Customer Training

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CANCELLED! BioMonth: Using CSC services for bioscientists

30.3.2022 09:00 +03:00 EEST - 1.4.2022 12:00 +03:00 EEST



 Due to low number of participants, we are cancelling this course. 

Please note that we have self-learning courses open for research data management and CSC computing environment.

We are also planning some webinars on related topics, stay tuned!


Our BioMonth training continues in 2022, too!

Join our BioMonth 2022 course to get the most out of our services. In the course, you can spend your mornings with us to learn CSC supercomputing and its use, especially for containerised bioapplications. And also, you can sharpen your data management skills to help you handle your research data not only during the analysis but also before and after that! In addition, you can learn CSC sensitive data services for processing and storing your data.

Course description

This biomonth course starts by providing a brief review of Puhti supercomputing environment for your scientific data analysis. A particular emphasis will be given to run analysis tools as contaienrised bioapplications. Singularity and biocontainers will be the core focus of the day. We will introduce HPC-compliant Singularity containers which allow you to run your analysis tools on Puhti. These containers can serve as an alternative approach to conda packages.

Good research data management is the basis of successful research and ensures that your data is reproducible and FAIR. In this data management session we get familiar with interoperability, which is one important part of FAIR data management. We also discuss the importance of data management planning and publishing data as well as where to find data repositories for life science data. In the end we deepen into specialties of sensitive data management.

Protecting your sensitive data against unauthorized access is becoming critical nowadays. CSC provides easy-to-use sensitive data services for your scientific needs. Easy-to-use solutions provide a secure workspace to facilitate sensitive data management. This course gives an introduction to new sensitive data services of CSC: SD Connect and SD Desktop. These services are essential when working with for example with clinical or other genetic data.


One should be comfortable working with the command line environment in Linux and able to use an editor (e.g., vi, nano, emacs, etc.) in order to get the maximum benefit from this course. You will need an CSC account and an computing project. Make sure you have access to Puhti.

So, ideal candidates for this course are:

  • Bioinformaticians or computer scientists with some bio-background
  • Biologists with Linux skills

If you are unsure of your prerequisite skills, we recommend that you take our course, Using CSC HPC environment efficiently to learn efficient use of CSC HPC environment.

Tentative schedule

Wednesday 30.3. 9:00-12:00

Recap of Puhti supercomputer environment
Singularity and biocontainers

Thursday 31.3. 9:00-12:00

  • Interoperability and reproducibility in FAIR data management
  • Data management planning
  • Publishing data
  • Sensitive data management

Friday 1.4. 9:00-12:00

Sensitive Data services
This day provides introduction to the new sensitive data services of CSC: SD Connect and SD Desktop. These services are essential if you are working with clinical or other sensitive data. In the course you will learn when and how you should use these services.

Registration for this event is currently stopped.

Event time


30.3.2022 09:00 +03:00 EEST


1.4.2022 12:00 +03:00 EEST

Event location