PlantLink bioinformatics

Bioinformatics has become increasingly important for the plant research community. During PlantLink’s first year the need to strengthen the bioinformatical competence in plant research in Southern Sweden was recognized. Therefore, PlantLink’s first bioinformatician, Estelle Proux-Wéra, was recruited in 2012. Estelle and the bioinformaticians following her have among other things established the PlantLink server, which has been mainly used for the analysis of sequence data. This server has since been complemented with the server Udda – named after Udda Lundquist for her life-long contribution to plant science – in 2018 and now most recently with a third server, Even, in 2020.

The PlantLink bioinformatician has offered support to SLU Alnarp and LU plant researchers, also working as a facilitator to keep contact between bioinformaticians at the two universities, and the bioinformatician has therefore been located at both campuses. Further, PlantLink’s bioinformaticians have over the years provided training in workshops and courses and offered bioinformatics cafés giving researchers the opportunity to drop in with their questions. Over the years, PlantLink support has gone to about 20 larger bioinformatics projects leading to more than 20 publications.

Initially (2012-2016) the PlantLink bioinformatician position was equal to full-time, but with the rise of SLUBI (The SLU Bioinformatics Infrastructure), PlantLink’s support has from 2017 decreased. Today, bioinformatics has become more integrated in plant sciences and there is additional strong local bioinformatics support available both through the presence of NBIS (National Bioinformatics Infrastructure Sweden) and SLUBI. Consequently, PlantLink stopped its active support to bioinformatics in May 2020. Our latest PlantLink-associated bioinformatician, Varma Saripella, is continuing as a full-time staff bioinformatician at SLU Alnarp as part of the SLUBI initiative. PlantLink now shift focus to further strengthen one of its core areas, to create a platform for network building. To strengthen this and to be able to build new links for plant researchers in the region, PlantLink recruited Sofia Marmon as a new coordinator from first half of 2020.