Team Lead - Research Information Services & Computing

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HC Informatics

Update

Douglas MacFadden, CBMI

June 2010

http://catalyst.harvard.edu

1

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.

2

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


3

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)


4

Informatics Foci

5


Cross Institutional


Collaboration


Aggregation


Education

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#

6

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

7

Major HC Informatics Areas

8


Portal


SHRINE


HC CRC
(former PCIR / GCRC)


EDC (Electronic Data Capture)


Community Connect to Research


CHILD


Workshops


Outside Collaborations

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

9



10

11

12

Semantic Search

13

Portal: Profiles

14

15

Portal: Grant Central

16

17

Portal: Education Catalog

Portal: Pilot Funding

18

Portal: Cede Review

19

Portal: Consulting Requests

20

Consulting Workflow

21

Portal: Usability

22


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

23

SHRINE Architecture

24

SHRINE Query Interface


25

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

26

HC CRC Protocol Review

27

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

28

Community Connect to
Research

29

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


30

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

31

REDCap

32

EDC
-

REDCap

33

Informatics Workshops

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


34

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

Lead
: Reddy Gali

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



35

Informatics Team

36

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

37

http://catalyst.harvard.edu