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Topics in BMI: Course Objectives
CSE
300
Prof. Steven A. Demurjian, Sr.
Computer Science & Engineering Department
The University of Connecticut
371 Fairfield Road, Box U-255
Storrs, CT 06269-2155
[email protected]
http://www.engr.uconn.edu/~steve
(860) 486 - 4818
IntroOH-1
What is Informatics?

CSE
300


Informatics is:
 Management and Processing of Data
 From Multiple Sources/Contexts
 Involves Classification (Ontologies), Collection,
Storage, Analysis, Dissemination
Informatics is Multi-Disciplinary
 Computing (Model, Store, Process Information)
 Social Science (User Interactions, HCI)
 Statistics (Analysis)
Informatics Can Apply to Multiple Domains:
 Business, Biology, Fine Arts, Humanities
 Pharmacology, Nursing, Medicine, etc.
IntroOH-2
What is Informatics?

CSE
300
Heterogeneous Field –
Interaction between
People, Information and
Technology
 Computer Science
and Engineering
 Social Science
(Human Computer
Interface)
 Information Science
(Data Storage,
Retrieval and
Mining)
Informatics
People
Information
Technology
Adapted from Shortcliff textbook
IntroOH-3
What is Biomedical Informatics (BMI)?

CSE
300
BMI is Information and its Usage Associated with the
Research and Practice of Medicine Including:
 Clinical Informatics for Patient Care
 Medical Record + Personal Health Record

Bioinformatics for Research/Biology to Bedside
 From Genomics To Proteomics

Public Health Informatics (State and Federal)
 Tracking Trends in Public Sector

Clinical Research Informatics
 Deidentified Repositories and Databases
 Facilitate Epidemiological Research and Ongong
Clinical Studies (Drug Trails, Data Analysis, etc.)
IntroOH-4
What are Key BMI Focal Areas?

CSE
300




T1 Research
 Transition Bench Results into  Clinical Research
Clinical Research
 Applying Clinical Research Results via Trials with
Patients on Medication, Devices, Treatment Plans
T2 Research
 Translating “Successful” Clinical Trials into
Practice and the Community
Clinical Practice
 Tracking all of the Information Associated with a
Patient and his/her Care
Integrated and Inter-Disciplinary Information
Spectrum
IntroOH-5
Where/How is BMI Utilized?
CSE
300
T1 Research (Bench  Clinical)
 Transfer of Knowledge from Laboratory or Bench to
Clinical Trials
 Move Genomic Research from Bench (Lab) to
Clinical Trial (or Genetic/Test Intervention)
 Transfer in Lab/Bench Research to Pre-Clinical and
Early Clinical Human Subject Research
 Exs:
 New Genetic Test for Autism
 Tested on Samples from DNA Repository
 Transition to Actual Patient Population

Growing new Jaw Bone in Mice for Dental
Implants – Transition to Human Tissue
IntroOH-6
Where/How is BMI Utilized?
CSE
300
Clinical Research (Trials)
 Wide Range of Implications from Medical Treatment
to Medication Regime
 Multi-Phased Process for Clinical Trials:
 Phase I: First Stage – 20-80 Healthy Patients
 Phase II: Second Stage – 20-300 Patients
 IIA – Dosing – How Much of Drug Should be Used
 IIB – Efficacy – How Well Does Drug Work
 Randomized Clinical Trials (Not all Get Drug)

Phase III: Multi-Center Trials – 300-3000
 Longer Term, Data Collected, Multiple Locations
 Preparation of Data for Regulatory Approval (FDA)

Phase IV: Ongoing Monitoring of Drug After
Approval
IntroOH-7
Where/How is BMI Utilized?
CSE
300
Clinical Research (Trials)
 Differing Perspectives for Carrying out Research:
 Patients: Drug, Treatment Regime, or Device
 Increased Dose of Existing Drug (Safety/Effective)
 Applying Drug to New Disease
 Compare Two or more Treatments

Epidemiological






Study Existing Data for Trend
Against Existing Data Repositories
Patients with CHF and Diabetes Taking Statins
Tracking Communicable Disease/Outbreaks
Phases I, II, III, and IV Apply
Bad Results in IV – Pull Drug (Vioxx)
IntroOH-8
Where/How is BMI Utilized?
CSE
300
T2 Research (Clinical Research Practice/Community)
 Practice-Oriented Translation Research
 Results: Clinical Trails  Clinical Practice
 Strategies for Establishing/Implementing New
Technologies
 Improvements in Practice
 New Evidence-Based Guidelines
 New Care Models
 Phase III Success Translated to Health Providers
 Examples
 Statin Drugs (Lipitor) and Exercise
 New Treatment Regime for Chronic Disease
IntroOH-9
Where/How is BMI Utilized?
CSE
300
Clinical Practice
 Dealing with Patients – Direct Medical Care
 Hospital or Clinic
 Physician’s Office
 Testing Facility
 Insurance/Reimbursement
 Tracking All Data Associated with Patients
 Medical Record
 Medical Tests (Lab, Diagnostic, Scans, etc.)
 Prescriptions
 Stringent Data Protection (HIPAA)
 Distributed Repositories, Inability to Access Data in
Emergent Situations, Competition, etc.
IntroOH-10
What is Medical Informatics?

CSE
300




Clinical Informatics, Pharmacy Informatics
Public Health Informatics
Consumer Health Informatics
Nursing Informatics
Systems and People Issues
 Intended to Improve Clinical outcomes,
Satisfaction and Efficiency
 Workflow Changes, Business Implications,
Implementation, etc…
 Patient Centered – Personal Health Record and
Medical Home
 Care Centered – Pay for Performance, Improving
Treatment Compliance
IntroOH-11
What is Bionformatics?

CSE
300


Focused on Research Tools for T1:
 Genomic and Proteomic Tools, Evaluation
Methods, Computing And Database Needs
 Information Retrieval and Manipulation of Large
Distributed (caBIG) Data Sets
(cabig.cancer.gov/index.asp)
 Often Requires Grid Computing
 Includes Cancer and Immunology Research
Increasing Need to Tie These Separate Types of
Systems Together = Personalized Medicine
Biology and the Bedside (www.i2b2.org)
IntroOH-12
Where is Data/How is it Used?

CSE
300


Medical And Administrative Data Found in Clinical
Information Systems (CIS) Such As:
 Hospital Info. Systems Electronic Medical Records
 Personal Health Records such as Google Health
and Microsoft Healthvault
 Pharmacy, Nursing, Picture Archiving Systems
 Complex Data Storage and Retrieval – Many
Different Systems
T1 Research Increasingly Reliant on CIS
T2 Research is Reliant on:
 End Systems for Embedding EBM (EvidenceBased Medicine) Guidelines
 Measuring Outcomes, Looking at Policy
IntroOH-13
What are Major Informatics Challenges?

CSE
300




Shortage of Trained People Nationally
Slows adoption of Health Information Technology
Results in Poor Planning and Coordination,
Duplication of Efforts and Incomplete Evaluation
What are Critical Needs?
 Dually Trained Clinicians or Researchers in
Leadership of some Initiatives
 Connect all folks with Informatics Roles across
Institutions to Improve Efficiency
 Multi-Disciplinary: CSE, Statistics, Biology,
Medicine, Nursing, Pharmacy, etc.
Emerging Standards for Information Modeling and
Exchange (www.hl7.org) based on XML
IntroOH-14
What is UConn Doing in this Area?

CSE
300

NIH’s CTSA Program: Transform the Way Clinical
and Translational Science Research is Conducted
 From Bench to Clinical Research to Translational
Research to the Bedside and Back Again
 45+ Academic Medical Centers Awarded to Date
see: http://www.ctsaweb.org/
Under President Mike Hogan’s Leadership
 UConn Submitted a CTSA Proposal in Oct 2008
 Formed CICaTS: Connecticut Institute for Clinical
and Translational Science (Sept. 29th 09)
 University Initiative with Partners
 John Dempsey, St. Francis, Hartford Hospital, CCMC,
Hospital for Central CT, Institute for Living, etc.

http://cicats.uconn.edu/
IntroOH-15
CICATS

CSE
300


Official Launching:
 Tuesday September 29, 10:30am-1:30pm
 UConn Global Business Learning Center, Hartford
 Speakers Include: Pres. M. Hogan, Provost P.
Nichols, and Dean Cato Laurencin (Med School)
Mission:
 to educate and nurture new scientists
 to increase clinical and translational
research being conducted at UCHC, regional
hospitals, UConn Storrs, and healthcare
organizations throughout greater Hartford
 to work collaboratively with regional stakeholders
to combat the leading causes of morbidity,
mortality, disability, and health disparities
CICATS will have Biomedical Informatics Center
IntroOH-16
Biomedical Informatics in CICATS
CSE
300
IntroOH-17
Summary of Web Sites of Note:

CSE
300

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
AMIA (www.amia.org)
IHE (http://www.ihe.net/)
Smartplatform (http://www.smartplatforms.org/)
Mysis MOSS (http://www.misys.com/OpenSource)
NSF Clinical and Translational Science Program
 http://www.ctsaweb.org/
Emerging Patient Data Standard
 http://www.hl7.org/
Informatics for Integrating Biology & the Bedside.
 https://www.i2b2.org/
Cancer Biomedical Informatics Grid
 http://cabig.cancer.gov/index.asp
IntroOH-18
Semester Topics (weeks)

CSE
300
Four Core Topics:
 Semester and Course Overview (0.5)
 Informatics/Information Engineering (1.5)
 Software Architectures (2)
 Security and Dynamic Coalition Problem (2)
 Service Based Computing (2)
 CORBA, JINI, .NET, Interoperability, Web
 Security



Discussion of Semester Project (0.5)
Presentations by Outside Speakers (2.5)
Student Presentations on Biomedical Informatics
Materials (3)
IntroOH-19
Planned Speakers

CSE
300



Dr. L. Fagan, Co-Director, Stanford Biomedical
Informatics Training Program, March 31
Dr. M. Smith, Pharmacy Practice, UConn, April 5
Dr. T. Shortliffe, President, AMIA, April 28
Others to be Scheduled:
 Dr. Thomas Agresta
 Dr. Michael Blechner
 Dr. Xiaoyan Wang
IntroOH-20
Class Materials, Textbook, Projects, etc.

CSE
300

Course Web Site:
http://www.engr.uconn.edu/~steve/Cse300/cse300.html
 Reading List
 Constant Updates and Changes
Textbook
Biomedical Informatics: Computer Applications in
Health Care and Biomedicine (Health Informatics),
Edward H. Shortliffe (Editor), James J. Cimino
(Editor), ISBN-10: 0387289860
Project 1 – Due in 2 weeks
Project 2 – Out in 2 weeks
Team Project – Out in 2 weeks as well
Questions? Comments? Suggestions?





IntroOH-21
Course Projects and Exam (???) …

CSE
300
Individual/Team Course Project(s) Throughout the
Semester
 Individual Projects have two Goals
 Increase Student Knowledge on BMI
 Assist in Creating Courseware

Project will be the Entire Class
 Explore and Learn about BMI Technologies
 Span Subset of: T1 Research - Clinical Research - T2
Research - Clinical Practice
 Explore Open Source and Other Solutions
 Develop Extensible Plug and Play Framework

Exam – At MOST Final Exam (Still open to debate!)
IntroOH-22
Individual Semester Projects

CSE
300


Readings, Readings, and More Readings
Project 1: Annotated Bibliography
 Accumulate Web/Hard Links on T1 Research Clinical Research - T2 Research - Clinical Practice
 Read 7 Papers on Clinical & Translational Science
Project 2: Courseware Materials
 Choose two Different Areas for Indepth
Examination
 Topics include (but not Limited to):





HIE I2b2
Standards (HL7, Common Data Architecture CDA)
caBIG
BIRN (Biomedical Informatics Research Network)
Another NIH Computing Initiative
IntroOH-23
Semester Project

CSE
300
Still Evolving – Possible Projects Include:
 Usage of SmartPlatform
 Utilization of Personal Health Records (PHR) Such
as Google Health and/or MS Healthvault in New or
Extended Context
 Interoperability with EMR
 Google Health Hibernate API Available

XML (HL7/CDA) to i2b2 DB Translation
 Supervised by M. Blechner (UCHC BMI Faculty)

Extending Cell Phone Applications (iphone,
blackberry, and android) for
 Maintaining Prescriptions
 Observations of Daily Living
 Prior Work by Undergraduate Teams (with Source)
IntroOH-24
Semester Project Objectives

CSE
300




Objective – Wide Scale Open Source Framework
Envision Plug and Play Architecture
High Reliance on Open Source Solutions for PHR and
EMR
Support Interoperability to Components via XML and
Standards
Develop Complete, Integrated, and Extensible
Framework
IntroOH-25
SmartPlatform

CSE
300



Substitutable Medical Apps, reusable technology
 (http://www.smartplatforms.org/)
NSF/NIH Funded SHARP Proposal at Harvard
Intended to:
“A platform with substitutable apps constructed
around core services is a promising approach to
driving down healthcare costs, supporting standards
evolution, accommodating differences in care
workflow, fostering competition in the market, and
accelerating innovation”
Likely Led by Timo Ziminski
IntroOH-26
Personal Health Records

CSE
300

Google Health
 Detailed Hibernate API to Allow Programmatic
Transfer of Information to/From Google Health
 Utilized in Web-Based Application
 Utilized by Cell Phone Projects (see later slides)
 Existing Platform Available for Future Design,
Development, and Usage
Explore EMR/PHR Interoperability
IntroOH-27
TMR Architecture
CSE
300
IntroOH-28
CSE
300
IntroOH-29
XML (HL7/CDA) to i2b2 DB Translation

CSE
300


Work with Dr. Michael Blechner (UCHC BMI Faculty
Member)
Explore a Prototype that can take:
 HL7/CDA Data (Simulated from an EMR)
 Store in a i2b2 Compatible Database
Utilization of Standards, New Technologies, etc.
IntroOH-30
Cell Phone Applications

CSE
300

RWJ Project Health Design
Observations of Daily Living and PHRs
 Passive – Once Initiated, Collects Data
 Accelerometer
 Pedometer
 Pill Bottle that Sends a Time Stamp Message (over
Bluetooth?) to SmartPhone

Active – Patient Initiated
 Providing Information via Smartphone on:
–
–
–
–

Diabetes (Glucose, Weight, Insulin)
Asthma (Peak Flow, use of Inhaler)
Heart Disease (Pulse, BP, Diet)
Pain, Functional status, Fatigue, etc.
http://www.engr.uconn.edu/~steve/Cse4904/cse4904.html
IntroOH-31
Focus of Grant

CSE
300

Management of Two Diseases in Women of Color
 Obesity and Osteoarthritis
Team
 TRIPP (Crowell, Fifield) and AHFP (Agresta)
 SisterTalk (Headley) and CHCAT (Granger)
 UConn Storrs (Demurjian) and Netsoft (Collins)
Providers
Web/Application
Server
SQL Server
Database
Microsoft
HealthVault
Patient Demographics
and ODLs
Patients
Researchers
Client Side Technologies
https, html, Ajax, XML
Server Side Technologies
Java, JSP, Hibernate,
Relational Database, XML
Lifelines
Repository
Figure 1: Architecture Diagram of the Proposed System.
IntroOH-32
CSE4904 – Spring 2010

CSE
300


Smartphone Projects on ODLs and Other Medical
Data Tracking and Alerts
Three Platforms:
 Google’s Android (Java)
 Blackberry (Java)
 iPhone (Objective C)
Three Teams of Three Students Each
IntroOH-33
Blackberry Team

CSE
300

Ability to Track Information on ODLs and
Prescriptions
 Login Screen
 Connection to Google Health
 Health Screen to Track ODLs
 Charting of ODLs over Time
 Loading Scripts from Google Health
 Prescription Alarms
Adam Siena, Kristopher Collins, William Fidrych
IntroOH-34
Screen Shots
CSE
300
IntroOH-35
Screen Shots
CSE
300
IntroOH-36
Screen Shots
CSE
300
IntroOH-37
Screen Shots
CSE
300
IntroOH-38
Screen Shots
CSE
300
IntroOH-39
Android Team

CSE
300
Similar Capabilities to Blackberry Project
 Wellness Diary and Medication Alarm
 Integration with Google Health
 Much Improved ODL Screens
 Male and Female Faces
 Change “Face” Based on Value
Tracking Prescriptions and Alarms
 Reports via. Google Charts
Ishmael Smyrnow, Kevin Morillo, James Redway


IntroOH-40
Screen Shots
CSE
300
IntroOH-41
Screen Shots
CSE
300
IntroOH-42
Screen Shots
CSE
300
IntroOH-43
Screen Shots
CSE
300
IntroOH-44
iPhone Team

CSE
300
Similar Capabilities to Blackberry Project
 Tracking of Conditions, Medications, and Allergies
 ODLs for:
 Blood-Glucose, Peak-Flow, and Hypertension
Generation of Reports
 Synchronization with Google Health
Brendan Heckman, Ryan McGivern, Matthew Fusaro


IntroOH-45
Screen Shots
CSE
300
IntroOH-46
Screen Shots
CSE
300
IntroOH-47
Screen Shots
CSE
300
IntroOH-48
Screen Shots
CSE
300
IntroOH-49
Questions?
CSE
300
IntroOH-50