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  • 1 min read

Unix Shell Basics training course March 3rd

Advanced computing power is hidden away in clouds/cluster/supercomputers that you do not have click and point access. As a general rule these high performance computer resources use Linux operating systems and are accessible only by a shell terminal.

This course is aimed to provide basic survival skills in Linux and terminal environment. We will teach you how to access files and folders, move around and hopefully shake off the fear of getting stuck somewhere along the way.

Objectives:

  • Obtain basic knowledge on dealing with files using command line (Linux or Mac)
  • Learn how to use search over several text files, combine files, extract certain knowledge.
  • Master tips and tricks for effective command line hacks that would save a lot of time.

Requirements:
Lecture venue is computer class with linux computers. In case you bring your own Windows laptop, please make sure to install Putty application (https://www.putty.org/) beforehand.

Materials:
https://elixirestonia.github.io/2020-03-03-tartu/

Registration:
The course is full!

Time:
March 3, 2020
10:15–14:00

Venue:
Auditorium 2005 (the Linux classroom)
UT Delta Centre
Narva mnt 18
51009 Tartu
Estonia

NB! Two weeks later we will run an Unix Shell Advanced course for people who have already basic knowledge.

  • 1 min read

Estonia Joined the Nordic e-Infrastructure Collaboration Initiative

On February 11th Estonia joined the Nordic e-Infrastructure Collaboration NeIC by signing the collaboration agreement at the Delta Centre in Tartu. This agreement gives Estonian research infrastructures the possibility to maintain and enhance their competitiveness and do more international cooperation.

The agreement was signed by Arne Flåøyen, Director for NordForsk, an institution  that facilitates and provides funding for cooperation on research across the Nordic region, and Andres Koppel, the chairman of the board of the Estonian Research Council.

More information is available at 

https://www.etag.ee/en/estonia-joined-the-nordic-e-infrastructure-collaboration-initiative/

https://neic.no/news/2020/01/09/estonia-joins-neic/

 

 

  • 2 min read

Weekly news 17.02.2020

ELIXIR Guest Webinar: Text mining of disease-gene networks 

19 February 2020 | Online | 14:00 GMT/15:00 CET

Most of what we know about human diseases and genes/proteins involved in them is buried in the biomedical literature. Text mining is thus a key tool for creating databases with structured data on disease-gene associations and the underlying gene networks.

In this webinar, Lars Juhl Jensen from the Novo Nordisk Foundation Center for Protein Research at the University of Copenhagen, Denmark, will describe a highly efficiently text-mining pipeline, which allows his team to systematically mine such information from very large corpora of full-text articles as well as abstracts. The presentation will also cover how this information is made available through interoperable, web-based databases, including the DISEASES database and the STRING database (an ELIXIR Core Data Resource). Finally, Lars will show how the Cytoscape stringApp brings together these databases, allowing users to easily retrieve, analyze, and visualize gene networks for diseases or other topics of interest.

Lars Juhl Jensen is a professor at the Novo Nordisk Foundation Center for Protein Research at the University of Copenhagen in Denmark. His research group develops state-of-the-art tools for generation and analysis of molecular interaction networks from proteomics data and text mining. The tools are freely available to the scientific community.

More: jensenlab.org

A paper on TeSS was recently accepted and published by Oxford University Press to review the training platform's features, workflows and future prospects.

 

ELIXIR events

3-Day Course Single-cell Transcriptomics
1-3 April 2020 | University of Lausanne, Switzerland 

Software Carpentry Course 
30-31 March 2020 | Cologne, Germany

Innovation and SME Forum: Data-Driven Innovation in the Agritech Sector
24 -25 March 2020 | Lyon, France

ELIXIR Bioinformatics Industry Forum 
28 April 2020 | London, UK

  • 2 min read

ELIXIR Estonia is part of the new ELIXIR-CONVERGE project

ELIXIR-CONVERGE — a new project to streamline data management practices

From accelerating to converging

After the completion of the successful ELIXIR-EXCELERATE project, which provided  ELIXIR with solid foundations, today ELIXIR kicks off a new project to support the provision of data management across Europe.

ELIXIR-CONVERGE, a €5 million three-year H2020 project, will bring together experts from all 23 ELIXIR Nodes, representing 29 research institutes and 22 countries across Europe to work collaboratively on some of the major challenges in data access, provisioning and distribution. The development of a data management toolkit will sit at the core of the project, providing researchers with a strategy to manage their data to international standards. 

The toolkit will be tested across multiple domains and data types against ‘Demonstrator Projects’ that cover:

  • Plant genotype and phenotype
  • Epitranscriptomics
  • Marine metagenomics
  • Human genomics
  • Toxicology
  • Bimolecular simulation

​ELIXIR CONVERGE map

Niklas Blomberg, Director of ELIXIR and Coordinator of ELIXIR-CONVERGE, said: “Many ELIXIR Nodes already provide local support and expertise with data management to national research projects and life scientists in that country. With the ELIXIR-CONVERGE project, we want to ensure that this data management provision is as developed as possible within each country and as connected as it can be across countries too. While data generation is a local process, often the expertise for the management of that dataset sits in another country, or the resource where the data will be deposited is in a different country. So there is a strong need to move beyond national data management support, we need to connect them across countries. ELIXIR-CONVERGE will allow us to construct that system across Europe”.

Further information

Dive into the ELIXIR-CONVERGE project to find out more about its key objectives, outputs and structure.

  • 1 min read

Bioinformatics Research and Education Workshop (BREW)

The Institute of Computer Science at the University of Tartu is organising this year's Bioinformatics Research and Education Workshop

The workshop will take place at Delta centre during May 21-22, 2020

BREW is a workshop for PhD students in bioinformatics, which aims to give an introduction to scientific conferences, including submission, peer review and presentation of scientific papers. All participants must submit a paper and take part in reviewing papers from other participants in order to attend the workshop. After the review deadline, students have a chance to make alterations to their paper and deliver a final version. All participants will present their paper at the conference-style meeting.

BREW is open for students and supervisors from the PhD programs in Bioinformatics and Computational Biology in participating universities. For particular details, please contact the organizers via email.

The workshop is free of charge, and will include lunch, snacks and a social evening. Accomodation is paid for by the local organizing committee. More details are available on the corresponding page.

Registration by March 1, 2020

More info at https://brew2020.cs.ut.ee/index.php

  • 1 min read

EMBO practical course in population genomics in Italy

ELIXIR-IIB is pleased to announce the fourth edition of the EMBO practical course in population genomics, this year there will be added emphasis on programming and machine learning applied to population genomics.

https://elixir-iib-training.github.io/website/2020/04/01/population-genomics-procida.html

Registration deadline is 28 January 2020

This EMBO Practical Course will cover coalescent theory, the effect of demography in space and time, genetic clustering, the detection and quantification of admixture and selection. Lectures on these topics will be complemented by hands-on computer practicals introducing a wide range of software packages, both in R and Python.

This course is aimed at evolutionary biologists who already have basic bioinformatics skills. The main criterion for selection will be how much a candidate can benefit from the course. This implies that PhD students and Postdoc researchers will likely be favoured; however, applications from candidates at all levels will be considered.

Fellowships to cover travel expenses and for childcare are available.

  • 1 min read

ELIXIR Weekly News 13.01.2020

ELIXIR Spain will be hosting ECCB 2020 in Sitges, near Barcelona 5 - 9 September 2020. Please note the deadline for the call for workshops/SIG applications and tutorial applications is 30 January. 

A publication on “Data Stewardship Wizard” has been released in the Data Science Journal. The Data Stewardship Wizard is a tool for data management focusing on getting the most value out of data management planning.

The Galaxy Machine Learning workbench is now available in Galaxy and provides you with the a Swiss Army knife of scikit-learn, Keras (a deep learning library based on TensorFlow) and various other tools to manipulate, convert and plot your data.

 

 

  • 1 min read

Weekly news 16.12.2019

The last Gallantries Project face-to-face meeting took place at INAB | CERTH, Thessaloniki, Greece 9-10 December. During this meeting the R and RStudio lessons within Galaxy were refactored, along with a pop-up course on making volcano plots in R. Helena Rache put out a blog-post on this, and materials were shared by the Galaxy twitter channel.

ELIXIR-CZ have created a very engaging animated video all about ELIXIR and the Czech Node. Features FAIR data and ELIXIR AAI. Well worth a watch! 

ELIXIR Finland has published a new article about ELIXIR Compute Platform for life and health sciences. Read to find out about how the Compute Platform has helped research across multiple ELIXIR Communities. 

The Dutch Techcentre for Life Sciences (DTL) have released their 2019 highlights newsletter. Read on to find out about their activities with ELIXIR and beyond. 

FAIRplus Innovation and SME Forum: Implementing FAIR data principles in industrial life science research
29 January 2020 | Hinxton, Cambridge, UK

Innovation and SME Forum: Data Driven Innovation in the Agritech Sector
24 -25 March 2020 | Lyon, France

  • 1 min read

Weekly news 09.12.2019

The Finnish IT Centre for Science (CSC) have published a new video: 'How do I authorise access to my sensitive data?'. Explaining the process of making your data open, the data access committee and authorisation tool. 

A recent article published in Science on how GDPR affects international biomedical research features comments from members of the Spanish National Bioinformatics Institute (INB) including Deputy Head of Node for ELIXIR Spain Salvador Capella. 

The European Open Science Cloud (EOSC) Life project recently released their second newsletter. You can sign up here to find out about their news and events. 

Best practices in research data management and stewardship 27 - 28 January 2020 | Esch-sur-Alzette, Luxembourg

Data visualisation for biology: A practical workshop on design, techniques and tools 16 - 20 March 2020 | Hinxton, Cambridge, UK

 

  • 1 min read

Weekly news 02.12.2019

Galaxy have loaded fully consented genome sequences from 10 individuals from the Personal Genomes Project (PGP) along with transcriptomic and methylomic data in collaboration with PGP to facilitate training within the platform. These data are open and available to be looked at within Galaxy and please feedback to bjoern.gruening@gmail.com if you require specific analysis on this data.

The ELIXIR Tools Platform published a paper "Towards FAIR principles for research software". The paper analyses how FAIR principles can be applied to software, as opposed to data. It also explores whether existing FAIR principles can be applied directly to software, or where they need to be adapted or reinterpreted. This publication coincides with the launch of fair-software.nl website, which provides recommendations on ways to improve the quality and reproducibility of software.

The programme of SIB training courses for 2020 is now online. Over 20 courses are already planned, and lots more are yet to come!  The topics covered span areas such as NGS and other omics data analysis, single-cell, statistics, programming, machine learning, and several SIB resources.