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Autumn semester Data Management courses

ELIXIR Estonia is continuing with the data management-related lectures and workshops this semester. To get more information about these courses, read below and visit https://elixir.ut.ee/training. 

 

Face-to-Face (F2F) lectures will take place at the Delta building in Tartu (Narva mnt 18, Tartu). 

ONLINE workshops will be held through Zoom (the meeting link will be sent a couple of days before the workshop). 


 

  • 13.09.2022 - Metadata and README (lecture, F2F, 2h) CLOSED

Register: https://forms.gle/6y2FaHMN7nrbA5bR7 

More information: https://elixir.ut.ee/node/448 

  • 27.09.2022 - Licensing Research Outputs (lecture, F2F, 2h) CLOSED

Register: https://forms.gle/ahVcG64FPJvTwuu68 

More information: https://elixir.ut.ee/node/450 

  • 4.10.2022 - How to Make Your Messy Data Usable? - PART 1 (workshop, ONLINE, 2h + independent work) CLOSED

Register: https://forms.gle/bWiBGrpanoot3YR59 

More information: https://elixir.ut.ee/node/456 

  • 25.10.2022 - Data Visualization I - Figures (lecture, F2F, 2h) CLOSED

Register: https://forms.gle/rjiGvJj32qweG5mj6 

More information: https://elixir.ut.ee/node/452 

  • 1.11.2022 - Crash Course of GDPR (lecture, F2F, 2h) - Cancelled

Register: https://forms.gle/dNVQPs3y35k5Ua8y8

More information: https://elixir.ut.ee/node/454 

  • 8.11.2022 - How to Make Your Messy Data Usable? - PART 2 (workshop, ONLINE, 1h + independent work) CLOSED

Register: https://forms.gle/2uMN9RN8LEyT8doM7 

More information: https://elixir.ut.ee/node/456 

 

We do ask you to register for the lecture responsibly. If you can’t attend the course, please let us know as soon as possible via email at elixir@ut.ee. 

Crash Course on GDPR lecture - 01.11.2022

On the 1st of November 2022, ELIXIR-Estonia will hold a new data management online course: Crash Course on GDPR. The course will be held in English. 

When handling any kind of information that may help to identify a person, whether directly or indirectly, it must be handled with care. Particular attention should be put to collecting, processing, handling, and storing the data throughout the research process. This is meant for both textual, but also audio, video, and picture data. However, what does this mean for the researcher?

In this lecture, we will go over what GDPR and the Estonian Personal Data Protection Act say when dealing with personal data. Also, we will concentrate on what it means for the researcher working with this data and what he/she/they need to do to abide by these laws. This lecture will also cover the consent form and anonymization/pseudonymization processes. 

 

Information about the lecture

Lecture: 1st of November, 2022 at 14:15 (lecture, 12h)

Place: Delta Building, r1022 (Narva mnt 18), TARTU

Register: REGISTRATION CLOSED

Registration closes at 23:59 on 27.10.2022 or when the course gets full.

 

Learning outcomes for the participants: 

  • Understand the rules and regulations you have to abide by when dealing with sensitive data
  • Understand the safety measures you need to take into account when working with sensitive data
  • Understand the difference between anonymization and pseudonymization

 

F2F lectures will take place at the Delta building in Tartu (Narva mnt 18, Tartu).

We do ask you to register for the lecture responsibly. If you can’t attend the course, please let us know as soon as possible via email at elixir@ut.ee. 

Data Visualization I - Figures lecture - 25.10.2022

On the 25th of October 2022, ELIXIR-Estonia will hold a new data management online course: Data Visualization I - Figures. The course will be held in English. 

All researchers will be handling some data at some point in their careers. However, the data, in its regular shape (tables), is quite hard to grasp for most people. Especially if there is a lot of it, this is where data visualization comes to help. The idea is to bring forth the essential aspects of the data - to tell a story. However, just putting data into a graph or figure might do more harm than good. Not only could it give wrong conclusions, but it also might be misleading. This is one of the main reasons why the exact way how you visualize the data is fundamental. 

This lecture is part of a series of lectures and workshops called “Data visualization.” The first lecture will discuss why data visualization is important and what we should consider when designing it. This means what chart type to pick, how much information to include, what (and how) to highlight, and so on. 

 

Information about the lecture

Lecture: 25th of October, 2022 at 14:15 (lecture, 2h)

Place: Delta Building, r1022 (Narva mnt 18), TARTU

Register: REGISTRATION CLOSED

Registration closes at 23:59 on 20.10.2022 or when the course gets full.

 

Learning outcomes for the participants: 

  • Understands how to tell a story through data visualization
  • Knows what chart type to pick for different kinds of data
  • Knows what to pay attention to while designing a figure

 

F2F lectures will take place at the Delta building in Tartu (Narva mnt 18, Tartu).

We do ask you to register for the lecture responsibly. If you can’t attend the course, please let us know as soon as possible via email at elixir@ut.ee. 

How to Make Your Messy Data Usable? - Beginner and Advanced workshop - 04.10.2022/8.11.2022

On the 4th of October 2022, ELIXIR-Estonia will be holding a data management online course: How to Make Your Messy Data Usable? - PART 1. The course will be held in English. This course will be in two parts: a 1.5-hour online lecture on how to make a spreadsheet usable for other people held on the 4th of October at 10:00 in Zoom. The practical workshop on cleaning your messy data with OpenRefine software will be a video lecture you can follow in your own time. Additionally, we will hold 2 Q&A sessions in Zoom, where you can talk about any problems you encountered with the OpenRefine software.

This course will cover how to name your files and variables, version control, compile a data dictionary, and what to do with empty cells. In the second part of this lecture, OpenRefine software is introduced. With this, you can easily clean up the messy data. For the more practical aspect of using the OpenRefine software, we will share a video that will teach the basics. You can watch it anytime and do the lessons yourself. On two days (7.10 and 10.10), there will be a 1h slot (10:00-11:00) on Zoom, when you can come and ask any question you have regarding tables and OpenRefine software. 

 

Workshop information for PART 1: 

Lecture: 4th of October, 2022 at 10:00 (lecture, 1.5h)

Q&A session: 7.10 and 10.10 at 10:00 (Q&A, feedback, 1h)

Place: ZOOM (link will be sent to your email)

Register: CLOSED

Registration closes at 23:59 on 30.09.2022 or when the course gets full.

 

Learning outcomes for the participants: 

  • Compile a data table that abides by the FAIR Principles
  • Recognize what a clean table for others to use looks like
  • Explain how to use OpenRefine to clean the messy data


 

On the 8th of November 2022, ELIXIR-Estonia will be holding a data management online course: How to Make Your Messy Data Usable? - PART 2. The course will be held in English. This course will be in two parts: a 1-hour online lecture on what you can do in OpenRefine, including transformations, expressions, and extensions for the software, held on the 8th of November at 10:00 in Zoom. The practical workshop on how to transform your previously cleaned data with OpenRefine software will be a video lecture that you can follow in your own time. Additionally, we will hold 2 Q&A sessions in Zoom, where you can talk about any problems you encountered with the OpenRefine software.

This is a follow-up workshop for “How to make your messy data usable - PART 1”, where we talked about spreadsheets but also introduced the OpenRefine software. This course will explore the depths of OpenRefine software and see what else it can offer. This will include cleaning the data in bigger batches and unifying the data in one sweep. These include transformations and expressions. Additionally, we will introduce the possibility of downloading additional data from other databases and different extensions OpenRefine software has. 

You should have participated in the PART 1 workshop in order to register for the PART 2. 

 

Workshop information for PART 2: 

Lecture: 8th of November, 2022 at 10:00 (lecture, 1h)

Q&A session: 10.11 at 11:00 and 14.11 at 10:00 (Q&A, feedback, 1h)

Place: ZOOM (link will be sent to your email)

Register: CLOSED

Registration closes at 23:59 on 04.11.2022 or when the course gets full.

 

Learning outcomes for the participants: 

  • Understands what OpenRefine software can do with data
  • Knows what kind of transformations OpenRefine software supports
  • Knows how to write transformations and expressions in OpenRefine software

 

ONLINE workshops will be held through Zoom (the meeting link will be sent a couple of days before the workshop). 

We do ask you to register for the lecture responsibly. If you can’t attend the course, please let us know as soon as possible via email at elixir@ut.ee. 

Licensing Research Outputs lecture - 27.09.2022

On the 27th of September 2022, ELIXIR-Estonia will hold a new data management lecture: Licensing Research Outputs. The course will be held in English. 

While doing scientific research, you handle different kinds of research outputs, whether they are produced by you or by somebody else. So, how can you ensure that other people will give you credit when using your produced materials? And how will you know how exactly you can use the resources produced by others? This is a topic that copyright laws handle. 

This lecture will cover what copyright laws do, who has the rights to the materials, and how you can use them. Most of this information is protected with licenses, whether they are meant for figures, data, or software. This lecture will discuss what licenses to use for different materials and what each license covers (this means how people can use the materials). We will also show how exactly you can apply a license to your research outputs. 

 

Information about the lecture

Lecture: 27th of September, 2022 at 14:15 (lecture, 2h)

Place: Delta Building, r1022 (Narva mnt 18), TARTU

Register: CLOSED

Registration closes at 23:59 on 22.09.2022 or when the course gets full.

 

Learning outcomes for the participants: 

  • Knows what items need a license
  • Knows the restrictions on licensing a dataset
  • Knows what licenses to use for what research output
  • Knows how to apply a license to a research output practically

 

F2F lectures will take place at the Delta building in Tartu (Narva mnt 18, Tartu). 

Parking: You can park for free for 3h in the parking lot of the University of Tartu Academic Sports Club. 

We do ask you to register for the lecture responsibly. If you can’t attend the course, please let us know as soon as possible via email at elixir@ut.ee. 

Metadata and README lecture - 13.09.2022

On the 13th of September, 2022, ELIXIR-Estonia will hold a data management lecture: Metadata and README. This lecture will be held in English. 

In general, metadata is the descriptive information about your data. However, what exactly is metadata, and how much of it should be included with your data? 

Good metadata can make up for human fallibilities. People forget and misplace things and leave research projects with their knowledge of the research methodology and the data. Metadata ensures that we will be able to find the data, use it, preserve and reuse it in the future.

  • Finding Data: Metadata makes it much easier to find relevant data. Most searches are done using text (like a Google search), so formats like audio, images, and video are limited unless text metadata is available. Metadata also makes text documents easier to find because it explains exactly what the document is about.
  • Using Data: To use a dataset, researchers need to understand how the data is structured, definitions of terms used, how it was collected, and how it should be read.
  • Reusing Data: Researchers often want to reuse data collected for another project for their own project. The data still needs to be found and used, but often at a higher level of trust and understanding. Reusing data usually requires careful preservation and documentation of the metadata.

This means that the metadata provides additional information that helps data consumers better to understand the meaning and the structure of the dataset and to clarify other issues, such as rights and license terms, the organization that generated the data, data quality, data access methods, and the update schedule of datasets. Additionally, metadata also gives information about the data in general. What an actual metadata file includes varies between disciplines and types of data you are working with. However, the documentation for your data should contain the minimum information required to be able to reuse (or understand) the data described. 

In the lecture, we will be going over what exactly metadata is, the minimum information that should be included with each of the scientific results you are sharing, and how exactly you can write a README file. 

 

Information about the lecture

Dates: 13th of September, 2022 at 14:15 (lecture, 2h)

Place: Delta Building, r1022 (Narva mnt 18), TARTU

Register: CLOSED

Registration closes at 23:59 on 08.09.2022 or when the course gets full.

 

Learning outcomes for the participants: 

  • Understands the importance of good data management
  • Knows what metadata means in data files
  • Knows how to add metadata to the data
  • Knows what should be included in the README file
  • Can write a simple README file to accompany the data

 

F2F lectures will take place at the Delta building in Tartu (Narva mnt 18, Tartu). 

Parking: You can park for free for 3h in the parking lot of the University of Tartu Academic Sports Club. 

We do ask you to register for the lecture responsibly. If you can’t attend the course, please let us know as soon as possible via email at elixir@ut.ee. 

  • 2 min read

“Bring Your Own Data Management Plan” workshop - Invitations only

According to the Estonian Research Council funding agreement, all the projects that have started from 2022 have to submit a data management plan (DMP) within the first 6 months. Since this will be a new thing for a lot of researchers, University of Tartu, University of Tartu Library,  ELIXIR Estonia and The Estonian Research Council will be doing a data management writing course for this purpose. This workshop will be with invitations only. “Bring Your Own Data Management Plan” workshop (in English) will consist of two sessions: one online introduction and one face-to-face writing session. The writing sessions will be held both in Tartu and in Tallinn. 

The online session will be held 20th of May at 11:00 - 14:30, with one 15 min break in between the sessions. Within this time, Tiiu Tarkpea will give an overview of Open Science in Estonia. We have also invited people from the Estonian Research Council, so they can answer your questions in person. Additionally, there are also two DMP writing tool introductions: DMPonline by Tiiu Tarkpea (University of Tartu Library) and Data Stewardship Wizard by Federico Bianchini (ELIXIR Norway). 

After that you can pick from two face-to-face sessions, in case you need any help with the writing of the DMP part (participation not mandatory). The 26th of May (14:00-17:00) session will be held in Tartu and the 6th of June (14:00-17:00) session will be held at Tallinn (the precise location will be sent with an email). In this, we will be talking about the theory of different aspects of the DMP, giving more practical advice  and there will be two 1h writing sessions, where you can write most of your DMP. Also, if you have any questions, the organizers (Tiiu Tarkpea and Heleri Inno) will help as best as they can. 

 

The registration information should arrive through the Grant Office, via invitations only.

In case of questions, you can contact ELIXIR Estonia (elixir@ut.ee). 

 

Useful materials: 

 

  • 1 min read

Virtual meeting: Handling Pandemic Omics Data in the Nordics

A two-days online meeting that will bring perspectives on Nordic infrastructures and approaches used to handle SARS-Cov-2 sequencing data. The event will take place on 18-19 May 2022 from 09:00-13:00 CEST (Central European Summer Time). The meeting is organised by members of ELIXIR Norway, ELIXIR Estonia, and SciLifeLab Data Centre.

 

The current COVID-19 pandemic has understandably received considerable attention worldwide over the last few years. As it spread across the globe, the pandemic posed significant challenges for society, governmental bodies, healthcare systems, and research communities. Unprecedented efforts were necessary to generate, handle, and report the sheer amount of complex data required to be able to understand how SARS-CoV-2 was spreading, and develop efficient policies to fight the pandemic. I

n this online event, we will focus on how the Nordic region handled omics data. We will focus in particular on how sequencing efforts were coordinated, how data was managed and shared, and how data was used and communicated to different groups. We will also discuss the importance of the FAIR principles in pandemic data management, and which tools and pipelines facilitated efforts. We also hope to identify key resources that have wider applicability and can be reused further.

You can register for the event in here: https://nettskjema.no/a/nordic-data

The meeting programme is available here: https://nordic-compbio.iscbsc.org/omics-data

  • 1 min read

ELIXIR launches new Toxicology Community

ELIXIR launches a new community to represent the field of toxicology, which is the study of the negative consequences of the interaction of chemicals and living things and the safety of those chemicals. 

ELIXIR Communities bring together experts across ELIXIR Nodes and external partners to coordinate activities within specific life science domains. The addition of toxicology brings the number of Communities in ELIXIR to thirteen, spanning domains such as human data, plant sciences and marine metagenomics and technologies such as Galaxy and proteomics. 

More information at https://elixir-europe.org/news/new-toxicology-community