are open to life scientists who want to learn Computing skills for reproducible research: Software Carpentry 24-25 October, Ghent Belgium

ELIXIR is offering an internship position relating to Beacon. The candidate will support the ELIXIR Beacon implementation study and the Beacon activities driven by the Human Genomics and Translational Data Services at the ELIXIR Hub.

 

 

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Weekly news 20.08.2018

ELIXIR and The Carpentries initiative (Software Carpentry and Data Carpentry), have extended their collaboration in organising and delivering training in ELIXIR Nodes. The Carpentries will organise close to 20 Software and Data Carpentry training workshops across ELIXIR Nodes, and two Instructor Training workshops to train a number of specialised instructors.

The Training Platform is organising a workshop “Implementation of DMPs and Data Stewardship in practice” at ECCB 2018 in Athens on Tuesday 11 September at 17:30-19:00. This is organized by ELIXIR Luxembourg, ELIXIR SIovenia and ELIXIR Netherlands, and is part of the ELIXIR Implementations Study about Data stewardship in ELIXIR.

ELIXIR Finland organizes two ELIXIR-EXCELERATE courses: Single cell RNA-seq data analysis with Chipster (19 September) and Single cell RNA-seq data analysis using R and command line tools (21 September). You can also attend an international single cell symposium on 20 September 2018 in Helsinki too

Registrations are open to life scientists who want to learn Computing skills for reproducible research: Software Carpentry, on 24-25 October in Ghent, Belgium.

Registrations are open for the SIB course on “NGS - Quality control, alignment, visualization”, in Bern (Switzerland), on 2-3 October 2018.