The facility provides different levels of service, support and training for a moderate fee.
- Short Term Service (STS): <2 weeks service-based projects; e.g. Next Generation Sequencing (NGS) data pre-processing.
- Long Term Support (LTS): collaborative support for projects from UPSC PIs that may require data pre-processing, data analysis and data interpretation
- Short Term Training (STT): hourly support to help a biologist or bioinformatician solve a specific issue
- Long Term Training (LTT): The corresponding PIs assigns a PhD or PostDoc from their group to be involved in the data pre-processing, data analysis and data interpretation. The facility only has a supervisory and advisory role to the trainee. The trainee learns how to perform the relevant analysis and bring this knowledge to the PI’s lab.
The facility conducts its own research in bioinformatics and related fields. The rationale for this is that the facility needs to be attractive to collaborators within UPSC, to researchers outside of UPSC, while also, and most importantly, to funding agencies. Stand-alone research, originating from the facility’s personal is also fostered, and is essential to maintain current knowledge at the forefront of developing bioinformatics approaches. Current topics of interest at the facility include:
- gene regulatory network approaches
- cloud computing to enable Big Data management and analysis
- systems biology approaches
The facility organises bioinformatics lectures, seminars and workshops both within and outside UPSC. Within UPSC, training includes regular sessions as an introduction to the UNIX environment, to bioinformatics tools, to the UPSC computational infrastructure and UPSC web-resources (primarily the PlantGenIE platform). Outside UPSC, the facility is involved in international workshops covering the design, analysis and interpretation of high-throughput technologies. The facility also contributes to teaching courses organised by UPSC at Umeå University or SLU.
A few numbers
The facility has been involved in multiple genome projects, including Picea abies (Norway spruce) and Populus tremula (Eurasian aspen). As of end of 2016, we have processed3000 RNA-Seq samples, representing a total of 1000 Gbps (the equivalent of 50 spruce or 6,000 arabidopsis genomes) and a storage size of tens of TBs.
Since early 2016, the facility has contracted 28 projects (see Figure; x-axis: number of projects; y-axis: project types).
The facility members are:
- Kristina Benevides, Research engineer in bioinformatics and sequencing, contact person/coordinator for NGI sequencing projects
- Nicolas Delhomme, PhD, bioinformatician, manager of the platform and researcher at SLU
- Chanaka Mannapperuma, PhD student at UmU, computer scientist, designer and developer of the PlantGenIE resource
- Bastian Schiffthaler, bioinformatician, PhD student at UmU with a focus on high-throughput sequencing technologies, genome assembly, gene regulatory networks and systems biology
The facility is funded through UPSC’s the Knut and Alice Wallenberg Foundation and the TC4F program support.
UPSC Bioinformatics Website