10-12 December 2019

Stockholm and Umeå, Sweden;
Ljubljana, Slovenia;
also available for remote online participants.

NBIS (the Swedish node of ELIXIR) and ELIXIR Slovenia are offering an "Introduction to Linux" course targeted at life scientists who want to extend their skills and knowledge.

Big data (usually in the form of large text files) are generated nowadays in many fields of science. Trying to handle this data with applications like Word or Excel is difficult or impossible, while using the Linux command line can improve data processing efficiency. Unix/Linux provides an excellent computing environment for several disciplines (such as bioinformatics, physics, engineering) and the command line interpreter (shell) serves as an interface to many big-data processing programs.

The course provides a basic introduction to Unix/Linux commands and covers how Unix/Linux commands can be used to manage and inspect your data and results, and how to generate and run pipelines and workflows using basic shell scripting. Finally, we will show you how the command line is used for access to supercomputers for boosting your scientific research.

Participants will be able to attend the course either by traveling to Stockholm or to Umeå in Sweden, to Ljubljana in Slovenia, or by connecting remotely via the ELIXIR Slovenia eLearning Platform (EeLP). The number of remote students is limited to 30. The number of students per classroom is limited to 15 for Stockholm and Umeå, and 20 for Ljubljana. Additional participants will be placed on a waiting list and contacted as soon as space becomes available. The course will be broadcast from Sweden.

The registration deadline has been extended until Friday, November 22. You can register for the course on Eventbrite by following this link.

Metadynminer webinar

Friday, 31 May 2019 at 15:00 CEST

Metadynminer is an R package for analysis and visualization of metadynamics results. It can load results from Plumed, a popular open-source metadynamics package. We will show basic and advanced options how to use Metadynminer and present plans for a future version.

Agenda:

• 20 min presentation
  
• 10 min discussion
  

You can register for the webinar by filling in a registration form available at this link.

The webinar is organised by Vojtech Spiwok from UCT Prague and ELIXIR Czech Republic, in cooperation with ELIXIR Slovenia.

ELIXIR Software Carpentry - Ljubljana

16-17 May 2019, Faculty of Medicine, Vrazov trg 2, Ljubljana (Slovenia)

ELIXIR Software Carpentry is a workshop intended for all those who would like to learn more about the basics of R - software environment used in bioinformatics for statistical computing and graphics. The workshop will include a keynote lecture about data management in ELIXIR-SI.

The workshop will be in English.

Registration:

• here is a link to the registration form
• the limit of participants is 20
• the course is free of charge
• course participants have to bring their own laptops

The course will take place at the University of Ljubljana, Faculty of Medicine, Vrazov trg 2, Ljubljana. The classroom will be announced later.

The limit of participants is 20. If the number of registered applicants exceeds this limit, selection of participants will be made. It will be based on the time of their registration and their affiliations, as well as geographic distribution.

Sessions will be intensive and hands-on, and taught by experienced software carpentry instructors. The course is recommended for anyone who would like to learn more about using statistical computing and graphics in the bioinformatics field, both for research or operational work.

Program topics:

• Keynote lecture about ELIXIR-SI data management
  
• Introduction to Linux/Unix command line
  
• R

The course is organised by ELIXIR Slovenia in collaboration with Data & Software Carpentry.

ELIXIR is an European ESFRI priority research infrastructure for bioinformatics that provides databases, (software) tools, services and training (including training materials) for information, cloud storage and supercomputers in the area of life sciences. It coordinates, develops, integrates and sustains life science (bioinformatics) resources across Europe.

This is an OPEN-ACCESS online tutorial where you can learn how to install and deploy Beacon.

The tutorial contains learning materials provided by Beacon developers. Among these materials you can find instructions for Beacon installation and deployment - as both PDF file and tutorial video.

ELIXIR Data Carpentry for Genomics - Ljubljana

29-30 Jan 2019, Faculty of Medicine, Vrazov trg 2, Ljubljana (Slovenia)

ELIXIR Data Carpentry for Genomics is a course intended for all those who would like to learn more about the basics of data processing and data management in the field of genomics.

The course will be in English.

Registration:

• register here
• the limit of participants is 20
• the course is free of charge

The course will take place in the computer classroom at the Institute of Biostatistics and Medical Informatics (IBMI), Faculty of Medicine, Vrazov trg 2, Ljubljana.

The limit of participants is 20. They will be selected on the time of registration and organisation and geographic widespread.

Sessions will be intensive and hands-on, and taught by experienced data carpentry instructors. The course is recommended for anyone who would like to learn more about how to process and manage big scale genomic data.

Program topics:

• Introduction - Presentation of ELIXIR Slovenia and ELIXIR-SI eLearning Platform
  
• Project management in genomics and introduction to cloud computing
  
• Introduction to Linux/Unix command line
  
• Data wrangling and processing for genomics

Instructors will be Vasilis Lenis (University of Plymouth, UK) and Živa Ramšak (ELIXIR Slovenia; National Institute of Biology Ljubljana).

The course is organised by ELIXIR Slovenia in collaboration with ELIXIR Hub and Data & Software Carpentry.

ELIXIR is an European ESFRI priority research infrastructure for bioinformatics that provides databases, (software) tools, services and training (including training materials) for information, cloud storage and supercomputers in the area of life sciences. It coordinates, develops, integrates and sustains life science (bioinformatics) resources across Europe.

26-30 Nov 2018, Tromsø, NO

ELIXIR Norway in cooperation with ELIXIR Slovenia is pleased to announce the first Hands-on workshop in Marine Metagenomics

The aim of the workshop is to introduce the participants to the research field of metagenomics with focus on samples from the marine environment. The theoretical part for each subject will be introduced via lectures, followed by a practical Hands-on session.

Place: The Arctic University of Norway, each day from 09.00 until 16.00

Target audience: Researchers and students above bachelor level

Prerequisite: None, but study or research interest in metagenomics is expected

COURSE FEE: € 250,-

Deadline for application 1st Nov 2018

Register here

The maximum number of participants is 20. If the interest for the course is greater than this, we will select participants based on a geographical distribution and on how relevant the workshop will be to the participant.

24-28 Sep 2018, France

A course is being organized in Montpellier, hosted by the French ELIXIR Node and in cooperation with the nodes involved in ELIXIR-EXCELERATE task 10.3 “Capacity Building in Genome Assembly and Annotation”. Some of the most experienced assembly and annotation experts in Europe will be teaching at the course.

The course is aimed at researchers interested in learning more about genome assembly and annotation. It will include information useful for both the beginner and the more advanced user. We will start by introducing general concepts and then continue to step-by-step describe all major components of a genome assembly and annotation workflow, from raw data all the way to a final assembled and annotated genome. There will be a mix of lectures and hands-on practical exercises using command line Linux. After the course the participants will be aware of common practices and commonly used tools and be able to run assembly and annotation projects on their own.

Prerequisites:

• knowledge of using command line Linux
• prepare info about your own project and tentatively bring your own data

13-15 Feb 2018

Linköping & Umeå, SE; Ljubljana, SI

21 November 2017

19-23 Jun 2017, Ljubljana, SI

A course is being organized in Ljubljana, hosted by the Slovenian ELIXIR Node leading organisation and in cooperation with the nodes involved in ELIXIR-EXCELERATE task 10.3 “Capacity Building in Genome Assembly and Annotation”. Some of the most experienced assembly and annotation experts in Europe will be teaching at the course.

The course is aimed at researchers interested in learning more about genome assembly and annotation. It will include information useful for both the beginner and the more advanced user. We will start by introducing general concepts and then continue to step-by-step describe all major components of a genome assembly and annotation workflow, from raw data all the way to a final assembled and annotated genome. There will be a mix of lectures and hands-on practical exercises using command line Linux. After the course the participants will be aware of common practices and commonly used tools and be able to run assembly and annotation projects on their own.

Prerequisites:

• knowledge of using command line Linux
• prepare info about your own project and tentatively bring your own data

Registration and venue

27-29 Mar 2017

Linköping & Umeå, SE; Ljubljana, SI

30 Nov 2016, Ljubljana, SI

12-14 Oct 2016, Prague, CZ

A course is being organized in Prague, hosted by the Czech ELIXIR Node leading institute and in cooperation with the nodes involved in ELIXIR-EXCELERATE task 10.3 “Capacity Building in Genome Assembly and Annotation”. Some of the most experienced assembly and annotation experts in Europe will be teaching at the course.

The course is aimed at researchers interested in learning more about genome assembly and annotation. It will include information useful for both the beginner and the more advanced user. We will start by introducing general concepts and then continue to step-by-step describe all major components of a genome assembly and annotation workflow, from raw data all the way to a final assembled and annotated genome. There will be a mix of lectures and hands-on practical exercises using command line Linux. After the course the participants will be aware of common practices and commonly used tools and be able to run assembly and annotation projects on their own.

Registration and venue