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Bioinformatic platform at SciLifeLab

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Presentation on theme: "Bioinformatic platform at SciLifeLab"— Presentation transcript:

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 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

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