National Bioinformatics Infrastructure

National Bioinformatics Infrastructure Sweden (NBIS) constitutes the SciLifeLab Bioinformatics platform.

NBIS is a distributed infrastructure with staff at six sites (Göteborg, Linköping, Lund, Stockholm, Uppsala, and Umeå), providing a range of services to support life sciences in Sweden, as summarized below.

Support

Custom-tailored support beyond the predefined analyses typically offered by the data-generating platforms at SciLifeLab.

• Weekly drop-in sessions at each of the six sites. Come by to discuss study design, data analysis or any other bioinformatics-related questions.
• Consultation meetings. Book a free meeting to discuss study design with one of our experts.
• Hands-on project support, ranging from assistance with smaller data processing/analysis tasks to long-term engagement. A user fee is charged.
• Free, extensive hands-on support to a limited set of scientifically outstanding projects selected in a rigorous peer-review process (enabled by a grant from Knut and Alice Wallenberg Foundation).

The topics covered by NBIS experts include genome assembly, genome annotation, genetic variation, comparative genomics, phylogenomics, transcriptomics, proteomics, metabolomics, systems biology, single-cell biology, biostatistics and multi-omics integration. We also provide support in systems development, such as interactive websites and data processing pipelines. Support services are available to both academic research groups and private companies, and not limited to data generated at SciLifeLab.

Infrastructure

Tools, data management, systems development and guidelines for the life science community.

Large datasets usually need to be analyzed on high-performance computing systems. Swedish academic researchers can apply for compute and storage allocations at systems provided by The Swedish National Infrastructure for Computing (SNIC), such as the UPPMAX systems. NBIS maintains bioinformatics software and data on UPPMAX and offers associated user support.

Training

NBIS offers a spectrum of training events, ranging from introductory classes to advanced workshops, e.g. on R and Python programming, general high-throughput sequencing data analysis, RNA-seq and single-cell RNA-seq.

NBIS also provides a 2-year advisory program for PhD students interested in having a bioinformatics expert as an additional mentor.

Further information