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Partners Research Computing Overview

Partners Research Computing Overview

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Partners Research Computing Overview

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  1. Partners Research Computing Overview Diane Keogh Corporate Director, Research Computing July 1, 2009

  2. Partners Research Enterprise Supporting Research Information Technology at Partners is important and unique • Research portfolio approximately $1B annually • Annual growth at double digit rates for the last 5 years • 15,000 research funds under management • 3500 principal investigators • Over 10,000 actively involved in research • 23 research space locations across Boston – international collaborations • 5600 grant applications/3000 IRB applications processed in last 12 months • Over 1800 sponsors – 60% NIH • Source of tremendous innovation across the network and critical to the vitality of the clinical enterprise As of last week - $21M in ARRA grants awarded, more on the way!

  3. IT impacts all areas of the Research Life Cycle Scientific Review (SRRP) Human Studies (IRB) *Source: PHS Research Administration Documentation IT is required from the beginning of an idea through review, award, scientific analysis, article published, new discovery through award close-out

  4. Overview of Research Computing at Partners • Research Computing - Functional groups • Administrative Systems • Infrastructure & Services • Research Patient Data Registry (RPDR) • I2b2 • Genetics and Genomics • Planning underway for new areas of support • Partners Personalized Medicine Biorepository • Pharmacovigilence • Personalized “Genetic” Medicine • Informatics support for Harvard Catalyst (CTSC)

  5. Research Computing

  6. Research Administrative Systems Scott McNeal • Insight • Administrator and PI web access to review and monitor research portfolio • All financial transactions integrated from People Soft and other sources • Clinical trial budget builder • Data warehouse to support financial and compliance reporting • COI – Conflict of Interest module • Grant and Contracts • Electronic proposal development/Grant submission – InfoED • eIRB • Electronic IRB -- workflow • Includes human and animal protocols • New project – Effort reporting module

  7. Research Infrastructure – Systems and SupportBrent Richter • HPC • Storage • Client Support • Dedicated BWH (RICS) and MGH Teams • Centralized support (ERIS) • Collaboration • DIPR (cloud)

  8. Research’s cloud requirements 8 • “need it now” • Difficult to predict funding • “need it to work” • Don’t always know sizing requirements • “need it to run [fill in]” • Flexible environments • Shared databases • Mysql, Oracle, Postgres

  9. Utility in Scientific Computing 9 • Developer-focus • Use development platforms they already know • Fast access to compute power and storage • Automatically scale to the needs of the application • Pay only for what you use, with no commitments • IT-focus • Secure, dependable, and fast infrastructure services • Easily provision resources for one‐off projects • Service the needs of the entire community without jeopardizing in‐progress projects

  10. Duality of Cloud Computing Using Internal (DIPR) and external clouds 10

  11. RPDR – Informatics Group

  12. De-identified Data Warehouse Research Patient Data Registry Query construction in web tool 1) Queries for aggregate patient numbers - Warehouse of in & outpatient clinical data- 4.0 million Partners Healthcare patients- 1.2 billion diagnoses, medications, procedures, laboratories, physical findings, & genomics coupled to demographics & visits- Authorized use by faculty status- Clinicians can construct complex queries- Queries cannot identify individuals, internally can produce identifiers for (2) Z731984X Z74902XX ... ... Encrypted identifiers 2) Returns detailed patient data OR 0000004 2185793 ... ... 0000004 2185793 ... ... - Start with list of specific patients, usually from (1)- Authorized use by IRB Protocol- Returns contact and PCP information, demographics, providers, visits, diagnoses, medications, procedures, laboratories, microbiology, reports (discharge, LMR, operative, radiology, pathology, cardiology, pulmonary, endoscopy), and images into a Microsoft Access database and text files. Real identifiers

  13. Research Patient Data Registry • 1900+ total users • 1000 detailed data sets delivered in last 12 mos (4 million patient records) • $94-136 million total research support critically dependent on RPDR from patient data received throughout life of funding. • Linkage to National Informatics for Integrating Biology and the Bedside (i2b2) efforts • Enhanced distribution of “user friendly” data marts from RPDR • Data visualization tools • Clinical Research Chart • “i2b2 Hive” Portfolio of tools (NLP, Patient de-identification, etc) • Linkage to biological samples • Crimson at BWH and soon to be at MGH is the first example • Pharmacovigilance • Ex: eHealth initiative - Collaboration between Pharmaceutical companies and the Life Sciences Industry to understand potential secondary uses of Healthcare Data for safety activities

  14. i2b2 Hive: A Translational Toolkit Adoption 18+ US AMC’s 5 International Commercial and academic development efforts Free and open source Project Management Natural Language Processing Visual Term Mapping File Repository De - Identification Of data Ontology Management Identity Management Annotating Genomic Data Data Repository (CRC) Workflow Framework Data Queries Data Visualization Correlation Analysis https://www.i2b2.org/software/

  15. Genetics and GenomicsSandy Aronson • IT support – Partners Center for Personalized Genetic Medicine • Partnership with Hewlett Packard provides hardware and offshore development resources to support “Personalized Medicine” • Gateway for integrated genomic/proteomic applications and data (GIGPAD) • Enterprise LIMS infrastructure -- supporting many core research labs and clinical genetics lab • Knowledge database of phonotype-genomic correlations (GeneInsight) • Genomic variant interpretation engine (GVIE) • Integration of structured clinical genetic results into the EMR • Developing clinical decision support rules using structured genetic results • “Personalized Medicine” roadmap project underway to understand clinical systems changes to incorporate expanding genetics into clinical practice

  16. Personalized MedicineServing the Need – PGE with Email Driven Alerts Email Alert on Update

  17. Partners Personalized Medicine BioRepositoryNatalie Boutin • Enterprise BioSample repository IT infrastructure • Access to discarded clinical samples • Initial focus – Blood, Tissue – Phase-II • Linking samples with clinical phenotypic data • IT infrastructure supporting research studies • Consent management and tracking • Capture research consent during the clinical encounter

  18. Use Case 1: Banking Consented Samples PHS Investigator Step 6. The RPDR returns data sets to the investigator. Timeline • Start collecting specimens in Sept 2009. • Enable queries of specimens in RPDR in Feb 2010. RPDR Step 4. Investigator makes specimen query in RPDR. Step 3. The EMSI assigns unique IDs to specimens. Enterprise Master Specimen Index (EMSI) EMPI Step 5. Banks distribute samples to the investigator. Step 2a. Specimens are accessioned in the CLR at MGH and Crimson at BWH. PCPGM (GIGPAD) MGH Tissue Bank (System TBD) BWH Tissue Bank (System TBD) CLR (Sunquest) Crimson (Crimson) Inventory Management Step 2b. The inventory of specimens is managed by the Inventory Mgt system. Step 1. Patients are consented. EMPI Consent Tracking System Research Coordinator Legend Existing system New system

  19. Harvard’s Clinical and Translational Science Center (CTSC) Collaboration Research Data Research Tools

  20. Learn more about us! • http://rc.partners.org