1. Bioinformatic platform at SciLifeLab

2. SciLifeLab organization
SAB
Board
NRK
Director &Co-Director
Executive management
Strategic management
Stockholm Steering committee
Uppsala Steering committee
Stockholm node management
Uppsala node management
Research programs
Health
Environment
Technology platforms
43 facilities – national and regional

3. Bioinformatics Custom-tailored support.
Bioinformatics provides custom-tailored support beyond the predefined analyses typically offered by the data-generating platforms at SciLifeLab. The bioinformatics platform also provides computing and storage resources for large-scale biological data in collaboration with the SNIC supercomputer centres.
Custom-tailored support.
Computing and storage resources for large-scale biological data.
Collaboration with the SNIC supercomputer centres.

4. Bioinformatics Bioinformatics Platform directors Bengt Persson (UU)
Siv Andersson (UU)
Erik Lindahl (KTH)
Gunnar von Heijne (SU)
Hans Karlsson(UU)
Bioinformatics
Bioinformatics Short-term Support and Local Infrastructure
Platform director Bengt Persson
Facility manager Mikael Borg
Bioinformatics Long-term Support (WABI)
Platform director Siv Andersson & Gunnar von Heijne
Facility manager Björn Nystedt & Thomas Svensson
Bioinformatics Compute and Storage (UPPNEX)
Platform director Hans Karlsson
Facility manager Ola Spjuth

5. SciLifeLab National Bioinformatics Support

6. System design/ development
Compute – Support – Education
Unique in the world:
A single NGS compute cluster for the entire country
Long-term
(13 FTE)
500 h / project
20 projects/year
Short-term
(40 FTE)
80 h / project
400 projects/year
Compute
(4 FTE)
System design/ development
400 projects/year (only NGS)
Number of projects
Support hours per project

8. Senior bioinformaticians working in your project 500 h for free!
Any NGS application
Anywhere in Sweden
Any bioinfo experience level

9. Current Staff Transcriptomics Proteomics Variation analyses
Johan Reimegård Ua
Mikael Huss
Sthlm
Åsa Björklund Ua
Pär Engström
Sthlm
Jakub Orzechowski Westholm, Sthlm
Estelle Proux- Wéra, Sthlm
Sanela Kjellqvist
Sthlm
Variation analyses
De novo/pop.genomics
Diana Ekman Sthlm
Pall Olason Ua
Anna Johansson Ua
Marcel Martin
Sthlm
Alvaro Martinez Barrio, Ua
Per Unneberg Sthlm

10. In a near future staff

12. Kind of projects that have been accepted
4 Variant analyses in medical research Human
1 Differential gene expression Human
1 Metagenomics Human microbiota 6
4 De novo genome assembly/analyses Animals/plants
4 Variant calling/Population genomics Animals/plants
2 Gene expression Animals/Plants
1 RNAseq + proteomics Fungus
1 Non-coding RNA Bacteria
1 RNAseq method development Universal 13

13. The number of applications per round is increasing

14. User survey in March 2014 (quotes)
Based on responses from 14 of 15 projects with >50h spent support at the end of February 2014

15. User survey in March 2014 (quotes)
“I think the WABI long-term support is an excellent resource“
“The bioinformatics support provided by WABI has been invaluable for the current project, both in terms of speeding up analyses and in ensuring that the scientific quality of those analyses is the highest possible. Running a small group, attracting bioinformaticians with this level of expertise can be difficult, and gaining access to people with such knowledge through WABI has really been extremely useful! I predict that my group will continue to benefit from this for years to come, even after the support is discontinued. In short, I consider this to be one of the best initiatives for supporting high-quality Swedish life science research in recent years.”
“Super!”

16. How to apply for long term support

17. Future dates for application 7. 2014 nov14 (PEC2)
How to apply for long term support
Future dates for application
nov14 (PEC2)
jan 30 (PEC1)
may15 (PEC2)
oct16 (PEC1)

18. System design/ development
Compute – Support – Education
Long-term
(13 FTE)
500 h / project
20 projects/year
Short-term
(40 FTE)
80 h / project
400 projects/year
Compute
(4 FTE)
System design/ development
400 projects/year (only NGS)
Number of projects
Support hours per project

19. BILS – Bioinformatics Infrastructure for Life Sciences
Technical
coordinator
Proteomics coordinator
BILS is a distributed national research infrastructure supported by the Swedish Research Council (VR)
Nodes at each of the 6 large univerisities
Coordination with other bioinformatics activities
Training activities, annual symposium/user meeting
BILS provides
Support/Consultancy (“human eCloud” for life sciences) 80 hours for free, additional hours for a subsidised fee
Databases and software tools Computing and storage in collaboration with SNIC
Annual budget ~35 MSEK
~22 MSEK from VR
~13 MSEK from SciLifeLab and participating universities
Director
Bengt Mikael Fredrik Persson Borg Levander
Syst. development
coordinator
Training
coordinator
Genomics coordinators
Magnus Henrik Jonas Sara
Alm-Rosenblad Lantz Hagberg Light

20. Current status of BILS 45 staff (including 4 fully SciLife-funded staff)
Umeå:
-- NGS
-- Metabolomics
-- Proteomics
-- Biostatistics
-- Metab. modelling
Stockholm:
-- Technical coordination
-- NGS incl. metagenomics
-- Protein bioinformatics
-- Proteomics pipelines
-- Phylogenomics
-- Systems biology
-- Software development
-- Cancer databases
-- 2 HPA integration into ELIXIR
-- Prediction servers
Uppsala:
-- NGS incl metagenomics
-- Biostatistics
-- Sw development
-- SLU platform
-- Proteomics
-- Genome annotation
-- Cancer genomics
-- Image analysis
-- Genome assembly
Linköping:
-- Host university
-- NGS & Biostatistics
-- Proteomics
-- Sw development (NSC)
Göteborg:
-- NGS
-- Marine genomics
-- Phenomics
-- Systems biology
-- Proteomics
Lund:
-- NGS
-- Plant genomes
-- Proteomics
-- Sw development

21. What can BILS help you with?
Consultancy – Current areas of expertise
Large scale sequencing (NGS) including metagenomics
Biostatistics
Phylogenomics
Metabolomics
Systems biology
Protein bioinformatics
Mass-spectrometry proteomics
Genome annotation
Infrastructure
data storage
data publishing
access to computing
access to bioinformatics tools

22. BILS support
BILS will support excellent science and our aim is to provide help in all relevant projects where our competence is asked for.
We aim at providing all users a basic fair amount of support (up to 2 weeks).
Additional support will be available at a subsidised cost. For 2014, this is 2000 SEK per day.
BILS staff has a national responsibility and should serve the users’ needs regardless of their affiliation. Thus, BILS staff is expected to work to a large extent outside their home department.

23. >400 projects in 2013

24. Focus areas 2014 Genome annotation platform Pipelines infrastructure
expansion with genome assembly activities
Pipelines infrastructure
Mosler – secure compute and storage
in close collaboration with SNIC/UPPMAX
Improved support request management
Data publishing
Increased training activities
Nordic collaborations – Nordic ELIXIR and NeIC
European collaborations – ELIXIR and RDA
Improved coordination with WABI and UPPNEX

25. Assembly and Annotation platform

26. Multiple ways to get in touch with BILS
Write an to
Contact your local BILS person
Our staff is listed at
Post a question on the support forum

27. System design/ development
"
Compute – Support – Education
Long-term
(13 FTE)
500 h / project
20 projects/year
Short-term
(40 FTE)
80 h / project
400 projects/year
Biosupport
System design/ development
400 projects/year (only NGS)
Number of projects
Support hours per project

28. SciLifeLab Bioinformatics Compute and Storage (UPPNEX)
Director
Manager
High performance resources for data-intensive biological research
High-performance computing and large scale storage dedicated for bioinformatics
3328-processor computer cluster
>7 Petabytes of storage
High-memory computers (2 TB RAM)
Backup and long-term storage
>120 bioinformatics software packages
Reference genomes, biological data collections
Technical user support and training
Hans Karlsson
Ola Spjuth
Specific needs for high-performance bioinformatics:
Rapid access to high-memory compute cluster
Large scale storage
The latest bioinformatics software available
Free of charge for all users

29. 2013: Over 400 active projects from all over Sweden
Other research fields
Large sequencing projects use UPPNEX
2013: Over 400 active projects from all over Sweden
Integrated in Swedish e-Science infrastructure

30. There are no stupid questions
Biosupport.se
There are no stupid questions
-even if they are we still have to answer them

31. Final word
We are here to help you!
Don’t be scared to contact us at any level
If you are unsure how to design of large data experiments
Just becuase you contacted us does not mean that you have to signed up for anything