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Bioinformatic platform at SciLifeLab. SciLifeLab organization Stockholm Steering committee Stockholm node management Research programs HealthEnvironment.

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Presentation on theme: "Bioinformatic platform at SciLifeLab. SciLifeLab organization Stockholm Steering committee Stockholm node management Research programs HealthEnvironment."— Presentation transcript:

1 Bioinformatic platform at SciLifeLab

2 SciLifeLab organization Stockholm Steering committee Stockholm node management Research programs HealthEnvironment Technology platforms 43 facilities – national and regional Uppsala Steering committee Uppsala node management Director &Co-Director Executive management Strategic management BoardNRK SAB

3 Bioinformatics Custom-tailored support. Computing and storage resources for large-scale biological data. Collaboration with the SNIC supercomputer centres.

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

5 SciLifeLab National Bioinformatics Support

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

7

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

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

10 In a near future staff

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12 4 Variant analyses in medical research Human 1 Differential gene expressionHuman 1 MetagenomicsHuman microbiota 6 4 De novo genome assembly/analysesAnimals/plants 4 Variant calling/Population genomicsAnimals/plants 2 Gene expression Animals/Plants 1 RNAseq + proteomicsFungus 1 Non-coding RNABacteria 1 RNAseq method development Universal 13 Kind of projects that have been accepted

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 nov14 (PEC2) jan 30 (PEC1) may15(PEC2) oct16 (PEC1) How to apply for long term support

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

19 BILS – Bioinformatics Infrastructure for Life Sciences Bengt Mikael Fredrik Persson Borg Levander 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 Training coordinator Magnus Henrik Jonas Sara Alm-Rosenblad Lantz Hagberg Light Technical coordinator Director Genomics coordinators Syst. development coordinator

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

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 21

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. 22

23 >400 projects in 2013

24 Focus areas 2014 Genome annotation platform –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 24

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 26

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

28 SciLifeLab Bioinformatics Compute and Storage (UPPNEX) High performance resources for data- intensive biological research Hans Karlsson Ola Spjuth 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 DirectorManager Free of charge for all users Specific needs for high- performance bioinformatics: -Rapid access to high-memory compute cluster -Large scale storage -The latest bioinformatics software available

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

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

31 We are here to help you! Final word 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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