Jim Dowling KTH Royal Institute of Technology, Stockholm SICS Swedish ICT CSHL Meeting on Biological Data Science, 2014
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1 Jim Dowling KTH Royal Institute of Technology, Stockholm SICS Swedish ICT CSHL Meeting on Biological Data Science, 2014
2 Definition of a Biobank The Biobank concept is defined (by Swedish law) as: biological material from one or several human beings collected and stored indefinitely or for a specified time and whose origin can be traced to the human or humans from whom it originates In Sweden, we have the goal of digitizing biological material in Biobanks. 500,000 people
3 Population-Scale WGS: $1325 per Genome HiSeq X Ten^ => Volume => Velocity => ^Cost ~$10 million ~18,000 genomes/year ~5.2 PB/year* ~45 MB/sec* *5.2 PB assumes a replication factor of 3 See:
4 Network effects: Biggest Dataset wins! Centralized dataset: technically feasible, politically hard. Federated dataset: technically hard, politically feasible. #diseases insights log(#samples)
5 Big Data means Commodity Hardware
6 180TB for $9,778 or 270TB for $15,763* *[
7 91,428 Whole Genomes: $782,240 (14.4PB) *Each genome is GB 35x coverage, Reed-Solomon erasure-coded. Nov 2014.
8 Hadoop can mean low administration costs Facebook Operations staffers manage 20-26,000 servers each^ ^
9 Population-based analysis needs scale-out Read genome on 1 machine*: ~1000 secs [Harddisk Image courtesy of sorapop / *112 GB, 35x coverage
10 Hadoop means Parallelization Read genome on 1000 machines: ~1 second* *112 GB, 35x coverage
11 Genomic data management solutions Outsource to SaaS providers Sequencing Centers High Performance Computing Centers In-House
12 BiobankCloud Users EU General Data Protection Regulation IT-Admin Biobanker Users, Data, Programs Ethics Auditor Bioinformatician
13 Never the Twain Shall Meet? Biobankers - NGS data producers Manage samples, metadata - Non-programmers Bioinformaticians - NGS data consumers Analyze samples - Programmers Python, R, Matlab, scripts BiobankCloud LIMS Cuneiform/HiWAY Hops-YARN Kerberos Overbank LDAP PaaS IT Admins Hops-HDFS
14 BiobankCloud LIMS (Lab Info Mgmt System)
15 Perimeter Security and Multi-Tenancy LIMS - J2EE Application LDAP, 2-Factor Authentication - Role-Based Access Control Study-level - Hadoop trusted proxy Kerberos - REST APIs LIMS Network Isolation Kerberos Related Hadoop Projects - Knox, Sentry, Rhino - Hue, Ambari LDAP
16 LIMS Authentication
17 Studies for Multi-Tenancy; Audit Trails Study Global Audit Trail
18 Study Membership
19 HDFS Files Browse Study Files
20 Upload Sample Data Low Volume Data ingestion (Overcome 3 GB browser upload limit) Apache Flume High Volume Data ingestion
21 Run Cuneiform Workflows on YARN
22 HiWay/Cuniform Variant Call Workflow TeraBytes of input data (1000 Genomes Project) read and reference parallel Scalability Experiments on up to 576 containers in a 28 node cluster reference parallel reference parallel
23 Runtime in Minutes HiWay/Cuniform Scalability* 128,00 Workflow Runtime with Increasing Number of Containers Container time spent at different stages of execution 64,00 32,00 16, Number of Nodes idle scheduling startup stage-in execution stage-out shutdown [*Unpublished Results]
24 Store Genomes in Hops-HDFS Block-id and a block placement policy minimizes re-identification risk. HDFS-6134, HDFS Transparent data at rest encryption Sample data is not fully compromised unless intruders also compromise the NameNode /genomes/jim.bam -> {2,4,3,6,9} NameNodes DataNodes Data nodes comprimised Hops-HDFS: Stateless NameNodes + MySQL Cluster Erasure-Coded Replication
25 PaaS support with Chef/Karamel Launch Hadoop and the LIMs on EC2, Vagrant.
26 Conclusions Open-source commodity hardware NGS data management solutions are feasible and economical - BiobankCloud is building such a system BiobankCloud status - First beta release coming in 2014 Ongoing work on regulatory and ethical compliance - BBC Newsletter on our website NGS Hadoop Workshop Feb 19-20, Stockholm - Signup at
27 The Team KTH Salman Niazi, Mahmoud Ismail, Kamal Hakimzadeh, Stig Viaene, Gautier Berthou, Roshan Sedar, Ali Gholami, Erwin Laure Humboldt University Ulf Leser, Jörgen Brandt, Marc Bux University of Lisbon Alysson Bessani, Vinicius Cogo Karolinska Institute Jan-Eric Litton, Roxana Martinez, Jane Reichel, Mats Hansson Charité University Hospital Michael Hummel, Lora Dimitrova, Karen Zimmermann Financed by the European Commission 7 th Framework Programme.
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