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: Siv Andersson 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

Bioinformatics know-how as infrastructure “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.” http://www.nature.com/news/core-services-reward-bioinformaticians-1.17251 Health and aging ENVIRONMENT and ECology Evolution and origin of life

NBIS Systems biology 5/y Training 30/y Long-term Support Novel/Customized Long time per project Systems biology 5/y Training 30/y Long-term Support Systems development Short-term Support 80/y Compute and storage 800/y Routine/Standardized Short time per project Data management

Support, tools and training

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) http://www.nbis.se/support http://www.scilifelab.se/platforms/bioinformatics

Short-term support Proteomics Systems biology 80 projects/year! Genomics Biostatistics Metabolomics Support decisions every 2nd week

A key Swedish unit for analyses of large-scale genomic data (24 FTE) 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 A key Swedish 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 RNA Metagenomics Spatial transcriptomics scRNA Göteborg Johan Reimegård Estelle P. Wéra Jakub O. Westholm Stefania Giacomello Leif Väremo Åsa Björklund John Sundh DNA Markus Mayrhofer Markus Ringnér Cancer Lund Linköping Lund Diana Ekman Anna Johansson Marcin Kierczak Malin Larsson Nikolay Oskolkov Marcel Martin Sergiu Netotea Göteborg Computer scientists Big data / Integrative Evolution Umeå Per Unneberg Allison Churcher Verena Kutchera Manfred Grabherr Sanela Kjellqvist Bengt Sennblad Mixed competence team Typically both technical and biological skills Average 7 years post PhD SysBio facility 10 Göteborg Göteborg Göteborg 1 physical + 1 video meeting per month Viktor Jonsson Rasmus Ågren Lena Hansson

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

Diversity of users

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

SciLifeLab Bioinformatics Courses Date Participants Evaluation score (max 5) Introduction to bioinformatics using NGS data April 2013 24 4.6   Nov 2013 4.3 March 2014 4.5 April 2014 3.8 Sept 2014 4.1 Nov 2014 Perl programming for biological sciences May 2013 20 4.4 Oct 2013 May 2014 4.7 Oct 2014 Genome Assembly Human Genetic Variation June 2013 15 Sept 2013 3.9 RNAseq 4.2 RNAseq and proteomics June 2014 Metagenomics TOTAL 2013 + 2014 394 www.scilifelab.se/education/courses/

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