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Enterprise Research Infrastructure & Services

Enterprise Research Infrastructure & Services. Updates Research Tech Lunch April 28, 2011. DATABASES: STRUCTURED DATA SERVICES. Enterprise Research Infrastructure Systems. Allan Harris/DBA ajharris@partners.org (*Updated from December 2009*). Overview.

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Enterprise Research Infrastructure & Services

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  1. Enterprise Research Infrastructure & Services Updates Research Tech Lunch April 28, 2011

  2. DATABASES: STRUCTUREDDATA SERVICES Enterprise Research Infrastructure Systems Allan Harris/DBA ajharris@partners.org (*Updated from December 2009*)

  3. Overview • What database services does ERIS offer? • Current realms of DB management • HPC • DIPR services • External DB support • Crimson – on track to move into DIPR • PCPGM – in discussions to utilize Oracle RAC cluster

  4. HPC Solutions • hpcdb.research.partners.org • PostgreSQL: 4 schemas • MySQL: 17 schemas • Bringing Oracle and MS SQL to the clusters • Integration with DIPR

  5. DIPR (Discovery Informatics Platform for Research) • PostgreSQL (13 schemas) • MySQL (69 schemas) • Oracle Database RAC (Real Application Clusters): • Version 11gR2, backwards compatibility available • 26 user schemas in 4 instances • Polyserve for MS SQL Server • Versions: 2005, 2008, 2008 R2 • 33 schemas in 6 instances • FileMaker Server Advanced • Version 11.0.2 (moving to 11.0.3) • 31 hosted database files

  6. Oracle RAC (Real Application Clusters) Extensible option of Oracle Database Oracle 11g Release 2 Single database accessed by multiple, coordinated instances on multiple hosts Leverages “Cache Fusion” over Infiniband interconnect for SGA unification Advanced connectivity capabilities can spread single service loads across multiple servers

  7. Oracle RAC (cont’d)

  8. Oracle RAC (cont’d) • Advantages • Built on commodity hardware – nodes can be dissimilar • Durability/scalability/flexibility • Cache Fusion • License consolidation • Implementation plans • Currently running on 2 (2 more available) HP BL685c AMD-based blade servers • Each node has 16 processor cores and 64GB RAM • Can expand/contract as necessary

  9. PolyServe for Microsoft SQL Server NOT a replacement of TSO services Consolidation Ease of deployment and patching Simplified management Multi-instance access to RO datasets CITED

  10. PolyServe for SQL (cont’d)

  11. FileMaker Server Advanced Hosted FileMaker solution Exposes FileMaker databases for enterprise consumption Instant Web Publishing/XSLT/PHP

  12. Resources http://research.partners.org http://h18000.www1.hp.com/products/storage/software/polyserve/db_utility/sql/index.html http://www.oracle.com/technology/products/database/clustering/pdf/twp_rac11gR2.pdf

  13. Applications for HPC Linux/Windows • Schedulers – LSF / PBS / Torque (Maui) … • GENOMICS / SEQUENCING : BioScope / PicardTools / SAM BAM TOOLS / TopHat / CuffLinks/ CASAVA / BWA … • STATISTICS : R, SAS, Octave … • Special : SSE and MPI

  14. Total Number of Users: ~ 500 / Number of Cores ~ 800

  15. The Discovery Informatics Platform for ResearchVirtual Machines

  16. Infrastructure • 16 HP BL460c G1 Blades • 8 Cores (2x Xeon 5450 @ 3ghz) • 64GB Memory • EVA 8100 SAN Storage • VMWare ESXi 4.1

  17. Current Usage • 271 Virtual machines hosted • 339.2/1024GB Memory in use • 6.54TB provisioned/3.56TB utilized

  18. Recent improvements • Expanded each VM host memory from 32 to 64GB • New builds managed by Spacewalk • Standard build is now CentOS 5 • All new VMs are 64 bit

  19. Services Groups can request, free of charge, either: 2 “Small” VMs • 512MB memory • 8GB Disk 1 “Medium” VM • 1GB memory • 16GB Disk Standard OS build or Custom OS of choice.

  20. Standard OS Build • CentOS 5, 64 Bit • User authentication with Partners AD • We manage OS updates • Nagios monitoring • SSH access with local sudo • Standard package software installed upon request • User has access to yum for package installs

  21. Custom OS Build • Any VMWare compatible OS can be installed • User is responsible for security updates • User is responsible for software installs • User must provide OS media/license • Single local admin account configured with remote access • SSH for Linux, RDP for windows

  22. External Sites • Research Web Proxy • Can proxy http/https traffic to DIPR VMs • Running apache mod_proxy • *.partners.org wildcard cert installed for SSL

  23. Future Improvements • CentOS 6 will be available once released/tested • Existing VMs will be converted to CentOS • Additional standard build configurations

  24. EDC/Survey • 3 options EDC • REDCap, Velos, StudyTrax • 2 options Surveys • REDCap, LimeSurvey

  25. REDCap • Went Live May 2010 • Today: • 6th in PRODUCTION projects • 2nd in DEVELOPMENT projects • 2nd in TOTAL projects • 2nd in TOTAL USERS

  26. Future Features 21CFR Part 11 Merging REDCap + REDCap-Survey External Systems Interoperability REDCap Unplugged (No Internet) Improved Language Rendering Matrix Question Type / Table Format 29

  27. Interesting Use Cases In development / production: • Student/Class, Program Evaluations • Longitudinal Survey Studies • Project Management Calendar • Study Bio-specimen Tracking/Scheduling Checklist … So many possibilities! 30

  28. Frequently Asked Questions (FAQ) • Q: How much training is required to use and design in REDCap? • A: Minimal training is needed. Development support available in the form of: • Online Tutorials and Videos • Periodic Training • Refined User Guides • Direct phone/email contact with support staff • Q: How much experience with programming, networking and/or database construction is required to use and design EDC tools in REDCap? • A: No programming, networking or database experience required. • Use Point-and-Click interface to design your EDC tool(s). 31

  29. Contacts Contact Information for Harvard Catalyst REDCap Support Staff Lynn Simpson MGH, BWH & McLean edcsupport@partners.org Phone: 617.643.7711 http://rc.partners.org/edcredcap Chris Botte BIDMC, Children’s & Joslin edc@bidmc.harvard.edu Phone: 617.754.8828 For support for other Harvard schools or affiliated academic health care centers, contact either Lynn or Chris. 32

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