1. The National Bioinformatics Infrastructure Sweden (NBIS) www
The National Bioinformatics Infrastructure Sweden (NBIS)
Björn Nystedt, Pär Engström
Joint Heads of Bioinformatics Long-term Support

2. 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

3. 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 National, distributed

4. Custom-tailored support
Study design consultation (free) + drop-in sessions every 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)

5. Tailored solutions – high impact
Bioinformatics Long-term Support
Wallenberg Advanced Bioinformatics Infrastructure
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!

6. 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

7. 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

8. 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

9. Happy users, high demand

10. Distribution across universities

11. 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 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

12. 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

13. 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

14. 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.
Recent call (2017/2018): 111 applicants for 15 places (!)