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NBIS, SciLifeLab, ELIXIR-SE, ELIXIR-SI

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.

ELIXIR-NO ELIXIR-SI

University of Tromsø
Medisin og helsefagbygget: Datarom (U7.110)
Tuesday 26th November 09.00-15.00

We are pleased to announce the second hands-on bioinformatics NeLS workshop organised in Tromsø by ELIXIR Norway (https://www.elixir-norway.org/).  The topic is on how you can use the Norwegian e-Infrastructure for Life Sciences (NeLS) (nels.bioinfo.no) to store and share data, and to run analyses via customisable analysis workflows in Galaxy. More specifically, we will go through how you can store data in NeLS and upload it directly into Galaxy. We will also construct and run a complete sequence analysis workflow for taxonomic profiling on a metagenomic sample.  There are no requirements for programming skills or experience using the command line, as Galaxy provides a web interface for running analysis.

Teachers:
    Erik Hjerde, University of Tromsø
    Ståle Nygård, University of Oslo
    Nils Peder Willassen, University of Tromsø

ELIXIR-IT ELIXIR-SE
ELIXIR-FR ELIXIR-SI

Genome assembly and annotation course 5

1-5 Jul 2019, University of Milano-Bicocca, Milan, Italy

A genome assembly and annotation course will take place on July 1-5, 2019 in Milan, Italy, hosted by the Italian ELIXIR Node in cooperation with other ELIXIR nodes that are involved in the 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 with a step-by-step description of 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 Unix/Linux command line.

After the course, the participants will have knowledge of commonly used assembly practices and tools. They will be able to run assembly and annotation projects on their own.

Prerequisites:

  • Working knowledge of Unix/Linux command line
  • Please prepare information about your own projects (PowerPoint / PDF presentation IS NOT NEEDED) so that you will be be able to discuss about your research. Optionally, you may also bring your own data.

Please follow this link to register for the course.
You will be able to access the course after you register and your registration is approved by the course organizers.

Everyone interested can learn more about the course on the ELIXIR-IIB Training Platform webpage.

elixir-cz-si

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-SI ELIXIR-hub
excelerate

ELIXIR e-learning workshop 2019 - Ljubljana

23-24 May 2019, Faculty of Medicine, Vrazov trg 2, Ljubljana (Slovenia)

ELIXIR e-learning workshop is intended for ELIXIR Nodes that are actively participating in the eLearning subtask within the EXCELERATE project, as well as for Training coordinators or e-learning experts from other ELIXIR Nodes.

The workshop will be in English.

Please click here to complete the registration form. The registration is possible with invitation only.

The event will take place at the Institute of Biostatistics and Medical Informatics (IBMI), Faculty of Medicine, Vrazov trg 2, Ljubljana in the conference room next to the library.

Workshop agenda:

  • Registration and welcome
  • Presentation of EXCELERATE report of eLearning subtask
  • e-learning beyond EXCELERATE
  • Discussion of candidate topics for production of new e-learning materials
  • TeSS and e-learning
  • Wrap up and future meetings plan

Travel and accommodation suggestions:

  • ELIXIR-SI can pre-book rooms for workshop participants, participants themselves cover their accommodation costs.
  • Optimal airports are Ljubljana and Trieste, easy to reach also from Venice, Treviso, Zagreb, Graz, Klagenfurt.
  • Instructions how to travel from nearby airports to the venue will be provided.

The workshop is organized by ELIXIR Slovenia. Programme committee: Brane Leskošek, Jure Dimec, Alex Botzki and Patricia Palagi.

ELIXIR-SI ELIXIR-hub

excelerate

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.

cwl-logo       elixir-si-logo

This is an open-access online tutorial where you can learn how to write tool wrappers and workflows using the Common Workflow Language (CWL). The materials provided here describe the first stable version of the CWL - Version 1.0. When newer stable CWL versions are released, the materials will be updated.

The tutorial is hosted on the ELIXIR-SI eLearning Platform (EeLP). The main part of the tutorial are learning materials with instructions how to use the CWL to write your workflows. These materials start with the most basic lessons and then continue with more advanced topics, so no previous knowledge about the CWL is required to follow this tutorial.

ELIXIR Finland ELIXIR Spain
ELIXIR Slovenia Beacon Network

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-SI ELIXIR-hub

excelerate

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.

ELIXIR-SI ELIXIR-FR

ELIXIR TtR course: Basic genomics using advanced analysis tools

Genomic Data Science with Galaxy

Dec 20-21, University of Ljubljana, Faculty of Medicine, Ljubljana (Slovenia)

Galaxy is an open source, web-based platform for data intensive biomedical research. The Galaxy Platform provides user friendly software for producing reproducible genomic pipelines for data analysis. This workshop will provide a 2 day introductory session to Galaxy software system.

The course will be in English.

Registration:

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

This course will focus on introducing the Galaxy user interface and how it can be used for basic genomic analyses. Sessions will be intensive and hands-on, and taught by experienced instructors from the Galaxy Community. We will cover the basic features of Galaxy, including where to find tools, how to import and use your data, and an introduction to workflows. This session is recommended for anyone who has not used, or only rarely uses Galaxy.

Program topics:

  • Quick introduction to Galaxy GUI
  • From peaks to genes
  • Reference-based RNA-seq - Quality control
  • Reference-based RNA-Seq - Sequencing

Lecturers will be Christophe Antoniewski and Olivier Inizan from ELIXIR France.

Course is organised by ELIXIR Slovenia in collaboration with ELIXIR France.

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.

Prerequisites:

  • Wi-Fi enabled laptop with a modern web browser. Latest versions of Google Chrome, Firefox, Safari and Opera will work best.
logo_embric_final_transparent
ELIXIR-NO ELIXIR-SI

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.

ELIXIR-CZ

4-5 Oct 2018, Prague

Workshop organised by ELIXIR CZ at the Institute of Organic Chemistry and Biochemistry of the CAS in cooperation with the Czech Society for Mass Spectrometry.

Analysing proteomics data involves a multitude of computational steps. This workshop will introduce the basics of how to design and run these steps within Galaxy, a free and easy-to-use web platform that enables users to connect bioinformatics tools into a workflow.

The focus will be on proteomics tools available for Galaxy and development of workflows to combine processing steps.

IMPORTANT: For access to the course, please register here.

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
ELIXIR-LU ELIXIR-NL
ELIXIR-SI

Materials from
ECCB18 Workshop “Implementation of Data Management Plans & Data Stewardship in practice
11 Sep 2018 in Athens

Summary

Collecting, curating storing and exchange or sharing research data is a constant challenge that has become more difficult with the complete digitalisation of the modern research. Larger projects and organisations now bring into play data stewards who organise research data and support researchers in these efforts.

The FAIR principles help to assess the quality of one’s data management. In this workshop, we will present tools to help data management and stewardship as well as bring examples of how such principles of data management perform in larger studies. We will touch on ethical, legal and data protection issues as well as the limitations imposed by data owners. We will also have an open discussion on better data management from practical aspects. It aims at larger projects with considerable contributions from bioinformatics.

Organizers

  • Celia van Gelder (ELIXIR-Netherlands)
  • Mateusz Kuzak (ELIXIR-Netherlands)
  • Roland Krause (ELIXIR-Luxembourg)
  • Brane Leskosek (ELIXIR-Slovenia)
  • Marko Vidak (ELIXIR-Slovenia)

Target audience

Researchers and bioinformaticians supporting researchers in making Data Management Plans.

Wednesday 30 May 2018, Seminar 5, 14:30 – 16:30

bitlab UMA
ELIXIR-ES

ELIXIR-SI

PRACE

NBIS, SciLifeLab, ELIXIR-SE, ELIXIR-SI
13-15 Feb 2018

Linköping & Umeå, SE; Ljubljana, SI

CHARMEELIXIR-SI

6-7 Feb 2018, Ljubljana

23-27 Oct 2017, Portugal

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

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

NBIS, SciLifeLab, ELIXIR-SE, ELIXIR-SI
27-29 Mar 2017

Linköping & Umeå, SE; Ljubljana, SI

How to get the most out of your microarray experiment – from design to biology“. The joint webinar is hosted by ELIXIR Sweden and ELIXIR Slovenia. It takes place on February 14th 2017 from 12:30 pm to 2:30 pm CET. The webinar presenters are

  • Eva Freyhult, NBIS/Elixir Sweden,
  • Jessica Lindvall, NBIS/Elixir Sweden, and
  • Mihaela Martis, NBIS/Elixir Sweden.

30 Nov 2016, Ljubljana, SI

28-30 Nov 2016, Ljubljana, SI

ELIXIR-CZ

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

ELIXIR-SW & ELIXIR-SI

17-19 Oct 2016, Linköping & Umeå, SE

International Network for Translating Research on Perinatal Derivatives into Therapeutic Approaches