ELIXIR Training eSupport System TeSS had its kick off meeting on October 23rd.
ELIXIR TeSS club brings together all parties interested in further developing TeSS further.
The group gathered for the first time on 23 October and will take place biweekly on Fridays betwen 10–11 CET.
The next meeting will be on 6 November to discuss the prioritisation of tasks for 2021.
ELIXIR Estonia is one of the Nodes helping to develop TeSS further.
The COVID-1 Viral Beacon is an ELIXIR Spain platform that allows researchers to browse SARS-CoV-2 variability at the genome, amino acid, structural and motif level
Bioinformaticians from the Center for Genomic Regulation (CRG) have built this time-saving tool with an extremely friendly interface.
More information at https://elixir-europe.org/news/beacon-ocean-sars-cov-2-data
If you are a researcher working in -omics (genomics, proteomics, metabolomics) and / or deal with data analysis, integration & stewardship join the online X-omics festival. Read more on the event website.
WE HAVE POSTPONED THE COURSES TO UNFORESEEN FUTURE.
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 streamline your skills in Linux and terminal environment. We will teach you how to make your life easier by creating maintainable and flexible bash scripts for your commonly used workflows or SLURM jobs.
Objectives:
Expected prior knowledge:
Experience in using the basic commands covered in the Basics course (e.g. cd, ls, mkdir, mv, cp, head, cat, find, less, pwd).
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/2020-03-17-tartu/
Registration:
Application is open at https://forms.gle/pzWrKDNcxpStEADk8
Time:
March 17, 2020
10:15–14:00
March 20, 2020
10:15–14:00
Venue:
Auditorium 2005 (the Linux classroom)
UT Delta Centre
Narva mnt 18
51009 Tartu
Estonia
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 streamline your skills in Linux and terminal environment. We will teach you how to make your life easier by creating maintainable and flexible bash scripts for your commonly used workflows or SLURM jobs.
Objectives:
Expected prior knowledge:
Experience in using the basic commands covered in the Basics course (e.g. cd, ls, mkdir, mv, cp, head, cat, find, less, pwd).
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/2020-03-17-tartu/
Registration:
Application is open at https://forms.gle/pzWrKDNcxpStEADk8
Time:
March 17, 2020
10:15–14:00
March 20, 2020
10:15–14:00
Venue:
Auditorium 2005 (the Linux classroom)
UT Delta Centre
Narva mnt 18
51009 Tartu
Estonia
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.
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:
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.
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/
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
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:
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”.
Dive into the ELIXIR-CONVERGE project to find out more about its key objectives, outputs and structure.
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