Solutions to Core Facility Problems<br />Matt Stine<br />2008 NERLSCD Meeting<br />
Agenda<br />Introduction to St. Jude and Information Sciences<br />Case Studies<br />Day-to-Day Facility Operations Manage...
Introduction to St. Jude and Information Sciences<br />
Research Landscape<br />16 Academic Departments<br />5 Academic Divisions<br />Cancer Center<br />First and only NCI-desig...
Shared Resources<br />Human Applications Laboratory<br />Information Sciences<br />Laboratory Services<br />MHC Tetramer<b...
The Hartwell Center<br />A unique integration of:<br />High-throughput biotechnology resources (core facilities)<br />Bioi...
Information Sciences<br />Formed in July 2007<br />Integrated the major IT groups on campus<br />Clayton Naeve, Ph.D. – CI...
Landscape Summary<br />Great diversity of shared resources/core facilities<br />IT leadership comes from core management b...
Case Study #1<br />Day-to-Day Facility Operations Management<br />
Day-to-Day Operational Issues<br />Ordering<br />Service Requests<br />Shared Instrumentation Booking<br />Workflow/Proces...
Shared Resource Management (SRM)<br />Web-based application providing a single, integrated portal for management of shared...
Web-based request for services:<br />Client fills order form with PI, grant/cost center, sample information, service reque...
Models the laboratory process as a workflow with multiple ordered modules.<br />Data is collected within each module:<br /...
SRM Data Management/Retrieval<br />Facilities archive the deliverable data associated with each module through its web int...
SRM Billing<br />Facilities bills for the “current cycle” are automatically generated by SRM and sent on demand by the bil...
SRM supports two reporting modes:<br />Prepared (Canned) Reports<br />Sample counts<br />Turnaround time<br />Investigator...
Case Study #2<br />Cancer Center Support Grant (CCSG) Competitive Renewal<br />
Problem Statement<br />Currently 12 shared resources are supported by the CCSG.<br />Every five years the CCSG comes up fo...
The Old Way<br />Usage statistics:<br />TODO<br />Publications<br />Shared resource directors independently contact invest...
SRM<br />SRM maintains an updated list of the<br />
TrakIT #1<br />
TrakIT #2<br />
Future Challenges & Plans<br />
Future Challenges & Plans<br />IS FY09-FY13 Strategic Plan<br />Expand the SRM system to include all laboratory-based SJCR...
SRM 2.0<br />Metadata-based data model<br />Enhanced flexibility and configurability<br />Rapid rollout of new facilities ...
Future Challenges & Plans<br />“Next Generation” Sequencing Data Deluge<br />First test run of Hartwell Center’s Illumina ...
SRM 2.0<br />Distributed Data Management Grid<br />Eliminate data management related network traffic between SRM applicati...
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Information Sciences Solutions to Core Facility Problems at St. Jude Children's Research Hospital

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

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

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