Information Sciences Solutions to Core Facility Problems at St. Jude Children's Research Hospital

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  • 1. Solutions to Core Facility Problems
    Matt Stine
    2008 NERLSCD Meeting
  • 2. Agenda
    Introduction to St. Jude and Information Sciences
    Case Studies
    Day-to-Day Facility Operations Management
    CCSG Competitive Renewal
    Future Challenges & Plans
  • 3. Introduction to St. Jude and Information Sciences
  • 4. Research Landscape
    16 Academic Departments
    5 Academic Divisions
    Cancer Center
    First and only NCI-designated Comprehensive Cancer Center solely focused on pediatric cancer
    6 Programs:
    Cancer Prevention and Control
    Developmental Therapeutics for Solid Malignancies
    Hematological Malignancies
    Molecular Oncology
    Neurobiology and Brain Tumor
    Signal Transduction
  • 5. Shared Resources
    Human Applications Laboratory
    Information Sciences
    Laboratory Services
    MHC Tetramer
    Molecular Clinical Trials Core
    Mouse Immunophenotyping/Cytokine Assay
    Office of Technology Licensing
    Process Development Group
    Protein Production Facility
    Protocol-Specific Research Support
    Scientific Communications
    Scientific Editing
    Tissue Repository
    Transgenic/Gene Knockout
    Translational Trials Unit
    Vector Development and Production
    Word Processing
    Bold/italicized resources are CCSG Funded
    Animal Imaging Center
    Animal Resources Center
    Biomedical Communications
    Biomedical Engineering
    Biomedical Library
    Cell & Tissue Imaging
    Central Trial and Data Monitoring Office
    Clinical Protocol Scientific Review & Monitoring
    Clinical Research Education Program
    Environmental Health & Safety
    Flow Cytometry & Cell Sorting
    Grant and Contract Management Office
    Hartwell Center for Bioinformatics and Biotechnology
    Clinical Applications Core Technology (Affymetrix)
    DNA Sequencing
    Genome Sequencing
    Functional Genomics
    Macromolecular Synthesis
    Molecular Interaction Analysis
  • 6. The Hartwell Center
    A unique integration of:
    High-throughput biotechnology resources (core facilities)
    Bioinformatics/Research Computing
    Bioinformatics Support
    Client Services/Desktop Support
    Operations/High Performance Computing
    Software Development
    Academic programs
    Designed to provide St. Jude with state-of-the-art tools for discovery
    Clayton Naeve, Ph.D. - Director
  • 7. Information Sciences
    Formed in July 2007
    Integrated the major IT groups on campus
    Clayton Naeve, Ph.D. – CIO
    Three divisions:
    Enterprise Informatics
    Client Services/Desktop Support
    Clinical Informatics
    Research Informatics:
    Bioinformatics Support
    High Performance Computing
    Software Development (Research Application Development)
  • 8. Landscape Summary
    Great diversity of shared resources/core facilities
    IT leadership comes from core management background
    IT expertise with long history of core facility support
    Research Application Development alone has 25+ combined years of experience supporting cores
    St. Jude is in a unique position to solve core facility information management problems
  • 9. Case Study #1
    Day-to-Day Facility Operations Management
  • 10. Day-to-Day Operational Issues
    Service Requests
    Shared Instrumentation Booking
    Workflow/Process Management (LIMS)
    Data Management/Retrieval
    Usage Statistics
    Turnaround Time
    Service Request History
  • 11. Shared Resource Management (SRM)
    Web-based application providing a single, integrated portal for management of shared resource (core) facility activities.
    Currently supports 11 St. Jude facilities offering more than 20 distinct services.
    Available under the GNU Lesser General Public License (LGPL) v3.0 at
  • 12. Web-based request for services:
    Client fills order form with PI, grant/cost center, sample information, service request
    Client brings physical samples to facility
    Facility “checks-in” the samples
    Web-based booking of shared instrumentation:
    Client selects from available time slots on desired instrument, unassisted vs. technician-assisted usage, etc.
    SRM Ordering
  • 13. Models the laboratory process as a workflow with multiple ordered modules.
    Data is collected within each module:
    QC Information
    Facilities can design multiple “workflow templates.”
    Individual sample workflows can be edited “on-the-fly.”
  • 14. SRM Data Management/Retrieval
    Facilities archive the deliverable data associated with each module through its web interface.
    Data are “picked up” by SRM from a network drive and moved to the RI flat-file archive, organized by PI.
    Clients are notified via email that their data is ready and can download it to their PC/Mac via a web interface.
  • 15. SRM Billing
    Facilities bills for the “current cycle” are automatically generated by SRM and sent on demand by the billing administrator.
    Faculty members (or delegates) login to SRM to approve bills and make desired changes to assigned grants/cost centers.
    SRM generates Excel spreadsheets for approved bills which are submitted to Financial Services.
  • 16. SRM supports two reporting modes:
    Prepared (Canned) Reports
    Sample counts
    Turnaround time
    Investigator usage statistics
    Custom (Ad-hoc) Reports
    Custom queries
    History for individual service requests
    SRM Reporting
  • 17. Case Study #2
    Cancer Center Support Grant (CCSG) Competitive Renewal
  • 18. Problem Statement
    Currently 12 shared resources are supported by the CCSG.
    Every five years the CCSG comes up for competitive renewal.
    As part of the renewal process, shared resources must provide:
    Usage statistics for Cancer Center investigators
    Cancer Center publications resulting from shared resource supported research
  • 19. The Old Way
    Usage statistics:
    Shared resource directors independently contact investigators.
    Investigators highlight publications supported by facility ‘X.’
    12 SR’s times 129 investigators = 1548 manual requests
    Shared resource directors collate these data into a report.
  • 20. SRM
    SRM maintains an updated list of the
  • 21. TrakIT #1
  • 22. TrakIT #2
  • 23. Future Challenges & Plans
  • 24. Future Challenges & Plans
    IS FY09-FY13 Strategic Plan
    Expand the SRM system to include all laboratory-based SJCRH shared resources
    Build SRM ordering and billing functionality for ~10 additional lab-based shared resources
    Build SRM LIMS for those shared resources needing this infrastructure
    Establish links to the Tissue Repository and other databases on campus as required
  • 25. SRM 2.0
    Metadata-based data model
    Enhanced flexibility and configurability
    Rapid rollout of new facilities and services
    Easy modification of existing services
    Microkernel/Plug-in architecture
    Microkernel core supporting base functionality
    Plug-ins to support facility/service-specific functionality
    caBIG Bronze level compatibility
  • 26. Future Challenges & Plans
    “Next Generation” Sequencing Data Deluge
    First test run of Hartwell Center’s Illumina platform produced 1.5 billion bases of DNA sequence data
    1.5 billion bp = three times the amount of DNA sequence data produced by St. Jude in the past 20 YEARS
    Early runs producing 40GB of deliverable client data per sample on the high-end
    3730xl runs producing average of 0.5 MB of deliverable client data per sample
  • 27. SRM 2.0
    Distributed Data Management Grid
    Eliminate data management related network traffic between SRM application servers and