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  • 1 min read

Weekly news 19.11.2018

The Biohackathon took place this week in Paris. Around 150 participants worked on 29 projects that support the operations across ELIXIR technical Platforms. See photos by Bérénice Batut (ELIXIR Germany), read the Daily reports from the event. From ELIXIR-Estonia Ivan and Erik took part.

 

Registrations are open for the course on “High Performance Computing for genomic applications”, organized for the D-BIOL researchers by Scientific IT Services, in Zürich, Switzerland, on 26-27 November 2018.

de.NBI (ELIXIR Germany) organises the  4th FAIRDOM/de.NBI Systems Biology Developers Foundry on 6-7 December in Frankfurt.

de.NBI also hosts COMBINE (Computational Modellig in Biology Network) 2019 Conference on 15-19 July 2019 in Heidelberg.

  • 2 min read

ELIXIR ESFRI 5y Celebration Week

The Life Science Infrastructure ELIXIR is celebrating its 5 year anniversary this December. On December 18th 2013 Estonia was the 5th member country that signed the collaboration agreement, thus officially launching ELIXIR (see the old news items (eng),(est)). Therefore, to bring ELIXIR knowledge closer to our life science community in Estonia we are celebrating the 5th anniversary with a series of events in Tartu.

The main event will be ELIXIR Info Day on 14th of December where Estonian ELIXIR team gives an overview of the actions taking place in Estonia and international speakers add flavour with demonstrating what is done in different countries across Europe.

The main event is accompanied by several smaller events happening in Tartu.

On Wednesday 12th, we are organising a Train the Trainer refreshment event for the people who are actively training researchers. This event is brought to us by EMBL-EBI training team members Sarah Morgan and Melissa Burke.  

On Thursday 13th, we have Data Management - what to consider when you manage your data workshop that is targetted for the life scientists who need to handle the data they create or use. This event is also delivered to us by EMBL-EBI training team members Sarah Morgan and Melissa Burke. 

On Thursday 13th in the afternoon we have a working seminar with Ilkka Lappalainen from CSC (ELIXIR-Finland) to exchange his and Estonian experience in handling sensitive data. For participation please contact Ulvi Gerst-Talas.

On Monday the 17th, we have Kim Gurwitz from ELIXIR-UK running a workshop "Facilitating communication between individuals from different academic backgrounds in the bioinformatics space”.



Please contact Laura Altin for further information about the events (laura.altin@ut.ee).

  • 1 min read

Weekly news 22.10.2018

EMBL-EBI is organising training course Introduction to RNA-Seq and Functional Interpretation on 26-29 March 2019 in Hinxton, UK. Registration is now open!

Registrations are open of the SIB course on “Data Visualization with Cytoscape, in Lausanne, on 1 November 2018. This workshop will directly follow a 3-day course about “Introduction to Network Analysis” and we recommend to attend both. It will focus on understanding sources of biological data and how to approach visualizing the data.

 

There are still free places for the SIB course on “Ligand-protein docking, and computer-aided drug design, in Basel, Switzerland, on 27-28 November 2018.

Booking now open for the course Bioinformatics for Biologists: An introduction to programming, analysis, and reproducibilityin Cambridge, United Kingdom, on 3-7 December 2018. The course will cover introduction to R, version control, statistical analyses, data management and reproducibility.

Registrations are open for the RNA Seq Data Analysis by using the Galaxy platform in Debrecen, Hungary, on 17-18 November. The course is free!

Join us in Ghent, Belgium, for the workshop NGS introduction using Galaxy on 6 November 2018. The registration is free.

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Weekly news 08.10.2018

ELIXIR Training is organising a satellite event at NETTAB in Genova, Italy on 22 October 2018 Adopting Open Source Software FAIR Practices.

The registration is now open for the EMBL-EBI course ‘Introduction to Metabolomics Analysis Course’ on 5-8 February 2019 in Hinxton, UK.

Members of ELIXIR Slovenia are co-organising  the largest Systems Medicine symposium in Europe, the 2nd Conference of the European Association of Systems Medicine on 7 – 9 November 2018 in Utrecht, the Netherlands. Registration is still open. Please consider joining the conference that represents a unique occasion for closer links between ELIXIR and the leaders in the field of Systems Medicine.

Registrations are open for the SIB course on “Single-cell RNA-Seq Analysis”, in Bern (Switzerland), on 28-30 November 2018. This course will close with a minisymposium consisting of short scientific talks from SIB researchers on single-cell.

There are still free seats available for the 1st de.NBI Cloud User Meeting. In a 3-day event on 29 - 31 October 2018 at Bielefeld University you can learn about life science projects hosted in the de.NBI Cloud. Talks and workshops will be given about current de.NBI Cloud projects and state of the art cloud computing technologies like Spark, Docker and Kubernetes.

 

 

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.

 

  • 1 min read

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.