News
18/01/23 - Second bulk RNA-seq course at the University of Copenhagen¶
On 18th of January we taught the second iteration of our bulk RNA-seq course to researchers (from PhD students to professors) at SUND at the University of Copenhagen. We had ~50 workshop participants joining us for three days of lectures and exercises on UCloud. This time, we introduced preprocessing theory (read QC, alignment and quantification) and the use of automated workflows using the nf-core rnaseq pipeline.
For those that could not enroll for this session, you can find the updated material here. We have moved the datasets and slides to a zenodo repository
We'd like to extend our thanks to our workshop collaborators, data scientists from the SUND DataLab at KU's Center for Health Data Science as well as the genomics platform at the NNF Center for Stem Cell Medicine (reNEW).
10/12/22 - Transcriptomics Sandbox app launched on UCloud!¶
We have deployed our second standalone Sandbox app on UCloud! Please see the Access page for instructions on how to find our Sandbox apps on UCloud - This one is titled 'Transcriptomics Sandbox' and module documentation is linked from the UCloud app page as well as here in Modules.
06/09/22 - Genomics Sandbox app launched on UCloud!¶
We have deployed our first standalone Sandbox app on UCloud! Please see the Access page for instructions on how to find our Sandbox apps on UCloud - this first one is titled 'Genomics Sandbox' and module documentation is linked from the UCloud app page as well as here in Modules.
18/08/22 - Bulk RNA-seq course at University of Copenhagen¶
Today we began teaching our brand new bulk RNA-seq course to researchers (from PhD students to professors) at SUND at the University of Copenhagen. We had 32 workshop participants join us for two days of lectures and exercises on UCloud. We'd like to extend our thanks to our workshop collaborators, data scientists from the SUND DataLab at KU's Center for Health Data Science as well as the genomics platform at the NNF Center for Stem Cell Medicine (reNEW).
For those that could not enroll for this session, you can find the relevant material here.
01/06/22 - Genomics course at Aarhus University¶
A month-long course in Genomics taught by Professors Mikkel Schierup and Stig Andersen has started with lead supercomputing support on UCloud by Sandbox data scientist and course instructor Samuele Soraggi. Computational exercises in NGS analysis were deployed in a UCloud project for use by 47 graduate students with primarily molecular biology and clinical backgrounds and no prior supercomputing experience! Post-course update: We received many positive reviews on use of the Genomics Sandbox training materials on UCloud!
22/04/22 - Basics of Personalized Medicine - final wrap-up¶
Our first course, Basics of Personalized Medicine, wrapped up this month with student project presentations which described their approaches to analysis of the synthetic Chronic Lymphocytic Leukemia dataset created for the course. Course reviews highlighted the helpfulness of Sandbox staff in troubleshooting R problems and the tremendous amount that students learned about predictive modeling.
04/01/22 - Basics of Personalized Medicine - MS in Personal Medicine program¶
The first course supported by the Sandbox is launching this month - 'Basics of Personalized Medicine' - where students in the new Master in Personal Medicine program at University of Copenhagen are introduced to predictive modeling using electronic health records.