1. The National Bioinformatics Infrastructure Sweden (NBIS) www
The National Bioinformatics Infrastructure Sweden (NBIS)
Björn Nystedt, Head 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 provides state-of-the art services
NGI (One of the largest sequencing centers in Europe) X-Ten, HiSeq, MiSeq, PacBio, IonTorrent, MinIon, Optical mapping
Next Generation Diagnostics Sequencing and other omics for new clinical applications
Bioinformatics ~65 FTE for custom-tailored project support, methods and systems development, data publishing, training
Single-cell omics Single-cell transcriptomics, genomics, and proteomics …

4. SciLifeLab national service
SciLifeLab platforms
SciLifeLab national service VR
National Genomics Infrastructure
Next Generation Diagnostics
National Bioinformatics Infrastructure
Sweden
SNIC
Single-cell omics
Bengt Persson
Computer resources free for Swedish researchers
Ongoing merge of BILS, WABI and more; complete National, distributed

5. Support, tools and training

6. Support

7. Custom-tailored support
Study design consultation (free) + drop-in sessions every all 6 sites
Short- and Medium-term support (8h free, then user fee 800 kr/h)
Long-term support (500h, free, scientific evaluation)
Systems biology (start-up phase)
(Recent increase in user fees, due to general infrastructure cut-down by VR)

8. Bioinformatics support
Proteomics
Systems biology
300 projects/year
Genomics
~25 FTE
Biostatistics
Metabolomics
Support decisions every 2nd week
800 SEK/h

9. Genome assembly and annotation
Henrik Lantz
projects per year
Highly specialized staff and robust pipelines
Tight user interaction
Numerous manual and semi-manual QC steps
Supports ENA submission
Editable user interface
Cost effective with high quality!

10. 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
Basic science!
Björn Nystedt
Pär Engström

11. The team 2013 2014/15 2015/16 RNA Cancer Protein evolution DNA
Lund
Johan Reimegård
Pär Engström
Mikael Huss
Estelle P. Wéra
Jakub O. Westholm
Stefania Giacomello
Markus Ringnér
Protein
evolution
DNA
Linköping
Lund
Umeå
Diana Ekman
Páll Ólason
Anna Johansson
Alvaro M. Barrio
Programmer
Malin Larsson
Nikolay Oskolkov
SystBio/
Integrative
Allison Churcher
Proteomics
Multivariate
Everything
scRNA
Göteborg
Göteborg
Sanela Kjellqvist
Per Unneberg
Åsa Björklund
Marcel Martin
Sergiu Netotea
Leif Väremo
Bengt Sennblad
Mixed competence team
Typically both technical and biological skills
Average 7 years post PhD 11
Göteborg
Göteborg
1 physical + 1 video meeting per month
Rasmus Ågren
Lena Hansson

12. 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
Next deadline Oct 28!

13. 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

14. Single-cell Already ~20% of our active projects
Newt limb regeneration
(A Simón, KI)
Epigenetic states in oligodendrocytes
(Castelo-Branco, KI)
Development of dopamine neurons (Perlmann, KI)
Neural stem cell characteristics
(Muhr, KI)
Development of lung epithelium
(Samakovlis, SU)
Lineage tracing of single cells by WGS
(Frisén, KI)
In vitro differentiation of human iPS cells from human neurological disorders
(Dahl, UU)
Fibroblast signatures in breast cancer
(Pietras, LU)

15. BigData/Integrative omics
4 FTE, joint effort by Long-term Support and Systems Biology
Combine data from SciLifeLab platforms
Building tools and resources for handling very large and/or complex biological data sets
Typically performed in the context of longer support projects
State-of-the-art analytical methods for integrating multi-modal biological data sets, eg
- Machine learning/deep learning
- Graph-based models
- Genome-scale metabolic models
Support track for integrative projects
First call Feb 2016; First few projects initiated
Involves extensive integration of data

16. Happy users, high demand

17. Tools

18. Tools and infrastructure
Compute and storage of sensitive data
Local EGA
ePouta integration pilot
microMosler
Pouta Blueprints
web-servers with EGI cloud vo.NBIS.se
WGS tools and resources
SweGen 1000 genomes
WGS somatic variant calling WF
WGS structural variation WF
Software maintenance
MrBayes
Structure prediction web services
Assembly and annotation
Falcon on Milou
ENA submission help
Other tools and resources
Human Metabolic Atlas (HMA)
Haloplex variant calling pipeline
WhatsHap: Genomic phasing
IgDiscover: Immunorepertoire
Open prioritization and background descriptions
Tools and development projects needs to be much more visible! Work in progress…

19. SweGen: 1000 Swedish genomes
SweGen Variant Frequency Database
950 twin registry + 50 Northern Sweden
Deep coverage WGS (30X)
ExAC browser interface
Data Beacon
Full SNP frequency table download
1st release yesterday!
Funding: SciLifeLab
Sequencing: NGI
Variant calling: NGI
QC: NBIS
Data access interface: NBIS

20. Training

21. National PhD level bioinformatics courses at SciLifeLab
Joint efforts by SciLifeLab staff and researchers (+ more)
Introduction to omics data analysis
4 x Introduction to Bioinformatics using NGS data, 5 days (Manfred Grabherr)
1 x Omics data analysis, 10 days (Erik Fredlund, Lukas Orre)
Advanced topical courses
2 x RNAseq, 3 days (Johan Reimegård)
1 x Genome assembly, 2 days (Henrik Lantz)
1 x Genome annotation, 2 days (Henrik Lantz)
1 x Metagenomics, 2 days (Anders Andersson, Thijs Ettema)
1 x Proteomics, 4 days (Fredrik Levander)
Programming
2 x Python, 2 days (Frédéric Haziza, Sergiu Netotea)
2 x Perl, 5 days (Matt Webster)
1 x R programming Foundations for Life Scientists, 5 days (Marcin Kierczak) 1 x Unix/Linux Tutorial for beginners, 3 days (Mihaela Martis)
Suggested additions
Human WGS, genetic variation
Human WGS, cancer
>200 students/year
Very positive course evaluations
Teacher-dense
Good for networking

22. 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.
New call out soon!

23. Looking ahead

24. The future is bright  ..and integrated! ..and unbalanced! Volume
Integration
Systems/processes
Data scientists
Mikael Huss
BigData/Integrative bioinformatics
Data

25. We’re here for you! www.nbis.se