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Nextflow for beginners - 3-day course (19.04; 26.04; 3.05), Tartu - Course is full

This 3-day Nextflow course by ELIXIR Estonia, in collaboration with the University of Tartu HPC Center, comprehensively introduces the powerful workflow language. Nextflow is renowned for its robust, scalable, and reproducible methods of running computational pipelines. Through efficient, interactive lessons, participants will gain a solid understanding of Nextflow technology, from fundamental to advanced concepts.

ETAIS & ELIXIR seminar UT HPC Usage 101 18.11.2021

During this UT HPC Usage 101 lecture course we will provide the participants basic knowledge required to use to submit, monitor, and control jobs on the compute nodes of UT HPC. We will talk about the principles of computing in a cluster and the difference between computing directly from the command line of a private server. We will introduce the good practices and standards of behavior that good cluster usage practice requires. Also the convenient graphical tools for monitoring the resource of your work will be covered. Finally, we might touch on the basic Slurm commands.

We expect the users to have basic LINUX command line experience, but very little or no cluster compute experience yet.

Learning outcome:
Knowing how to submit, monitor and control jobs at UT HPC.

The seminar will take place in Zoom on 18th of November 2021 at 14.00 and will last approximately 90 minutes. The seminar will not be recorded.

Registration is open at https://forms.gle/pVe86HVqjWB6GpLg8 and will close on 16th of November or when the course gets full. 

The seminar is held in English by Ulvi Gerst Talas and Ott Eric Oopkaup from UT HPC/ETAIS.

 

 

GTN Smörgåsbord: A Global Galaxy Course, February 15-19 2021

 

For Estonian scientists the most important facts are:

  • https://galaxy.hpc.ut.ee/ will ensure that all the tools covered during the course will be available afterwards at the local instance
  • If you register to the Global Galaxy Course, please notify the UT Galaxy team (galaxy@hpc.ut.ee) as well, so you would be informed about future Galaxy events and local developments among the first ones.
  • Also, in case you have not used UT Galaxy instance at https://galaxy.hpc.ut.ee before, then please include your UT username (in case you have it) to the email above (galaxy@hpc.ut.ee) so your local Galaxy account can be created.


Galaxy Training event showcasing a wide variety of GTN (Galaxy Training Network) tutorials. This will be an online event, spanning all time zones. All training sessions are pre-recorded, so you can work through them at your own pace, and manage your own time. A large community of GTN trainers will be available via online support to answer all your questions.

The program covers a general introduction to the Galaxy platform, NGS Analysis (DNA-seq and RNA-seq), Proteomics, and also features a Choose your own adventure day on Friday, where we encourage you to explore all the tutorials that the GTN training repository has to offer, and follow those that are of interest to you. The GTN tutorials cover a wide range of scientific topics, from NGS to ecology, climate science, machine learning, visualization, and many more. All the tutorials can be found on the GTN website

When: February 15-19, 2021 (all time zones)
Who: Open for everybody
Cost: Free
Format: Virtual event, all training session are pre-recorded, you can work through these at your own pace, with instructors available online for support
Support: Slack Channel (link will be provided here before the course)
Organized by: The Galaxy Training Network (GTN), CINECA, The Galaxy Project, Australian BioCommons, Erasmus Medical Center, Albert-Ludwigs-Universität Freiburg, Avans Hogeschool, The Gallantries Project, The GalaxyP Team, The ProteoRE Team, INAB-CERTH, EMBL-EBI, Institute of Surgical Pathology - University Medical Center Freiburg.

More info and registration is available at https://shiltemann.github.io/global-galaxy-course/. 

Do not miss the great opportunity!

Single cell RNA-seq analysis courses by ELIXIR-FI in Espoo

Please note that registration is now open for the following two single cell RNA-seq data analysis courses, which cover the processing of transcript counts from quality control and filtering to dimensional reduction, clustering, and differential expression analysis. You will also learn how to do integrated analysis of two samples. 

 

18.-19.9.2019 Single cell RNA-seq data analysis using R

In order to participate in this course, you need to have prior experience in using R.

Teachers: Heli Pessa, Bishwa Ghimire, Iivari Kleino

For more information and registration, please see https://www.csc.fi/web/training/-/single-cell-r-2019

 

24.9.2019 Single cell RNA-seq data analysis using Chipster

As the R-based tools are used via the graphical user interface of Chipster, no experience of R is required, and the course is thus suitable for everybody.

Teachers: Maria Lehtivaara and Eija Korpelainen

For more information and registration, please see https://www.csc.fi/web/training/-/single-cell-chipster-2019

 

Note that you can combine these courses with the international Single cell transcriptomics symposium, which takes place in Biomedicum Helsinki 23.9.2019. 

For more information and registration, please see 

https://www.helsinki.fi/en/researchgroups/immunomics/single-cell-course-week/single-cell-transcriptomics-symposium-2019

 

Finally, all the material from the ELIXIR course "Single cell RNA-seq data analysis with R" (27.-29.5.2019) is now available at 

https://www.csc.fi/web/training/-/scrnaseq

The material includes lecture videos, slides, exercises with code, and exercise data.

FAIR Data Stewardship – digital data scholarship for wetlab scientists - course in the Netherlands

From 27-29 May, 2019, we will organize the first course in  Data Analysis and Stewardship theme of the Helis Academy:  

FAIR Data Stewardship – digital data scholarship for wetlab scientists

The target audience is wet-lab scientists – from industry and academia – and graduate students in the Life Sciences who wish to improve their digital scholarship on data handling. Some basic experience with programming and scripting languages like python, perl, R, matlab, etc. are an advantage, but not needed.

The course will introduce the trainees to important concepts of data stewardship. We start with a general introduction covering the data life cycle, the FAIR principles and a definition of data stewardship and data stewards. The course is also relevant for Data Stewards who are supporting the life science researchers.

 

We will pass the stages of the data life cycle in more detail in the training modules of this 3 day course.

  • On day one trainees will investigate data management plans, which types are there and how they should be used.
  • On day two the course highlights how to work with data during the research phase, explaining how to create well formatted data which helps in the second module of day two to make data interoperable already during the active research phase.
  • On day three trainees will have an in-depth at persistent identifiers, different use cases and types of identifiers. Finally we are closing the data life cycle by making data fit for sharing, archiving and publishing. 

This course is part of the Data Analysis and Stewardship theme of Helis Academy and is organised by DTL and DTL collaborators. Info about other courses in the theme of Data Analysis and Stewardship can be found on the Helis Academy website and on the Helis Academy page on the DTL website.

You can find all the information, including the full programme and registration possibilities here: https://www.aanmelder.nl/helis-fair-data-stewardship-course