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Solutions to Core Facility Problems Matt Stine 2008 NERLSCD Meeting
Agenda Introduction to St. Jude and Information Sciences Case Studies Day-to-Day Facility Operations Management CCSG Competitive Renewal Future Challenges & Plans
Introduction to St. Jude and Information Sciences
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
Shared Resources Human Applications Laboratory Information Sciences Laboratory Services MHC Tetramer Molecular Clinical Trials Core Mouse Immunophenotyping/Cytokine Assay Office of Technology Licensing Pharmacokinetcs 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 Biostatistics Cell & Tissue Imaging Central Trial and Data Monitoring Office Clinical Protocol Scientific Review & Monitoring Clinical Research Education Program Cytogenetics Environmental Health & Safety Flow Cytometry & Cell Sorting Grant and Contract Management Office Hartwell Center for Bioinformatics and Biotechnology Clinical Applications Core Technology (Affymetrix) Bioinformatics DNA Sequencing Genome Sequencing Functional Genomics Genotyping Macromolecular Synthesis Molecular Interaction Analysis Proteomics
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
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)
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
Case Study #1 Day-to-Day Facility Operations Management
Day-to-Day Operational Issues Ordering Service Requests Shared Instrumentation Booking Workflow/Process Management (LIMS) Data Management/Retrieval Billing Reporting Usage Statistics Turnaround Time Service Request History
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.
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
Models the laboratory process as a workflow with multiple ordered modules. Data is collected within each module: QC Information Results Observations Facilities can design multiple “workflow templates.” Individual sample workflows can be edited “on-the-fly.” SRM LIMS
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.
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.
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
Case Study #2 Cancer Center Support Grant (CCSG) Competitive Renewal
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
The Old Way Usage statistics: TODO Publications 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.
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
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
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
SRM 2.0 Distributed Data Management Grid Eliminate data management related network traffic between SRM application servers and