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

2. National service The Swiss army knife for Swedish Life Science researchers National service The Swiss army knife for Swedish Life Science researchers Local scientific center SciLifeLab Director: Olli Kallioniemi Co-director: Lena Claesson-Welsh Vision: To be an internationally leading center that develops, uses and provides access to advanced technologies for molecular biosciences with focus on health and environment. www.scilifelab.se 2010: Strategic research initiative 2013: National resource 2015: New management/chairman 2010: Strategic research initiative 2013: National resource 2015: New management/chairman SciLifeLab

3. SciLifeLab platforms SciLifeLab national service National Genomics Infrastructure National Bioinformatics Infrastructure Sweden Bengt Persson Clinical Diagnostics Computer resources free for Swedish researchers VR SNIC Ongoing merge of BILS, WABI and more; complete 2016. National, distributed Functional Genomics

4. Bioinformatics know-how as infrastructure 4 http://www.nature.com/news/core-services-reward-bioinformaticians-1.17251 “The scientific community has failed to craft attractive career paths for those who do the analyses it increasingly requires. Institutions and funding bodies must carve out a viable place for bioinformaticians who focus on collaborations, and reward them for their abilities to navigate the myriad demands of multidisciplinary projects.”

5. Support Training Tools Support, tools and training 5 Support Tools Training

6. 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://bils.se/resources/supportform/index.php http://bils.se/resources/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) (Recent increase in user fees, due to general infrastructure cut-down by VR) New contact routes later 2016, stay tuned at www.scilifelab.se/platforms/bioinformatics/ www.nbis.se

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

8. 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!

9. Bioinformatics Long-term Support 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

10. Application procedure Open to all research groups in Sweden Applications 3 times every year (accept 5-10 projects per call) Requires hands-on involvement from the research group 500h effective time over ~6-18 calendar months Co-authors according to normal contribution criteria Staff 100% support (not driving own research) National committee www.scilifelab.se/facilities/wabi/

11. 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

12. Happy users, high demand

13. Distribution across universities 13

14. 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/

15. 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

16. Your Long-term Support Effective time 450h + 50h follow-up - excluding: vacations, sick leaves, internal admin - including: within-project admin, 2 weeks follow-up time - including reading-up/testing on project-specific topics - hours reported to PI each calendar month Aim to exit after ~12 calendar months - can be negotiated based on needs Involved people might change over time - The Long-term Support management has the last word on who works in the project Contract violations - Research group much less personnel resources than stated in application

17. IP Data always owned by the PI - normally never leaves the Uppmax project folder The Long-term Support staff appear on scientific papers according to normal contribution criteria Tools developed by the bioinformatics platform are open source by default, and can be immediately used in other projects - exceptions needs to be agreed on