The National Bioinformatics Infrastructure Sweden (NBIS) Björn Nystedt, Head of Bioinformatics Long-term Support

Support Training Tools Support, tools and training 3 Support Tools Training

Custom-tailored support Study design consultation (free) + drop-in sessions every all 6 sites Short- and Medium-term support (8h free, then user fee 800 kr/h) Long-term support (500h, free, scientific evaluation) Systems biology (start-up phase) New contact routes later 2016, stay tuned at

Short-term support 400 projects/year! Genomics Proteomics Metabolomics Biostatistics Systems biology Support decisions every 2 nd week

Bioinformatics Long-term Support Wallenberg Advanced Bioinformatics Infrastructure Björn Nystedt Pär Engström Tailored solutions – high impact Siv Andersson Gunnar von Heijne Applied bioinformatics: 500h free support/project Variant analyses Transcriptomics Single-cell analyses Epigenetics Metagenomics Directors Managers Sweden’s strongest unit for analyses of large-scale genomic data (24 FTE) National committee reviews and selects projects based on scientific quality 70% of funding Basic science!

Bioinformatics Long-term Support staff Per Unneberg Páll Ólason Johan Reimegård Diana Ekman Anna Johansson Mikael Huss Sanela Kjellqvist Pär Engström Åsa Björklund Jakub Orzechowski Westholm Alvaro Martinez Barrio Marcel Martin Estelle Proux-Wéra Stefania Giacomello Bengt Sennblad Malin Larsson Allison Churcher Rasmus Ågren Leif Väremo Sergiu Netotea Nikolay Oskolkov Markus Ringnér Björn Nystedt Thomas Svensson Lena Hansson

Working model Web portal Facility management National Proposals Evaluation Committee Support staff Research project Hands-on scientist priority time allocation feasibility application Scientific value Feasibility Involvement 500h effective time over ~6-18 calendar months Co-authors according to normal contribution criteria Staff 100% support (not driving own research) Hands-on involvement from the research group is mandatory 3 times per year 2 months to decision Accept 5-10 project per call

Custom-tailored support “Routinely unique” Difficult to forsee/automate Human health and disease (13) 5 Variant analyses (cohort, family, cell fate) 3 Epigenetics 2 RNA, method 1 Differential gene expression 1 Lipidomics 1 Integrative (Medical) animal models (10) 4 single-cell RNA 2 Differential gene expression 2 Targeted 1 ChipSeq 1 miRNA Ecology/Evolution (8) 3 Population genomics 2 De novo genome assembly/analyses 2 Phylogenomics/genome evolution 1 Epigenetics

Single-cell projects 10 6 (of 40) ongoing support projects are single-cell Development and differentiation of midbrain dopamine neurons Thomas Perlmann KI/LICR Neural stem cell characteristics Jonas Muhr KI/LICR Fibroblast signatures in breast cancer Kristian Pietras, LU Cellular composition of blastema in newt limb regeneration Andras Simón, KI Epigenetic states in oligodendrocyte lineage development Goncalo Castelo-Branco, KI Development of lung epithelium Cristos Samakovlis, SU Lineage tracing of single cells through whole genome amplification Jonas Frisén, KI Shiny Apps

Happy users, high demand

SciLifeLab Bioinformatics Courses CourseDateParticipantsEvaluation score (max 5) Introduction to bioinformatics using NGS data April Nov March April Sept Nov Perl programming for biological sciences May Oct May Oct Genome AssemblyNov Nov Human Genetic VariationJune Sept RNAseqJune Sept Oct RNAseq and proteomicsJune MetagenomicsNov TOTAL

The Swedish Bioinformatics Advisory Program PhD students get a senior bioinformatician as a personal advisor during 2 years of their PhD. Monthly project meetings + two grand meetings per year to aid networking and knowledge transfer. advisory-program/ Currently ~30 PhD students enrolled

Swedish ELIXIR contributions within the ELIXIR-EXCELERATE project ELIXIR Node Capacity Building ELIXIR Data Nodes Construction –Including data flow Lab -> National -> European/International Computing and Storage of Sensitive Data Data Storage and Transfer within the Compute Platform Data Interoperability –”FAIR” – Findable, Accessible, Interoperable, Reusable Genome Annotation Competence Network Additional HPA Integration Activities Training