Sandbox Workshop

Autumn 2023

Welcome to the homepage for in-person workshops introducing the Health Data Science Sandbox to potential users. Thanks for joining us!

Agenda

The Sandbox concept

The Health Data Science Sandbox aims to be a training resource for bioinformaticians, data scientists, and those generally curious about how to investigate large biomedical datasets. We are an active and developing project seeking interested users (both trainees and educators). All of our open-source materials are available on our Github page and much more information is available on the rest of the website you are currently visiting! We work with both UCloud and Computerome (major Danish academic supercomputers) - see our HPC Access page for more info on each set up.

Access Sandbox resources

We currently provide training materials and resources as topical apps on UCloud, the supercomputer located at the University of Southern Denmark. To use these resources, you’ll need the following:

  1. a Danish university ID so you can sign on to UCloud via WAYF. See this guide and/or follow along with our live demo.
  2. the ability to navigate in linux / RStudio / Jupyter. You don’t need to be an expert, but it is beyond our ambitions (and course material) to teach you how to code and how to run analyses simultaneously. We recommend a basic R or Python course before diving in.
  3. our invite link to the correct UCloud project that will be shared on the day of the workshop. This way, we can provide you compute resources for the active sessions of the workshop. To use Sandbox materials outside of the workshop, you’ll need to check with the local DeiC office at your university about how to request compute hours on UCloud.

Try out a module

So our Sandbox data scientists have finished their intro at the workshop? Great, now it’s time to choose your poison (cough) topic of interest for today. Your options are below:

Genomics ### Genomics If you’re interested in NGS technologies and applications ranging from genome assembly to variant calling to metagenomics, join Sandbox Data Scientist Samuele Soraggi in testing out our Genomics Sandbox app. This app supports a semester-length course on NGS as well as a Population Genomics course run regularly at Aarhus University. Sign into UCloud and then click this invite link.

Transcriptomics ### Transcriptomics If you’re interested in bulk or single cell RNA sequencing analysis and visualization, join Sandbox Data Scientist Jose Alejandro Romero Herrera (Alex) in testing out our Transcriptomics Sandbox app. This app supports regular 3-4 day workshops at University of Copenhagen and provides stand-alone visualisation tools. Sign into UCloud and then click this invite link.

proteomics ### Proteomics Interested in modern methods for protein structure prediction? Join Sandbox Data Scientist Jacob Fredegaard Hansen as he walks you through how to use ColabFold on UCloud. Jacob can also demo our Proteomics Sandbox, which contains a suite of proteomics analysis tools that will support a future course in clinical proteomics but is already available on UCloud for interested users. Sign into UCloud and then click this invite link.

Discussion and feedback

We hope you enjoyed the live demo. If you have broader questions, suggestions, or concerns, now is the time to raise them! If you are totally toast for the day, remember that you can check out longer versions of our tutorials as well as other topics and tools in each of the Sandbox modules or join us for a multi-day in person course.

As data scientists, we also would be really happy for some quantifiable info and feedback - we want to build things that the Danish health data science community is excited to use. Please answer these 5 questions for us before you head out for the day (link activated on day of the workshop).

Nice meeting you and we hope to see you again!