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: 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

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

4. 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.”
Health and aging
ENVIRONMENT and ECology
Evolution and
origin of life

5. 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

6. Support, tools and training

7. 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)

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

9. A key Swedish unit for analyses of large-scale genomic data (24 FTE)
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
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!

10. 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

11. 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

12. 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

13. Happy users, high demand

14. Distribution across universities

15. Diversity of users

16. 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

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 need to be agreed on

18. 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
394

19. 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.
Currently ~30 PhD students enrolled