An Overview of
Biomedical Informatics and Computing
Prof. Steven A. Demurjian, Sr.
Computer Science & Engineering Department
The University of Connecticut
371 Fairfield Road, Box U-255
Storrs, CT 06269-2155
steve@engr.uconn.edu
http://www.engr.uconn.edu/~steve
(860) 486 - 4818
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What is Informatics?
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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.
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What is Informatics?
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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
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What is Biomedical Informatics (BMI)?
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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
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Bioinformatics for Research/Biology to Bedside
 From Genomics to Proteomics
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Public Health Informatics (State and Federal)
 Tracking Trends in Public Sector
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Clinical Research Informatics
 Deidentified Repositories and Databases
 Facilitate Epidemiological Research and Ongong
Clinical Studies (Drug Trails, Data Analysis, etc.)
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Clinical Informatics, Pharmacy Informatics,
Consumer Health Informatics, Nursing Informatics
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What is Biomedical Informatics (BMI)?
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A Exciting Emerging Discipline
Biomedical Informatics/Health Information
Technology Rapidly Emerging Discipline
Cutting Edge, Incredible Career and Research
Opportunities
Wide Range of Data
 Clinical Data on Patients
 Diagnostic Data (Scans, Labs, EKG, etc.)
 Population Data (Public Health Surveillance)
 Research on Genomic and Biological Data
Any Data Involved in
 Care of Patients
 Medical and Clinical Research
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Why is BMI/Clinical Practice Important?
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Tracking all Information for Patient and his/her Care
 Medical Record, Medical Tests (Lab, Diagnostic,
Scans, etc.), Prescriptions
Dealing with Patients – Direct Medical Care
 Hospital or Clinic, Physician’s Office
 Testing Facility, Insurance/Reimbursement
Bringing Together Information for Different Sources
 Health Information Exchange
 Gather Data from MD Offices, Clinics, Hospitals
Informatics Support via:
 Personal Health Records
 Electronic Medical Record
 Linking/Accessing Data Repositories
 Collaborative and Secure (HIPPA) Web Portals
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© T. Shortliffe 2006 Columbia University
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© T. Shortliffe 2006 Columbia University
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© T. Shortliffe 2006 Columbia University
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BMI and Computer Science & Engineering
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Significant Impact Across CS&E Fields Including:
 Security and Data Protection/Privacy
 Sensor Networks to Monitor Elderly
 Artificial Intelligence &Clinical Decision Support
 Software Architectures for Integrating Health
Information
 Bioinformatics (BI) to Process Biological Data
 Supercomputing for Genomic and Clinical Data
Analysis
 Visualization to Conceptualize BMI/BI Data
 Algorithms for BMI/Clinical Data Analysis
 Mobile Computing to Impact Patient Health and
Data Availability
 Etc…
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What is BMI Used to Support?
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.
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What is Medical Informatics?
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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
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What is Bionformatics?
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Focused on Research :
 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)
Significant Expertise in BI in CS&E, MCB, Statistics,
and UCHC
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Where is Data/How is it Used?
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Medical and Administrative Data Found in Clinical
Information Systems (CIS) Such As:
 Personal Health Records - Microsoft Healthvault
 Electronic Medical Records – OpenEMR
 Patient Portals
 E Prescribing (electronic Rx)
 Hospital Info. Systems
 Laboratory, Imaging and Other Systems
 Pharmacy, Nursing, Picture Archiving Systems
 Complex Data Storage and Retrieval – Many
Different Systems
Research Increasingly Reliant on CIS
Jump to PDF Presentation with Screenshots
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What are Major Informatics Challenges?
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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?
 CS/CSE/CompE with Health/Medical Domain
Knowledge
 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
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Summary of Web Sites of Note:
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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
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BMI in Computing: Interoperability
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Need to Integrate Across Health Care Enterprise
 Practice management systems (PMS) for
management of non-medical patient information
 Electronic medical records (EMR)
 Decision Support Systems (both within and
external to EMRs)
 Medical laboratory information systems (MLIS)
 Personal health records (PHR)
 Electronic Prescribing
 Patient Portal (Tests, Appointments, Refills)
 Billing Systems
Employ Computing w.r.t. Standards, Interoperability,
Software Architectures, Security, Privacy, Decision
Support, etc.
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Stakeholders for HIE and Virtual Chart
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Who are the Major Stakeholders?
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Patients that require short-term treatments, long-term
treatments, emergency help, inpatient care, ambulatory
care, home care, etc.
Providers that administer care (MDs, medical
specialists, ER MDs, nurses, hospitals, long term care
facilities, home health care, nurse practitioners, etc.)
Public health organizations that monitor health trends
and include disease control and prevention
organizations, medical associations, etc.
Researchers that explore new health treatments,
medications, and medical devices
Laboratories that conduct tests and include chemistry,
microbiology, radiology, blood, genome, etc.
Payers that are responsible for cost management
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What are Interoperability Issues?
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In Computing: For heterogeneous software systems,
interoperability means exchanging information
efficiently and without any additional effort of the user
For Medical Software Systems:
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Syntactic Interoperability
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Defined as the Ability to read and Write the Same File
Formats and Communicate over Same Protocols
Available Solutions Include:
 Custom Adapter Interfaces
 XML
 Web Services
 Cloud Computing
 Standards and their Usage
 CDA and HL7 (both in XML)
 OpenEHR (http://www.open-emr.org/)
 Continuity of Care Record (CCR
http://www.ccrstandard.com/)
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Semantic Interoperability
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Defined as ability of systems to exchange data and
interpret information while automatically allowing
said information to be used across the systems without
user intervention and without additional agreements
between the communicating parties
Must Understand the Data to be Integrated
 In a PHR – Patient may refer to “Stroke”
 In an EMR – Provider may indicate
“cerebrovascular incident”
 These need to be Reconciled Semantically
Available Technologies Include:
 SNOMED
 LOINC
 NDC
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BMI in Computing: SW Architectures
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Can we Leverage Software Architectural Alternatives
from Computing:
 Data Warehouse
 Service-Oriented Architectures
 Grid Computing
 Cloud Computing
 Publisher-Subscriber Paradigm
 Web-Architectures and Services
Objectives:
 Understand their Capabilities in Support of Health
Information Exchange
 A Solution may Require a Combination of
Approaches
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Hybrid Architecture: Applied to Real Setting
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Hybrid Architecture: Applied to Real Setting
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Hybrid Architecture: Applied to Real Setting
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Hybrid Architecture: Applied to Real Setting
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Hybrid Architecture: Applied to Real Setting
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BMI in Computing: Security
Patients
Patient GUI
Providers
for RN vs. MD
XML
https
https
html
Web Server
Encryption
Firewall
Appl Server
Web - Control Services
Clinical
Researchers
Appl. – Control Methods
Encryption
Secure Communication
Web Content
DB Server
Encryption
GUI Look and Feel
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Security Issues for Patients
Patients
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Providers
Web-Based
Portal(XML + HL7)
Open Source XML DB
HIPPA Overriding Concern
All Patient Interfaces Web-Based
Secure Communication
 To/From Web Server (https)
 Among Discussion Group Members
Is this https or Peer-to-Peer?
Role-Based Access Control to Authorize
 Providers to Interact
 PHR Data to Individual Providers
Clinical
Researchers
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Security Issues for Providers
Providers
Patients
EMR
Web-Based
Portal(XML + HL7)
Open Source XML DB
Clinical
Researchers
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HIPPA Concerns for any EMR Data
Transmitted into Portal
Need to Consider Delegation
 Provider P Access to Portal for
Patient X
 Provider Q on Call
 Can P Delegate his Permission to
Access Portal to Q?
 Will Q’s Role (e.g., EMT) Limit
Access Even with Delegation?
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Motivation: General Concepts
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Authentication
 Proving you are who you are
 Signing a Message
 Is Client who s/he Says they are?
Authorization
 Granting/Denying Access
 Revoking Access
 Does Client have Permission to do what s/he
Wants?
Encryption
 Establishing Communications Such that No One
but Receiver will Get the Content of the Message
 Symmetric Encryption and Public Key Encryption
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Motivation: Type of Security Issues
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Legal and Ethical Issues
 Information that Must be Protected
 Information that Must be Accessible
 HIPPA vs. Emergent Health Situations
Policy Issues
 Who Can See What Information When?
 Applications Limits w.r.t. Data vs. Users?
System Level Enforcement
 What is Provided by the DBMS? Programming
Language? OS? Application? Web Server? Client?
 How Do All of the Pieces Interact?
Multiple Security Levels/Organizational Enforcement
 Mapping Security to Organizational Hierarchy
 Protecting Information in Organization
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BMI: Security
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Security is Multi-Step, Multi-Discipline Process
 Definition of Security Requirements
 Realization of Security at Web, Application, and
Database Levels
 Integration of Security from Client to Web to
Application to DB
 Rigorous Definition of Security Policy
 Dynamic Nature of Security Privileges
 Enforcement of Defined Privileges Across and
within Multiple Tiers
Overall, Security in Today’s World Integral Part of
Everyday Life - Some Key Concerns
 Confidentiality of an Individuals Data – PHR/EMR
 Identity Theft
 Protecting National Infrastructure
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BMI Cell Phone Applications
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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
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Active – Patient Initiated
 Providing Information via Smartphone on:
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Diabetes (Glucose, Weight, Insulin)
Asthma (Peak Flow, use of Inhaler)
Heart Disease (Pulse, BP, Diet)
Pain, Functional status, Fatigue, etc.
 Medication/OTC/Supplement Tracking
http://www.engr.uconn.edu/~steve/Cse4904/cse4904.html
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History of Mobile Computing 2009
Table 1: SmartPhone Varieties and Market Share in 2009.
Platform
Symbian
BlackBerry
iPhone
Windows
Mobile
Android
World market share
47.10%
19.50%
10.70%
12.40%
> 1%
# US users
888,535
9,668,977
5,258,254
6,807,554
427,914
US market share
3.9%
41.9%
22.8%
29.5%
1.9%
Development
C++
Java
Objective C
Windows
Linux
Dev Environment
Visual Studio
Blackerry/Java
Mac OSX
Visual Studio
Linux
Resolution
various
various
480x320
various
various
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History of Mobile Computing – Aug 2013
Table 2: SmartPhone Varieties and Market Share in August 2013.
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History of Mobile Computing - Tablets
Table 3: Tablet Market Share in Q2 2013.
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Semester Project in CSE2102 – Fall 2013
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Personal Health Assistant (PHA)
 Patient Version for Medication and Chronic
Disease Management and Authorizing Providers
 Identify Overmedication , adverse interactions, and
adverse reactions
Provider Version for Viewing Patient Data that has
been Authorized
Personal Health Record Microsoft HealthVault
 A Person Can Track Medical Information
 Used as Backend Repository to PHA
OpenEMR Standalone version for Providers
 Seek to Integrate into PHA
 Support Medication Reconciliation
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Software Architecture Diagram
Medication/
Supplement
Interaction Checker
PHA Provider
ODL and Chronic
Disease Analyzer
Medication & Observations of
Chronic Disease Daily Living (ODL)
Management
PHA Patient
Apache/Tomcat
Web/Application
Server
MySQL
Database
Server
OpenEMR
Personal Health
Record (PHR)
Microsoft
Healtvault
Figure 1: Architecture Diagram of the CSE2102 Project this Semester.
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Architecture for CSE2102 in Fall 2013
New External Sources
XML
MS
Health
Vault
Middle-Layer Server
With REST API
NDF-RT
ASP.Net API
RxNorm
XML
OpenEMR
JSON
XML
JAVA APIs
XML
JSON
RxTerms
FDA
Daily
Meds
Personal Health Assistant (PHA)
Patient App
•
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•
•
Medications
Allergies
Procedures
Demographic
Provider List
Security Policies
Proivder App
•
•
•
•
Medications
Allergies
Procedures
Demographic
Patient List
Authorization by Role
New
Interaction
Checker
Screen
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Four Part Semester Project in CSE2102
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Part 1: Installing Technologies
 Android SDK, EclipseUML, openEMR
Part 2a: Design and Implementation of Class Library
 Meds, ODLs, Diseases, Exercise, Nutrition
Part 2b: Expansion of PHA Android Source to
 Chronic Diseases,
 Exercise, Nutrition
Part 3: Integrating PHA with MS HealthVault
 Use of REST API – Linkage to Common Server
 Read/Store Data from HealthVault
Part 4: Extending PHA and Integrating with openEMR
 Medication Interactions – Use RxNorm, RxTerms,
NDF-RT and other Federal REST APIs
 Pull Medications from openEMR
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Android SDK
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Android SDK Manager
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Android Virtual Device Manager
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Android Virtual Device Manager
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PHA in Andriod Emulator
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openEMR
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iOS PHA – Patient Version
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iOS PHA – Patient Version
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iOS PHA – Patient Version
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iOS PHA – Provider Version
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Android PHA Screenshots
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Android PHA Screenshots
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Android PHA Screenshots
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Conclusions
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Please Contact me with Questions on these Topics
Look for CSE Offerings in Coming Years
 Undergrad Bioinformatics Course
 CSE3800 – Usually each Fall Semseter
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Undergrad Introduction to Biomedical Informatics
 In Spring – Cross Listed with CSE5810!
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Lab Based Courses
 Software and Hardware Foci
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Industry Sponsored Student Projects
Undergraduate Info and Data Security Course
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CSE4904 – Spring 2010
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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
Work ongoing this Semester
 Joint CSE (4 students) and PharmD (4 students)
 CSE Fac (Demurjian) and PharmD Fac (Smith)
CSE4939W in Spring 2012
 Industry Sponsored Projects
 Cell/Mobile Platform Based
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Blackberry Team
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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
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Screen Shots
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Screen Shots
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Screen Shots
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Screen Shots
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Screen Shots
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Android Team
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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
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Screen Shots
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Screen Shots
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Screen Shots
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Screen Shots
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iPhone Team
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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
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PHA iOS Application
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Main Menu & Settings Menu
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Profile
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Medications
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Wellness Diary
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Observations of Daily Living
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Dietary Management
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Screen Shots
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Screen Shots
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Screen Shots
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Screen Shots
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