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

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. 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.

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.

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.

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

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