The department of Plant Physiology at Umeå University hosts both local and national bioinformatics resources, making it a central hub for data-science driven research in Umeå. These are the research groups, initiatives and infrastuctures that are part of the bioinformatics environment at UPSC:
Affiliated UPSC Research groups
- Jian-Feng Mao, working on plant genomics (Umeå University)
- Nathaniel Street, working on systems biology (Umeå University)
- Kelly Swarts, DDLS Fellow, working on tree ring genomics (Swedish University of Agricultural Sciences)
DDLS
The DDLS is an initiative hosted by SciLifeLab: "Data-driven life science is a field of research that focuses on using data, computational methods and artificial intelligence to study biological systems and processes. Read more about the four strategic DDLS research areas, joint research projects, and Fellows".
The DDLS members are:
- data processing as a service: the facility runs states of the art tools to process the data (800 SEK / h)
- scientific project's data analysis training: a research group leader "contributes" a PhD / Post-doc who is to be supervised by the facility to learn doing the analyses (800 SEK / h)
- data science teaching: a group leader books us to give one or more lessons in a course they are running (500 SEK / h)
- data storage: we offer both hot (300 kr / TB / year, RAID6, unreplicated) and cold ( 800 kr / TB / year, in a 2-2-2 setup following the Swedish ordinance for research data archival: two copies on two different supports in two locations) data storage. We have a current capacity of 1 PB.
- gene regulatory network approaches
- cloud computing to enable Big Data management and analysis
- systems biology approaches (multi-omics)
- data curation
- ML and AI
NBIS
NBIS is the National Bioinformatics Infrastructure Sweden. It "constitutes the SciLifeLab Bioinformatics platform, and is the Swedish node in ELIXIR (the European infrastructure for biological information)" and "provides services in areas such as large-scale omics, bio- and medical image analysis, and structural biology. We offer competences in bioinformatics, image analysis, biostatistics, machine learning/AI, data management, and systems development to support individual research projects and research consortia, as well as the private and public sector. We also develop and host scalable computational and digital infrastructure services of broad interest at national and international level, and offer data publication support. NBIS offers a wide range of consultation, training and mentoring opportunities, and provides assistance at national compute clusters. Learn more about all NBIS services".
The NBIS members are:
SLUBI
SLUBI is the SLU (Swedish University of Agricultural Sciences) Bioinformatics Infrastructure. Its "mission is to provide support and training in bioinformatics for researchers, students, and faculty at SLU." One member of the UPSC Bioinformatics Facility is the local representative of SLUBI, the bioinformatician affiliated to the SLU Forestry Faculty in Umeå.
Training Hub
The Training Hub is the ScilifeLab capability dedicated to training and trainers. From a training perspective, they "share cutting-edge knowledge on the advanced techniques, data analysis methods, and essential research skills used in our infrastructure. Courses and workshops offer intensive, hands-on training that provides researchers with the skills they need to excel", while from a trainer perspective, they are "dedicated to fostering a diverse and inclusive community of instructors and learners, where we can all gain new skills and benefit from the minds of many."
The Training Hub members are:
UPSC Bioinformatics Facility
The UPSC Bioinformatics Facility (UPSCb) centralises bioinformatics competences, offering a range of bioinformatics services as well as participating in wider collaborative projects. The facility also delivers local bioinformatics training and contributes to international workshops and training programs. Since it was founded in 2016, the facility has been handling a total of 314 projects for 65 different research groups.
We have a strong expertise in High Throughput Sequencing (HTS) data analysis, having been involved in the genome assembly of several tree species, among which most recently spruce and pine, having handled several thousands bulk RNA-Seq samples, analysed single-cell sequencing and spatial transcriptomics, as well as metagemomics, metatranscriptomics, ribosome profiling, transcription starting site sequencing, methyl-seq, ATAC-seq, ...
Service
The facility provides different levels of service, support and training for a fee.
Research
While the facility has no mandate to conduct research, to maintain current knowledge at the forefront of developing bioinformatics approaches, it supports the further development of its staff by for example fostering projects originating from the facility’s personal. Current topics of interest at the facility include:
Education
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.
Internal
To access additional information from the UPSC Bioinformatics Facility, log in to the UPSC homepage and then follow this link.
Facility members
Funding
The facility is funded through UPSC and grants from the Knut and Alice Wallenberg Foundation and the TC4F program as well as by user fees.
Contact
NBIS
Contact: Jeanette Tångrot
Training Hub
Contact: Nina Norgren
UPSCb
You can reach us by email: bioinfo-facility (@) upsc.se