The course is about how to take advantage of high-performance computing facilities, like those provided by Sigma2 (e.g. Saga) and the Norwegian Research and Education Cloud (NREC) for bioinformatics applications. Topics like parallel programming, software containers, and queueing systems are taught. The bioinformatics application used as an example is known as ‘variant calling’, which is used to find out exactly where and how the genetic material from one sample differs from another or from a reference. For instance, it could be used after DNA sequencing to find out that a person has a C (cytosine) instead of the typical A (adenine) in position 43051071 on chromosome 17 as one of several differences.
The National research school in bioinformatics, biostatistics, and systems biology (NORBIS) provides financial support and usually pays for PhD students from all over Norway to travel and stay in Oslo to participate in the course. This time it was different: Less than two weeks before the course was supposed to start (on March 23), the university was closed due to the pandemic, and we had to decide if the course should be moved online or cancelled. Hands-on exercises where students can easily get help and direct feedback from the teachers comprises a major part of the course, and that would be difficult to do online. It is also the intention of the NORBIS research school to make PhD students get to know each other better and perhaps collaborate in the future; that would perhaps also be more challenging online. On the other hand, students could stay home and avoiding travelling. Luckily, all teachers involved, mainly from USIT and Oslo University Hospital (OUS), were happy to contribute to an online course, even if it demanded more in already challenging times. Few were familiar with online teaching, so teaching the course was also a crash course in this kind of instruction.
We decided to use a combination of Zoom, MatterMost, Microsoft GitHub, and Google Drive to communicate with the students. Most lectures were held live on Zoom, some were pre-recorded, and for a few topics self-study materials were provided. In total about thirty students participated from many of the universities in Norway (UiT, Nord, NTNU, NMBU, OsloMet, and UiO), and there was even a student from Denmark. Overall the course went very well and better than we had expected. Thanks to Abdulrahman Azab, Bjørn-Helge Mevik, Maiken Pedersen, Sabry Razick, Darren Starr, Ole Widar Saastad, and Leon Charl du Toit from USIT, as well as to Arvind Sundaram from OUS for making the course possible also this year.