Alvar Almstedt has a master’s in molecular biology from the University of Gothenburg and has since worked at Clinical Genomics Gothenburg and BDC. When he started, they were just three colleagues in total with one focus area each [Cancer, Rare Disease (RD), and Microbiology]. Alvar has during this time mainly worked with cancer, which he still does, but also dabbled in Rare Diseases and Microbiology.
- In the beginning, I mostly worked with validating and integrating bioinformatic pipelines* into Sahlgrenska University Hospital's (SU) routine diagnostics, as well as some administration of our compute clusters, says Alvar Almstedt.
In September 2021 the two bioinformatics units at Core Facilities merged into one: The Bioinformatics and Data Centre. Alvar Almstedt has been a part of this journey and has seen how the group has grown and developed.
Now the cancer group at BDC consists of four people and there are a total of five groups with different focus areas: Cancer, Rare diseases, Microbiology, IT, and DataOperations.
- The fact that our unit has grown and the collaboration with SU is a big part of why I find my work stimulating. The combination of both IT and biology makes my day-to-day work varied and I have the opportunity to continually develop my skills and expand my knowledge.
BDC has a close collaboration with KGG (Klinisk Genetik och Genomik), the department responsible for all clinical genetic analysis in VGR which is a part of Sahlgrenska University Hospital. The collaboration regards both personnel in the lab and hospital geneticists working closely together sharing facilities and infrastructure.
- My day-to-day is generally split between meetings, routine data operations, and development projects, generally prioritized in that order with some exceptions. If something is not running smoothly with the flow of genetic data through our systems, I try to assist in solving it as fast as possible. If everything is working well, I continue working on one of the many different projects running in parallel in either the DataOps- or Cancer groups.
The sequencing instruments used for clinical analysis at the hospital and research services at the University of Gothenburg are tightly integrated with the BDC infrastructure. The number of instruments grows each year as demands increase and the technology advances. In addition to the established short reads sequencers by Illumina and Thermo Fischer, Alvar is now also helping set up an Oxford Nanopore Instrument for long read sequencing.
*a pipeline is a series of software programs that run one after the other)
