SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN Biomedical Informatics Research Network.

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Presentation transcript:

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN Biomedical Informatics Research Network

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN Four Collaboratories BIRN Coordination Center –Distributed Research Center Mouse BIRN –Distributed Research Center –Community Data System Morphometry BIRN –Distributed Research Center –Community Data System Function BIRN –Distributed Research Center –Community Data System

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN BIRN Collaboratory Basics Federated databases –Neuroimaging data Integration of diverse data –Location –Scale, level of aggregation Tools for analysis –Visualization, statistical support Serving as a testbed for the idea of a biomedical knowledge infrastructure

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN Synchrotrons Molecules MacromolecularComplexes, Organelles, Cells Organs, Organ Systems, Organisms Microscopes Magnetic Resonance Imagers

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN BIRN Sites

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN BIRN Sites

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN BIRN Sites

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN BIRN Sites

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN Research Centers Mouse BIRN (44) UCSD Duke UCLA Cal Tech Morphometry (69) UCSD Duke UCLA BWH MGH Johns Hopkins Funtion BIRN (106) UCSD Duke UCLA BWH MGH UC-Irvine Stanford Minnesota Iowa New Mexico UNC BIRN-CC (34) UCSD Internet2 (3) Ohio State (2) National Cancer Institute

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN Mouse BIRN Animal Models of Disease /Multi Scale/Multi Method – –A model animal because of the corresponding disease symptoms ot pathology between its brain and the human brain Parkinson, Alzheimer, etc. Looking at different resolutions by combining data from multiple modalities Cal Tech, Duke, UCLA, UC San Diego

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN Mouse BIRN

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN Morphometry BIRN Human Brains Neuroanatomical correlates of neuropsychiatric illness –Unipolar Depression, –Alzheimer's disease, –Mild Cognitive Impairment Harvard (BWH and MGH), Duke, UCLA, UC San Diego, Johns Hopkins

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN Morphometry BIRN

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN Function BIRN Characterizing the collection and integration of fMRI data from multiple sites Study schizophrenia through fMRI images collected from patients around the country using standardized protocols Harvard (MGH and BWH), Duke, Iowa, Minnesota, New Mexico, North Carolina, Stanford, UCLA, UC San Diego, UC Irvine

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN Example Query of Federated Database fMRI Are chronic, but not first-onset patients, associated with superior temporal gyrus dysfunction (MMN)? Integrated View Receptor Density ERP Web PubMed, Expasy Wrapper Structure Wrapper Clinical Wrapper Mediator

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN BIRN Coordinating Center UC San Diego High-level project management Technical development center Expert-level technical support Center for training and experience exchange Best practices aggregator Oversight bodies’ point of contact

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN BIRN Funding The BIRN grants consist of four groups of awards totaling approximately $30,000,000. From NIH

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN Technology Gigabit/10/100 Network Switch – Cisco4006 Network Statistics System Gigabit Ethernet Network Probe Network Attached Storage – Gigabit Ether 1.0 to 8.0 TB Grid POP SRB, Globus Dual Processor Linux w/ 1GB memory DL 380 General purpose Specialized encryption UPS for Rack

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN Experiment Databases Data archive Domain knowledge User application BIRN System Metadata catalog Tell me about data relationships Tell me about the data Give me the data Experiment Databases Mediator

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN Experiment Databases SRB ServerDomain Knowledge Experiment Databases User Application BIRN System SRB Server MCAT Server Mediator

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN Experiment Databases SRB Server MCAT Server Mediator Domain Knowledge Client Application Query about “cerebellum” Experiment Databases

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN Experiment Databases SRB Server MCAT Server Mediator Domain Knowledge Client Application Translate into domain queries about “dentate” and “Purkinje cell” Experiment Databases

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN Experiment Database Domain Knowledge SRB Server MCAT Server MediatorClient Application Return metadata and data set handles Experiment Databases

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN Experiment Databases Domain Knowledge SRB Server MCAT Server MediatorClient Application Return metadata and data set handles Experiment Databases

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN Experiment Database SRB Server MCAT Server MediatorClient Application Query data set attributes Domain Knowledge Experiment Databases

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN Experiment Database SRB Server MCAT Server MediatorClient Application Return data set attributes Domain Knowledge Experiment Databases

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN Experiment Databases SRB Server MCAT Server MediatorClient Application Ask for data set Domain Knowledge SRB ServerExperiment Databases

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN Experiment Databases SRB Server MCAT Server MediatorClient Application Forward data set request to proper SRB server Domain Knowledge Experiment Databases

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN Experiment Databases SRB Server MCAT Server MediatorClient Application Return data set Domain Knowledge Experiment Databases

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN Experiment Databases SRB Server MCAT Server MediatorClient Application Return data set Domain Knowledge Experiment Databases

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN Access

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN Resource Diagram

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN Resource Diagram

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN Resource Diagram Function BIRN

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN Resource Diagram

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN Issues from Diagram BIRN money flows to each participating institution –Each site pays for rack and is responsible for on- site administration –Local site responsible for Backups Fix hardware Create DNS registration entries Interface with BIRN CC Provide local support

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN Files loaded

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN Number of Accounts

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN Usage

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN Usage

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN Issues across Collaboratories Technical readiness Infrastructure readiness Collaboration readiness Common ground Coupling of tasks Incentives to do something new

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN Technical and Infrastructure Readiness Participating sites are technically sophisticated BIRN in a box –Standard hardware/software –Configured at BIRN-CC

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN Collaboration Readiness Unknown How many people have collaborated already Early collaboration on –Instrument calibration –Software development –IRB issues –Governance

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN Common Ground Mouse and Morphometry BIRNs –Issue of researchers at different scales collaborating –Common terminology Atlas Metadata Mediator Function BIRN –Leveraging work done by Morphometry BIRN –Agreeing up front on common protocols

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN Coupling of Tasks Will there be collaboration beyond sharing of data? –Interpretation is an ambiguous task –Will there be video conferencing around interpretation?

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN Incentives Ostensibly, researchers who share get a bigger sample size Researchers can see things at various scales Better science But…. –Ownership of data Private, collaboration, BIRN Consortium, Public –Not being scooped

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN Early Successes Faster ramp up with experience

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN Points of Interest Provide a working set of BIRN technologies –BIRN in a box Many issues need to be resolved early –Declare a topic, expect participation from each institution, it happens E.g., IRB, protocols, calibration Lessons learned from one BIRN propagated to others.

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN Points of Interest Governance Manual 0.6 Organization, policies, methods –Responsibilities of local and CC –Common issues of protection of data HIPPA, etc. –Who gets an account Responsibilities –Communication through web site, newsletters, meeting –Copyright –IRB –Publication –Authorship

SCHOOL OF INFORMATION UNIVERSITY OF MICHIGAN BIRN Testbeds in brain imaging, discovery of correlates of diseases Also a model for –Cell biology –Comprehensive clinical research network