The National Bioinformatics Infrastructure Sweden (NBIS) www The National Bioinformatics Infrastructure Sweden (NBIS) www.scilifelab.se/platforms/bioinformatics/ Björn Nystedt, Pär Engström Joint Heads of Bioinformatics Long-term Support bjorn.nystedt@scilifelab.se, par.engstrom@scilifelab.se

SciLifeLab SciLifeLab National service Local scientific center The Swiss army knife for Swedish Life Science researchers Local scientific center 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. 2010: Strategic research initiative 2013: National resource 2015: New management/chairman www.scilifelab.se

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

Custom-tailored support Study design consultation (free) + drop-in sessions every week @ all 6 sites Short- and Medium-term support (user fee 800 kr/h) Long-term support (500h, free, scientific evaluation) (Recent increase in user fees, due to general infrastructure cut-down by VR) http://www.nbis.se/support http://www.scilifelab.se/platforms/bioinformatics

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

The team Mixed competence team Typically both technical and biological skills Average 7 years post PhD The team 1 physical + 1 video meeting per month Pär Engström Björn Nystedt Thomas Svensson Johan Reimegård Åsa Björklund Jakub Orzechowski Westholm Estelle Proux-Wéra Markus Ringnér Diana Ekman Anna Johansson Marcel Martin Malin Larsson Allison Churcher Sanela Kjellqvist Per Unneberg Leif Väremo Nikolay Oskolkov Lena Hansson Sergiu Netotea Mikael Huss Bengt Sennblad Rasmus Ågren Stefania Giacomello Marcin Kierczak John Sundh

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/

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

Happy users, high demand

Distribution across universities

Your Long-term Support Effective time 450h + 50h follow-up - excluding: vacations, sick leave, internal admin - including: within-project admin, 2 weeks follow-up time reading-up/testing on project-specific topics data submission facilitating easy reproduction of results - status and hours reported to PI each calendar month Aim to exit after 12-18 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 We may exit before all hours are used, if all project aims have been reached it turns out that the project is infeasible (e.g. poor data quality) the research group is not sufficiently involved

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 need to be agreed on

National bioinformatics courses About 20 courses per year Introduction to Bioinformatics using NGS Introduction to Linux Perl programming Introduction to genome annotation Introduction to multivariate analysis RNA-seq Advanced workshop on NGS data analysis Advanced functional genomics Advanced bioinformatics www.scilifelab.se/education/courses/ www.nbis.se/training/events.html

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/ Recent call (2017/2018): 111 applicants for 15 places (!)