1. The National Bioinformatics Infrastructure Sweden (NBIS) www.scilifelab.se/platforms/bioinformatics/ Björn Nystedt, Head of Bioinformatics Long-term Support bjorn.nystedt@scilifelab.se

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

4. Custom-tailored support Study design consultation (free) support@bils.se + drop-in sessions every week @ all 6 sites support@bils.se Short- and Medium-term support (8h free, then user fee 800 kr/h) http://nbis.se/support/supportform/index.php http://nbis.se/support/supportform/index.php Long-term support (500h, free, scientific evaluation) http://www.scilifelab.se/facilities/wabi/ http://www.scilifelab.se/facilities/wabi/ Systems biology (start-up phase) New contact routes later 2016, stay tuned at www.scilifelab.se/platforms/bioinformatics/ www.nbis.se

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

6. Bioinformatics Long-term Support Wallenberg Advanced Bioinformatics Infrastructure www.scilifelab.se/facilities/wabi/ 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!

7. 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

8. 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

9. 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

10. 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

11. Happy users, high demand

12. SciLifeLab Bioinformatics Courses CourseDateParticipantsEvaluation score (max 5) Introduction to bioinformatics using NGS data April 2013244.6 Nov 2013244.3 March 2014244.5 April 2014243.8 Sept 2014244.1 Nov 2014244.3 Perl programming for biological sciences May 2013204.4 Oct 2013204.4 May 2014204.7 Oct 2014204.5 Genome AssemblyNov 2013204.1 Nov 2014204.4 Human Genetic VariationJune 2013154.5 Sept 2013203.9 RNAseqJune 2013154.1 Sept 2013204.2 Oct 2014204.3 RNAseq and proteomicsJune 2014204.1 MetagenomicsNov 2014204.2 TOTAL 2013 + 20143944.3 www.scilifelab.se/education/courses/

13. 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. www.scilifelab.se/education/mentorship/the-swedish-bioinformatics- advisory-program/ Currently ~30 PhD students enrolled

14. 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