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- pen source, open data, &
- pen source & open data
open source, open data, & personalized medicine Benaroya - - PowerPoint PPT Presentation
open source, open data, & personalized medicine Benaroya - - PowerPoint PPT Presentation
open source, open data, & personalized medicine Benaroya Research Institute open source & open data Agenda a little about the Benaroya Research Institute what is personalized medicine? the project data collection analysis
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Agenda
a little about the Benaroya Research Institute what is personalized medicine? the project data collection analysis dissemination making our work (and tools) public
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Benaroya Research Institute
Benaroya Research Institute at Virginia Mason is located in Seattle 220 scientists and staff primarily focused on finding the causes and cures for autoimmune diseases 5 Core Laboratories 15 Laboratories 100 clinical trials enrolling patients at any time
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Benaroya Research Institute
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Systems Immunology
GENOMICS CORE BIOINFORMATICS BIOSTATISTICS SOFTWARE DEV.
SYSTEMS IMMUNOLOGY
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Personalized Medicine
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starting with just
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healthy
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not so healthy...
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technology platforms
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processing the results
CHAUSSABEL ET AL. IMMUNITY 2008
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query the reference DB
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disease progression
CHAUSSABEL ET AL. IMMUNITY 2008
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understanding disease
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category B pathogens
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clinical data & sample collection
logistics storing samples shipping samples access to computers language (i18n) naming conventions
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case report forms
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HTTPS://WWW.OPENCLINICA.COM/
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HTTP://WWW.PROJECT-REDCAP.ORG/
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adding in experimental data
genomics microarray NanoString rna-Seq flow cytometry luminex RT PCR ELISPOT etc
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adding in experimental data
custom systems LabKey
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HTTPS://WWW.LABKEY.ORG/
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Browsing the data together
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Browsing the data together
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more data (cross project)
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getting more data
collaborators (sharing between friends) NCBI GEO Array Express IMMPORT Supplemental Materials & Email
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- pen data
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OPEN != ACCESSIBLE
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OPEN != USEABLE
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CURATION SCIENTIST
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finding & open data
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where are we?
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making it available
Access through different science portals Immune Tolerance Network Cooperative Center for Human Immunology Systems Immunology at Benaroya Research Publications Interactive Figures Downloadable supplemental results
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making the data accessible
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publications
Modules (Chaussabel et al, Immunity 2008, http:// www.ncbi.nlm.nih.gov/pmc/articles/ PMC2727981/?tool=pubmed) Data Management (Chaussabel et al, Nature Immunology 2009, http://www.ncbi.nlm.nih.gov/ pmc/articles/PMC2788787/?tool=pubmed) Signature in Tuberculosis (Berry et al., Nature, 2010)
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publications pending
Modules Gene Expression Browser Knowledge Management
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Acknowledgements & Thanks
Immune Tolerance Network (http:// immunetolerance.org/) Atul Butte Lab, Stanford University (http:// buttelab.stanford.edu/) Cooperative Center for Human Immunology (http://www.humanimmunology.org/)
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thank you to the developers
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For more information...
cquinn@benaroyaresearch.org