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HC Informatics

HC Informatics. Update. Douglas MacFadden, CBMI. June 2010. HC Mission.

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HC Informatics

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  1. HC Informatics Update Douglas MacFadden, CBMI June 2010 http://catalyst.harvard.edu

  2. HC Mission We believe that the key elements for success in clinical and translational research already exist at Harvard including the intellectual force, technologies, and clinical expertise necessary to reduce the burden of human illness. What is missing is a systematic way for investigators from disparate disciplines and institutions to find each other and form teams, to gain open access to tools and technologies, and to obtain seed funding to embark upon new areas of investigation. This demands a systematic effort to remove the barriers and obstacles to cross-institutional collaboration. A catalyst lowers the barriers to reaction, and thus speeds a reaction that would normally have occurred at a much slower rate. Speeding the reduction of human illness is the only function of the Harvard Catalyst.

  3. Core Team • Lee M. Nadler, M.D. Harvard Catalyst Director, Principal Investigator of the Harvard CTSC, and Dean for Clinical and Translational Research Harvard Medical School • Steven D. Freedman, M.D., Ph.D. Co-Director Harvard Catalyst, co-Director of the Harvard CTSC, and Associate Dean for Clinical and Translational Research Harvard Medical School • Laura Weisel, M.B.A. Executive Director of Harvard Catalyst and Administrative Director of the Harvard CTSC • Lucy Kolessin, M.B.A. Harvard Catalyst Finance Manager • Seanne Hanke, M.B.A Harvard Catalyst Implementation Manager • Sabune Winkler, J.D. Harvard Catalyst Regulatory Affairs Support Manager • Jocelyn Kasper, Ph.D., Harvard Catalyst Research Navigator • Ann Schlesinger, Ph.D., Harvard Catalyst Research Navigator • Zeke Bernstein, Ph.D. Harvard Catalyst Research Navigator

  4. Programs • Biomedical Informatics (I. Kohane, Professor of Pediatrics, CHB • Community Engagement and Research (R. Platt, Professor of Ambulatory Care and Prevention, HMS) • Design and Biostatistics (J. Ware, Professor of Biostatistics, HSPH) • Ethics in Clinical and Translational Research (D. Brock, Professor of Global Health and Social Medicine, HMS) • Faculty Diversity and Development (J. Reede, Associate Professor of Medicine, HMS) • Health Disparities Research (J. Ayanian, Professor of Health Care Policy, HMS and Professor of Medicine, BWH) • Novel Clinical and Translational Methodologies (V. Sukhatme, Professor of Medicine, BIDMC) • Participant and Clinical Interactions Resource (In and Out-Patient Resources) (A. Klibanski, Professor of Medicine, MGH) • Pediatrics (E. Neufeld, Associate Professor of Pediatrics, CHB) • Pilot and Collaborative Translational and Clinical Studies (L. Nadler, Professor of Medicine DFCI) • Regulatory Knowledge and Support (B. Bierer, Professor of Medicine, BWH • Research Education, Training and Career Development (E. Antman, Professor of Medicine, BWH; and D. Golan, Professor of Biological Chemistry and Molecular Pharmacology, HMS) • Translational Technologies and Resources (G. Williams, Professor of Medicine, BWH)

  5. Informatics Foci • Cross Institutional • Collaboration • Aggregation • Education

  6. Technologies • Open Source centric • Linux Apache, MySQL • Tomcat, JSP, JSF • REST Web Services • Ruby on Rails • CMSs: Drupal and custom • Semantic Data: Pubmed, publication full text autocoding, clinical databases (i2b2), MeSH, ICD-9-CM, HITSP C32, RxNorm • Semantic Tools: XML, RDF, Cocoon, XSLT, Semantic Search • SharePoint, SQL Server, C#

  7. Methodologies • Project management • Iterative development • User centered design and usability testing • Open Source provider (open.med.harvard.edu coming soon) • Project model supports adaptive team structures and use of outside resources: • Offshore development teams • Domain/skill specific consultants • UI design firms • Hosting providers

  8. Major HC Informatics Areas • Portal • SHRINE • HC CRC (former PCIR / GCRC) • EDC (Electronic Data Capture) • Community Connect to Research • CHILD • Workshops • Outside Collaborations

  9. Portal • Team Lead: Maria Cervone • Portal Architecture – CMS, APPs, Multi-domain • Semantic Search • Profiles Module (Griffin Weber) • Medvane (Joon Lee) • Grant Central Module • Education Course Catalog Module • Course registrations • Pilot Grant submissions • IRB Ceded Review process • Consulting request submission and ticket management • Usability Study • Future: pathways, dashboard, user customization

  10. Semantic Search

  11. Portal: Profiles

  12. Portal: Grant Central

  13. Portal: Education Catalog

  14. Portal: Pilot Funding

  15. Portal: Cede Review

  16. Portal: Consulting Requests

  17. Consulting Workflow

  18. Portal: Usability

  19. SHRINE • Team Lead: Andrew McMurry, Bill Simons • Hospital leads: Shawn Murphy, Griffin Weber, Charles McGow & John Orechia • Released into Beta (February, 2010) • Demographics, diagnoses, medications and labs • BI, BWH, CHB, MGH now. DFCI in 2010 • Aggregate counts • Future: Limited Data Sets, Improved Search Usability

  20. SHRINE Architecture

  21. SHRINE Query Interface

  22. HC CRC • Team Lead: George de la Torre • Protocol Review 1.0 Released November 2009 • In 24x7 Production • Deployed for MGH, BI, BW, CHB, MIT • Follow-up releases in December, February • 1.x releases planned through Summer 2010 • Scheduling project in planning phase • Future: Scheduling system 1.0 release in Y3

  23. HC CRC Protocol Review

  24. Community Connect to Research • Lead: Alexa McCray • Greg Polumbo (technology) • Released and live • Repurposes and integrates content from Harvard Health Publications and clinicaltrials.gov • Uses MeSH as the organizational model • Targets a user community with broad levels of understanding about health care and research • Ruby on Rails

  25. Community Connect to Research

  26. CHILD • Team Lead: Ken Mandl • Focus on transition from pediatric to adult care • Open source software for personal health information sharing • Study: Patient Safety and Quality during transition • Pilot: Inflammatory Bowel Disease

  27. Electronic Data Capture • Champion: Diane Keogh • Support for small labs and young investigators • REDCap • Local resources for training and support • Lynn Simpson • Christian Botte • Future: workshops, brown bag lunches, training sessions and online resources

  28. REDCap

  29. EDC - REDCap

  30. Informatics Workshops Lead: Reddy Gali Institutional Affiliation of Students • BIDMC • BWH • CBMI • CCIB • CH • CTSC • DFCI • FAS • ERI • HRC • HMS • HRCA • HSDM • HSPH • MIT • IDI • JOSLIN • MCCLEAN • MEEI • MGH • OEB • PARTNERS • OTHERS Over 80 Workshops offered (most frequent first) • BLAST Tips and Tricks • Bioinformatics Consultings • ABCD Bioinformatics Sequencing analysis • MetaCore: Getting the most from your "omics" analysis • Introduction and analysis of MicroRNAs • NCBI MapViewer and Related Resources • Perl and BioPerl for Biologists • Introduction to Microarrays and Affymetrix Data analysis using R/Bioconductor • BIOBASE ExPlain Analysis System for microarray and proteomic data • Ensemble Workshop • Expression analysis using GenePattern • Microarray Data Analysis using Rosetta Resolver • Ensembl Fundamentals • Ensembl Genome Browser Workshop • Biomedical Imaging Analysis • Microarray Training at FAS Science Center • Bioinformatics Boot Camp - Credit offering • Microarray Data Analysis of Illumina Data Using R/Bioconductor • Metacore Pathway Analysis • Ingenuity Pathways Analysis 6.0 Training Workshop • LAMP for Biologists • EBI Proteomics Databases • Introduction and Fundamentals to R and Bioconductor • Making the Most of the UCSC Genome Browser • Bioinformatics - Credit offering • Browsing Genes and Genomes with Ensembl • Introduction and Fundamentals of Matlab • Making the Most of the UCSC Genome Browser • BIOBASE Biological Knowledge Library for microarray and proteomic data • Illumina Microarray Data Analysis Using R/Bioconductor • MapViewer and other NCBI tools • Genetics - Credit offering • Introduction to Ingenuity Pathway Analysis • Ingenuity Pathway Analysis Workshop • NCBI MapViewer and Related Resources • Blast • Two Color [cDNA] Microarray Data Analysis Using R/Bioconductor

  31. Collaborations and Related • CTSA Working Groups: • Integrated Data Repository • Data Sharing • Research Networking • Bibliographic • … • SHRINE: code sharing (U Washington, UCSF, …) • Profiles: code sharing (UCSF, 40 others) • Portal: code sharing • Collaborative for Community Engagement & Research (Tufts, BU, Harvard) • Eagle-I • Innocentive Crowd Sourcing • Randy Gollub & Shawn Murphy imaging i2b2 project

  32. Informatics Team Core team: Alex Romero Alexa T. McCray Bill Simons Charles McGow Chetan Patel Doug MacFadden Genoa Wall George de la Torre Joe Rezuke Ken Huling Kerry Foley Konstantin Merson Maria Cervone Marlon Violette Matt Sullivan Nich Wattanasin Nicholas Benik Paul Gomez Philip Trevvett Priti Patil Reddy Gali Shaun Kelly Smitha Madhavamurthy Zak Kohane - Program Director Major support staff: Andy McMurry Ann Schlesinger Britt Fitch David Hardwick Greg Polumbo Griffin Weber Halip Saifi Joanna Brownstein Jocelyn Kasper John Orechia Joon Lee Melissa Kenny Rob Frost Seanne Falconer Ted Bashor Tom Ulrich Wei Zhong Zeke Bernstein-Hanley Past Members: Abhinav Singh David Hummel Evan Pankey Hernando Barake Jonathan Abbett Josh Boughey Matt Johnson Matvey Palchuk Nicole Zanetti Patrick Sullivan Ricardo De Lima Steven Boscarine Steven Cheung Tom Monaghan Vineet Manohar Will Crawford OIC Committee: Alessandro Doria Alexa T. McCray Dan Nigrin Diane Keogh Doug MacFadden Frank Kuo Griffin Weber Henry Chueh Jeff Brown Joe Ronda John Halamka John Quackenbush Jomol Mathew Ken Mandl Laura Weisel Shawn Murphy Susanne Churchill Zak Kohane - Program Director

  33. http://catalyst.harvard.edu

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