Three data delivery cases for EMBL- EBI s Embassy. Guy Cochrane

Transcription

1 Three data delivery cases for EMBL- EBI s Embassy Guy Cochrane

2 EMBL European Bioinformatics Institute Genes, genomes & variation European Nucleotide Archive 1000 Genomes Ensembl Ensembl Genomes Ensembl Plants European Genome-phenome Archive Metagenomics portal GWAS Catalog browser Protein sequences InterPro Pfam UniProt Molecular structures Protein Data Bank in Europe Electron Microscopy Data Bank Literature & ontology Europe PubMed Central Gene Ontology Experimental Factor Ontology Expression ArrayExpress Expression Atlas Metabolights PRIDE Reactions, interactions & pathways IntAct Reactome MetaboLights Chemical biology ChEMBL ChEBI Systems BioModels Enzyme Portal BioSamples

3 Sequence data at EMBL-EBI Sample/method Sample/method Read Read Alignment Alignment Assembly European Genome-phenome Archive - Controlled access data - Human data around molecular medicine - Annotation European Nucleotide Archive - Unrestricted data - Pan-species and application -

4 Sequence data at EMBL-EBI Sample/method Sample/method Read Read Alignment Alignment Assembly Annotation European Nucleotide Archive - Unrestricted data - Pan-species and application - European Genome-phenome Archive - Controlled access data - Human data around molecular medicine - Infrastructure provision - BBSRC: RNAcentral, MG Portal - MRC: 100k Genomes data implementation - EC: COMPARE, MicroB3, ESGI, BASIS - etc.

5 Challenges Data have high volume and grow rapidly Data are dynamic (continuous feed) and their application has urgency Users require arbitrary and ad hoc access

6 Tara Oceans

7 Tara Oceans Capacity

8 Infectious disease Opportunity: A methodological revolution in clinical and public health towards shotgun sequencing-based methods Scientific power: Sequence harbours rich information Diagnostic: identification, typing, resistance profiling, etc. Public health: outbreak detection, response strategy, vaccine development Mechanistic: host interactions, pathogencity, virulence, transmission, antimicrobial resistance COMPARE: recently launched Horizon 2020 project in which EMBL-EBI is informatics provider Global Microbial Identifier: Initiative with EMBL-EBI involvement supporting technologies, standards and data sharing for pathogen surveillance Informatics roles for EMBL: COMPARE: Rapid global sharing of surveillance and outbreak data, systematic integrated analysis, compute provision (Embassy) Standards for reporting, analysis and the communication of results New algorithms and analysis methods User interfaces for surveillance data reporting, across the domains

9 COMPARE platform Sources Processes Portals and environments COMPARE Registry COMPARE Data Resource Public data COMPARE workflow engine Assembly & alignment Food workflow development COMPARE Portal Default tools API INSDC data exchange Managed access data Private data AnnotaHon Typing Workflow integrahon Clinical workflow development Outbreak workflow development Hosted tools API API EBI infrastructure Embassy infrastructure DTU infrastructure Embassy virtual domain

10 COMPARE platform Sources Processes Portals and environments COMPARE Registry COMPARE Data Resource Public data COMPARE workflow engine Assembly & alignment Food workflow development COMPARE Portal Default tools API INSDC data exchange Managed access data Private data AnnotaHon Urgency Typing Workflow integrahon Clinical workflow development Outbreak workflow development Hosted tools API API EBI infrastructure Embassy infrastructure DTU infrastructure Embassy virtual domain

11 Personalised medicine Motivation: Personalised studies of variation, cancer mutation, epigenetics, regulation, expression require references for comparison and interpretation As part of GA4GH, EMBL-EBI is working on Resources serving reference human genomic and transcriptomic data, including Google read API, variant Beacons, etc. CRAM compression supporting greater data fluidity and APIs to allow direct computational access Delivery and synchronisation of high volume datasets to local Embassy and remote cloud infrastructures Past and current FP7 projects include SLING, BASIS, ESGI

12 Personalised medicine Motivation: Personalised studies of variation, cancer mutation, epigenetics, regulation, expression require references for comparison and interpretation Arbitrary access As part of GA4GH, EMBL-EBI is working on Resources serving reference human genomic and transcriptomic data, including Google read API, variant Beacons, etc. CRAM compression supporting greater data fluidity and APIs to allow direct computational access Delivery and synchronisation of high volume datasets to local Embassy and remote cloud infrastructures Past and current FP7 projects include SLING, BASIS, ESGI

13 ENA conventional read data delivery Conventional infrastructure (FTP, Aspera, GridFTP) ENA metadata FIRE1 ENA data (NFS)

14 ENA Embassy read data delivery Conventional infrastructure (FTP, Aspera, GridFTP) ENA metadata FIRE2 ENA data (Cleversafe) FUSE HTTP

15 ENA Embassy read data delivery Conventional infrastructure (FTP, Aspera, GridFTP) Embassy cloud infrastructure (VMWare -> OpenStack) Marine cache Tara Oceans Embassy ENA metadata FIRE2 Pathogen cache COMPARE Embassy ENA data (Cleversafe) FUSE CRAM cache GA4GH Embassy HTTP

16 ENA external read data delivery phase II

17 EMBL-EBI Embassy Cloud Steven Newhouse Head of Technical Services

18 The Challenge Facing EMBL-EBI Volume and variety of genomic data expanding EMBL-EBI data doubling every year - replication is challenging Infrastructure currently 50,000 CPUs & 60+PB Need to support complex analysis scenarios Web and programmatic access to services (3M unique users) Access to both public and managed access data sets Bespoke workflows and tools across a variety of domains Hard for users to replicate data sets for local analysis Use the cloud to bring local analysis to EMBL-EBI data 18

19 EMBL-EBI Embassy Cloud Service hosted at EMBL-EBI data centres Direct network access to public and managed data sets Direct network to access public services Expect both academic and commercial users Technical Implementation Logically isolated outside EMBL-EBI s LANs Secure flexible infrastructure for both tenant and host Resources exposed using VMware s vcloud Director & OpenStack Provide isolated IaaS clouds to multiple users 19

20 Why Embassy Cloud? An embassy is sovereign territory in a host country Host Country: EMBL-EBI Data Centre Sovereign Territory: Host Country not allowed to enter Virtualisation provides the protection for tenant and host Host puts boundaries in place to protect it from the tenant Tenant has freedom and control within those boundaries 20

21 Embassy Cloud Concept PanCancer Public Data Public Services Managed Data Embassy Cloud 1 Embassy Cloud 2 Embassy Cloud 3 Private Data Virtualised EMBL-EBI Hardware 21

22 User Benefits for the IaaS Model Tenant organisations get an empty virtual infrastructure They establish their own virtual machines and networks System administration performed by the tenant EMBL-EBI staff have no access to the VMs Added value from EMBL-EBI over other clouds Machines and data hosted in known jurisdiction Direct network data sets (public & managed access) Direct network access to public EMBL-EBI services 22

23 Benefits to EMBL-EBI of the IaaS Model A secure collaborative workspace Work does not contend with main EMBL-EBI resources Clearly define the committed IT resources and data Explore how to build more data focused analysis services Move the analysis to where the big data is located Learn from and inform other big data scientific communities 23

24 Embassy Cloud: Typical Uses Collaborative Environment Neutral ground outside internal network CTTV: Resources and VMs to host intranet, databases, Data Staging Undertake submission from local machine (following data staging) rather from remote location BRAEMBL: Remote submission unreliable due to file upload Data Analysis Large scale management and analysis of data PanCancer: 1,000 cores, 2.5 TB RAM, 1.0 PB HDD

25 Issues Object Store Storage Infrastructure Essential for scalable high-performance storage Applications need to adapt to flat model Current caching strategy will have a limit Sharing resources between sites/communities/clouds Adopt a standards based model for federating resources Solutions for uploading and distributing VMs (+containers?) Replicating large data sets to attract workloads to a cloud 25

26 Gaps à Activities à Solutions? Data Set Replication Strategic pre-positioning of data into clouds Leverage JANET/GEANT, GridFTP + Globus Transfers, Cloud federation for mobile computing EGI has a federated cloud and VM distribution model ELIXIR plans to build on existing infrastructure where possible Wide-area file access needed for collaborative data analysis High performance wide-area object-store Need access control for human related data Coordinated investment in infrastructure Where is the UK coordination? What coordination is needed? Integrating commercial resources where they add value Integration with EU Infrastructure (ELIXIR) 26