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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.

Thursday, December 9, 2021, 9:00-16:30 CET
Veterinary Faculty, podiplomska soba (zgornje nadstropje na VF pri dekanatu)
Please bring your laptops.

You can register for the course by following this link.

Course participants will learn how to generate data management plans for research projects so that the plan meets the requirements of funding organisations. During the hands-on session you will set up a data management plan using the Data Stewardship Wizard (DSW) tool. DSW is more flexible and provides more domain-specific templates than other data management tools.

Course agenda:
Legal requirements for research projects
Introduction to Data Stewardship Wizard (DSW)
Persistent identifiers, controlled vocabularies and ontologies
Relevant deposition repositories and data archives
Licensing of data, biological material and software
Hands on training and assistance to generate a data management plan

The intended audience are researchers in life sciences (including PhD students) who would like to learn how to properly submit a grant application for a research project. Participants are required to bring their own laptops.

Participants are encouraged to bring their own data (BYOD) about their project for hands-on session on data management planning (DMP).

Teachers:
Korbinian Bösl (ELIXIR Norway - remote lecture via a video conference)
Brane Leskošek (ELIXIR Slovenia)

Helpers:
Marko Vidak (ELIXIR Slovenia)
Nadja Žlender (ELIXIR Slovenia)

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.

Vision of e-learning within ELIXIR

(extract from ELIXIR-EXCELERATE deliverable)

E-learning tools and services can be used in many different ways to complement ELIXIR training methods. In the future, ELIXIR training courses could use e-learning services (e-learning augmented training) to enable course participants and trainers to concentrate fully on the content of the course, moving away from the complexity of local installation of tools and services needed for a course. Such e-learning augmented training should enable teachers to follow participants' progress during course execution remotely or in situ, either synchronously or asynchronously.

EeLP follows Trainground principles and provides a single access point for trainers as well as trainees, to all necessary information, dynamic educational resources, tools and services for any training event, including access to registration, compute infrastructure (HPC), exams, comms and certificates.

For long term sustainability of ELIXIR e-learning it is important to have a specific e-learning community forum where e-learning information and experiences are exchanged. For that purpose, an ELIXIR e-learning group was established in January 2019 and will exist beyond the ELIXIR-EXCELERATE project. This group will set up and maintain the list of e-learning services and tools provided by the Nodes that will be displayed in TeSS, will provide an e-learning consultant service and will address issues such as transforming existing face-to-face course into e-learning courses or the needs of special e-learning tools or services for training events.

TtT template course

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