This document discusses solutions to core facility problems at St. Jude Children's Research Hospital. It describes a case study on using the Shared Resource Management (SRM) system to help with day-to-day operations and the Cancer Center Support Grant (CCSG) competitive renewal process. The document also outlines future challenges around managing large sequencing data and plans to expand SRM and develop a next generation version.

1. Solutions to Core Facility ProblemsMatt Stine2008 NERLSCD Meeting

2. AgendaIntroduction to St. Jude and Information SciencesCase StudiesDay-to-Day Facility Operations ManagementCCSG Competitive RenewalFuture Challenges & Plans

3. Introduction to St. Jude and Information Sciences

4. Research Landscape16 Academic Departments5 Academic DivisionsCancer CenterFirst and only NCI-designated Comprehensive Cancer Center solely focused on pediatric cancer6 Programs:Cancer Prevention and ControlDevelopmental Therapeutics for Solid MalignanciesHematological MalignanciesMolecular OncologyNeurobiology and Brain TumorSignal Transduction

5. Shared ResourcesHuman Applications LaboratoryInformation SciencesLaboratory ServicesMHC TetramerMolecular Clinical Trials CoreMouse Immunophenotyping/Cytokine AssayOffice of Technology LicensingPharmacokinetcsProcess Development GroupProtein Production FacilityProtocol-Specific Research SupportScientific CommunicationsScientific EditingTissue RepositoryTransgenic/Gene KnockoutTranslational Trials UnitVector Development and ProductionWord ProcessingBold/italicized resources are CCSG FundedAnimal Imaging CenterAnimal Resources CenterBiomedical CommunicationsBiomedical EngineeringBiomedical LibraryBiostatisticsCell & Tissue ImagingCentral Trial and Data Monitoring OfficeClinical Protocol Scientific Review & MonitoringClinical Research Education ProgramCytogeneticsEnvironmental Health & SafetyFlow Cytometry & Cell SortingGrant and Contract Management OfficeHartwell Center for Bioinformatics and BiotechnologyClinical Applications Core Technology (Affymetrix)BioinformaticsDNA SequencingGenome SequencingFunctional GenomicsGenotypingMacromolecular SynthesisMolecular Interaction AnalysisProteomics

6. The Hartwell CenterA unique integration of:High-throughput biotechnology resources (core facilities)Bioinformatics/Research ComputingBioinformatics SupportClient Services/Desktop SupportOperations/High Performance ComputingSoftware DevelopmentAcademic programsDesigned to provide St. Jude with state-of-the-art tools for discoveryClayton Naeve, Ph.D. - Director

7. Information SciencesFormed in July 2007Integrated the major IT groups on campusClayton Naeve, Ph.D. – CIOThree divisions:Enterprise InformaticsClient Services/Desktop SupportClinical InformaticsResearch Informatics:Bioinformatics SupportHigh Performance ComputingSoftware Development (Research Application Development)

8. Landscape SummaryGreat diversity of shared resources/core facilitiesIT leadership comes from core management backgroundIT expertise with long history of core facility supportResearch Application Development alone has 25+ combined years of experience supporting coresSt. Jude is in a unique position to solve core facility information management problems

9. Case Study #1Day-to-Day Facility Operations Management

10. Day-to-Day Operational IssuesOrderingService RequestsShared Instrumentation BookingWorkflow/Process Management (LIMS)Data Management/RetrievalBillingReportingUsage StatisticsTurnaround TimeService 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 http://stjude-srm.sourceforge.net.

12. Web-based request for services:Client fills order form with PI, grant/cost center, sample information, service requestClient brings physical samples to facilityFacility “checks-in” the samplesWeb-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 InformationResultsObservationsFacilities can design multiple “workflow templates.”Individual sample workflows can be edited “on-the-fly.”SRM LIMS

14. SRM Data Management/RetrievalFacilities 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 BillingFacilities 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) ReportsSample countsTurnaround timeInvestigator usage statisticsCustom (Ad-hoc) ReportsCustom queriesHistory for individual service requestsSRM Reporting

17. Case Study #2Cancer Center Support Grant (CCSG) Competitive Renewal

18. Problem StatementCurrently 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 investigatorsCancer Center publications resulting from shared resource supported research

19. The Old WayUsage statistics:TODOPublicationsShared resource directors independently contact investigators.Investigators highlight publications supported by facility ‘X.’12 SR’s times 129 investigators = 1548 manual requestsShared resource directors collate these data into a report.

20. SRMSRM maintains an updated list of the

21. TrakIT #1

22. TrakIT #2

23. Future Challenges & Plans

24. Future Challenges & PlansIS FY09-FY13 Strategic PlanExpand the SRM system to include all laboratory-based SJCRH shared resourcesBuild SRM ordering and billing functionality for ~10 additional lab-based shared resourcesBuild SRM LIMS for those shared resources needing this infrastructureEstablish links to the Tissue Repository and other databases on campus as required

25. SRM 2.0Metadata-based data modelEnhanced flexibility and configurabilityRapid rollout of new facilities and servicesEasy modification of existing servicesMicrokernel/Plug-in architectureMicrokernel core supporting base functionalityPlug-ins to support facility/service-specific functionalitycaBIG Bronze level compatibility

26. Future Challenges & Plans“Next Generation” Sequencing Data DelugeFirst test run of Hartwell Center’s Illumina platform produced 1.5 billion bases of DNA sequence data1.5 billion bp = three times the amount of DNA sequence data produced by St. Jude in the past 20 YEARSEarly runs producing 40GB of deliverable client data per sample on the high-end3730xl runs producing average of 0.5 MB of deliverable client data per sample

27. SRM 2.0Distributed Data Management GridEliminate data management related network traffic between SRM application servers and