Storage and Analysis of Sensitive Large-Scale Biomedical Data in Sweden
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This document summarizes the storage and analysis of sensitive large-scale biomedical data in Sweden. It discusses: 1) The Science for Life Laboratory, established in 2010, which is a leading center for developing and applying large-scale technologies for molecular biosciences. 2) Hardware resources available for bioinformatics analysis including high-performance computing clusters and large-scale storage facilities. 3) The generation of over 120 terabases of sequencing data in 2014 alone and resources for ongoing large-scale human genome sequencing efforts. 4) The SNIC-Sens project, a 4-year national security project funded to develop specifications for analyzing sensitive biomedical data within legal and ethical guidelines.
Storage and Analysis of Sensitive Large-Scale Biomedical Data in Sweden
- 1. Storage and Analysis of Sensitive Large-Scale Biomedical Data in Sweden Ola Spjuth SNIC, UPPMAX and Science for Life Laboratory Uppsala University, Sweden [email protected]
- 2. Ola Spjuth • Associate Professor in Pharmaceutical Bioinformatics • Guest Researcher • Co-Director • Manager of Bioinformatics Compute and Storage facility
- 4. 2003: First sequenced human genome - 13 years for $3 billions
- 5. 2015: Human whole genome sequenced in 3 days for ~$1150 …requires supercomputers for analysis and storage Massively parallel sequencing….
- 6. 2010: Science for Life Laboratory inaugurated An internationally leading center that develops and applies large-scale technologies for molecular biosciences with a focus on health and environment. National platform since 2013 Stockholm node Uppsala node
- 7. 2. Data delivery Data generation and delivery 3. Analysis Scientists www.uppmax.uu.se/uppnex High-performance computers and large scale storage for bioinformatics analysis. 1. Sample transfer
- 9. Sequence production 2014: • Generated > 120 Tbp of sequence data • 13.7 Gbp/hour, 3.8 Mbp/sec (on average)
- 10. Hardware resourcesmilou: HP cluster of 208 nodes pica: 6 (7) PB Hitachi storage halvan: 2 TB high- memory computer Fast network via SUNET Backup via SNIC Long-term storage at SweStore nestor: 48 nodes production cluster meles: 547 TB Hitachi storage mosler: 24 nodes, 223 TBSmog: 100 nodes, ~300 TB 2015: 250 nodes 2016: 200 new nodes +1 PB +2 PB
- 11. A national e-Infrastructure for NGS Software + reference data Support Education Compute resources Storage resources Efficiency + automation
- 12. What we sequenced at NGI /
- 13. Chipster workbench on UPPMAX UpCloud – smog - (OpenStack)
- 14. • Open catalogue of VMIs • Hosted at Uppsala University M. Dahlö, F. Haziza, A. Kallio, E. Korpelainen, E. Bongcam- Rudloff, and O. Spjuth. BioImg.org: A catalogue of virtual machine images for the life sciences. Accepted in Bioinformatics and Biology Insights. www.bioimg.org Managing Virtual Machine Images
- 15. Mosler overview • e-Infrastructure for working with sensitive data • Copy of Norwegian solution (TSD) • Designed to look like UPPMAX clusters
- 16. Mosler specifications • High-performance computing in a virtualized environment (OpenStack) • 2-factor authentication • Restricted data transfer in/out • Only accessible over remote desktop (ThinLinc) via Mosler dashboard • Aim: Compliant with all laws and regulations for analyzing sensitive data in Sweden
- 17. Consortia DBA Consortium member MyResearch Virtual environment storage compute Mosler Data hosting Data syncing Access, analysis Data hosting use case
- 18. Manager DBA Scientist LifeGene Virtual environment storage compute Mosler 1. Request for data 2. Approval 3. Data extraction 4. Data transfer 5. Access, analysis Data extraction use case
- 19. Nov 2014 20M € total grant 4M € IT-infrastructure
- 20. X-Ten System • First system able to deliver 1000$ genome • Each run 1.2TB data • 16 Human genome (30X) • 3 days per run • Population scale genomics • 15K genomes per year Swedish Genome Initiative Call for a reference variation Database (1000 genomes) and for Whole Human Genome (half price). Goal: 5.000 genomes 2015, 10.000 genomes 2016
- 21. -100000 0 100000 200000 300000 400000 500000 600000 700000 800000 900000 1000000 Aug-11 Mar-12 Sep-12 Apr-13 Nov-13 May-14 Dec-14 Jun-15 Jan-16 GigaBases Production date NGI-Stockholm Procution (Jan-12 to Dec-15) Data production Conservative Prediction (60% of maximum production)
- 22. Whole Genome Sequencing • Data on new scale, 80% expected to be sensitive New challenges • Funding for IT-infrastructure from KAW foundation – Resources for data production (2 M EUR) – Resources for scientists (2 M EUR) • A national security project funded by Swedish Research Council (5 M EUR over 4 years) – SNIC Sens
- 23. SNIC-Sens • 4-year project, started Jan 2015 • Project owner: SNIC (Ann-Charlotte Sonnhammer) • Project leader: Ola Spjuth (until end of this week) • Aims: – Specifications for analyzing sensitive data in SNIC (hardware, legal, contracts, processes etc.) – Evaluation on the use of public cloud providers (Google, Amazon) – Make available e-Infrastructure for production and research of data generated at NGI, blueprint for other domains
- 24. SNIC-Sens roadmap • Information classification workshop (21/5) • Risk/vulnerability analysis (2/6) • Specifications for hardware procurement • Public tender (end of this week) • Installation and testing of production system (Aug- Sept) • Installation, configuration and testing of research system (Q3-Q4) • Research system online (Q1 2016)
- 25. Two pilots for clinical data management
- 27. MDR, Åsa Melhus
Editor's Notes
- #7: Strategic funding to enable: Infrastructure for high-throughput analysis Multi-disciplinary research environment Competence in technology and analysis methodology
- #11: Bild på milou: 2 M compute hours Bild på pica: 7 PB storage Bild på halvan: High-memory machine Backup (via SNIC, currently to Linköping) Network (SUNET)
- #12: Access to computers (many if you need) Access to storage (a lot if you need) Pre-installed software and reference genomes Free
- #21: X-Ten system, some “scary” numbers and some screen shot about what we plan in the following months (the picture shows the thirst thee HiSeq X in our basement)