bioinformatic platform at scilifelab. scilifelab organization stockholm steering committee stockholm...
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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 [email protected]
• 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