Bioinformatic platform at SciLifeLab

SciLifeLab organization

Stockholm Steering committee

Stockholm node management

Research programs

Health Environment

Technology platforms

43 facilities – national and regional

Uppsala Steering committee

Uppsala node management

Director &Co-Director

Executive management

Strategic management

Board NRKSAB

Bioinformatics

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

Bioinformatics

Bioinformatics

Bioinformatics Short-term Support and Local Infrastructure

Bioinformatics Long-term Support (WABI)

Bioinformatics Compute and Storage (UPPNEX)

Platform directorsBengt Persson (UU)Siv Andersson (UU)Erik Lindahl (KTH)Gunnar von Heijne (SU)Hans Karlsson(UU)

Platform director Bengt PerssonFacility manager Mikael Borg

Platform director Siv Andersson & Gunnar von Heijne Facility manager Björn Nystedt & Thomas Svensson

Platform director Hans KarlssonFacility manager Ola Spjuth

SciLifeLab National Bioinformatics Support

www.scilifelab.se/platforms/bioinformatics

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

Compute – Support – Education

Senior bioinformaticians working in your project 500 h for free!

• Any NGS application• Anywhere in Sweden• Any bioinfo experience level

Per Unneberg Sthlm

Pall OlasonUa

Johan ReimegårdUa

Diana EkmanSthlm

Anna JohanssonUa

Mikael HussSthlm

Sanela KjellqvistSthlm

Pär EngströmSthlm

Åsa BjörklundUa

Jakub Orzechowski

Westholm, Sthlm

Alvaro Martinez Barrio, Ua

Marcel Martin Sthlm

Estelle Proux-Wéra, Sthlm

TranscriptomicsProteomics

Variation analyses De novo/pop.genomics

Current Staff

In a near future staff

4 Variant analyses in medical research Human 1 Differential gene expression Human 1 MetagenomicsHuman microbiota 6

4 De novo genome assembly/analyses Animals/plants 4 Variant calling/Population genomics Animals/plants 2 Gene expression

Animals/Plants 1 RNAseq + proteomicsFungus 1 Non-coding RNA

Bacteria 1 RNAseq method development Universal13

Kind of projects that have been accepted

1 2 3 40

10

20

30

40

50

60

70

# granted # applications

The number of applications per round is increasing

User survey in March 2014 (quotes)

Based on responses from 14 of 15 projects with >50h spent support at the end of February 2014

How content are you with the SciLifeLab Bioinformatics Long-term Support overall?

How much has the SciLifeLab Bioinformatics Long-term Support contributed to the technical quality of the project?

How content are you with the knowledge transfer to your group achieved by the SciLifeLab Bioinformatics Long-term Support?

How much do you believe that the results and knowledge gained from your current SciLifeLab Bioinformatics Long-term Support will aid your research in general over the next 2-3 years?

Are you in favour of SciLifeLab continuing to offer Bioinformatics Long-term Support on a national level?

0 1 2 3 4 5

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!”

How to apply for long term support

http://www.scilifelab.se/facilities/wabi/

Future dates for application7. 2014 nov14 (PEC2)8. 2015 jan 30 (PEC1)9. 2015 may15(PEC2)10. 2015 oct16 (PEC1)

How to apply for long term support

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

BILS – Bioinformatics Infrastructure for Life Sciences

Bengt Mikael Fredrik Persson Borg Levander

Proteomics coordinator

BILS is a distributed national research infrastructuresupported 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

Trainingcoordinator

Magnus Henrik Jonas SaraAlm-Rosenblad Lantz Hagberg Light

Technicalcoordinato

r

Director

Genomics coordinatorsSyst. development

coordinator

Current status of BILS 45 staff(including 4 fully SciLife-funded staff)

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Umeå:-- NGS-- Metabolomics-- Proteomics-- Biostatistics-- Metab. modelling

Göteborg:-- NGS-- Marine genomics-- Phenomics-- Systems biology-- Proteomics

Linköping:-- Host university-- NGS & Biostatistics-- Proteomics-- Sw development (NSC)

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

Uppsala:-- NGS incl. metagenomics-- Biostatistics-- Sw development-- SLU platform-- Proteomics-- Genome annotation-- Cancer genomics-- Image analysis-- Genome assembly

What can BILS help you with?

• Consultancy – Current areas of expertise

Large scale sequencing (NGS) including metagenomicsBiostatisticsPhylogenomicsMetabolomicsSystems biologyProtein bioinformaticsMass-spectrometry proteomicsGenome annotation

• Infrastructure data storage data publishing access to computing access to bioinformatics tools

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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.

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>400 projects in 2013

38

37

28

2823

22

22

17

11

96 3 211111111

PIs at different Swedish organisations KI

UU

GU

LU

UmU

LiU

NRM

SU

SLU

KTH

Chalmers

Sahlgrenska University Hospital

NGI

AstraZeneca

FOI

LTH

Norrlands Universitetssjukhus

Polismyndigheten

SVA

WABI

ÖrU

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

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Assembly and Annotation platform

Multiple ways to get in touch with BILS

• Write an E-mail to support@bils.se

• Contact your local BILS person– Our staff is listed at http://bils.se

• Post a question on the support forum

http://biosupport.se

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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)

SciLifeLab Bioinformatics Compute and Storage (UPPNEX)

www.scilifelab.se/facilities/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

Director Manager

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

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

There are no stupid questions

-even if they are we still have to answer them

http://www.biosupport.se/

Biosupport.se

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