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  • 1. CSE4904 Computer Science Design Lab Prof. Steven A. Demurjian, Sr. Computer Science & Engineering Department The University of Connecticut 191 Auditorium Road, Box U-155 Storrs, CT 06269-2155 [email_address] (860) 486 - 4818
  • 2. Course Goals
    • CSE4904: The “First” Project Based Course
      • Objective of Course
        • Expand Knowledge on Emerging Disciplines
        • Learn about New/Innovative Technology/Standards
        • Transition from Requirements to Design to Development
        • Work as a Loosely Organized Group
        • You Make Decisions, Resolve Problems, etc.
        • You “Apply” your Coursework/Experiences
    • What is Instructor’s Role?
      • Provide a Set of Potential Project Topics
      • Serve as Manager - Organize Meetings, Available for Questions, etc.
  • 3. Expand Knowledge on Emerging Disciplines
    • Biomedical Informatics/Health Information Technology Rapidly Emerging Discipline
    • Cutting Edge, Incredible Career and Research Opportunities
    • Improve Practice of Medicine Through Informatics
      • Patient Managed
      • Patient Care
      • Hospital Based
      • Research (Genomics/Trials)
    • What is Biomedical Informatics?
    • Where is the Future?
  • 4. What is Informatics?
    • Informatics is:
      • Management/Processing of Data
      • From Multiple Sources/Contexts
      • Classification (Ontologies), Collection, Storage, Analysis, Dissemination
    • Informatics is Multi-Disciplinary
      • Computing (Model, Store, Mine, Process Information)
      • Social Science (HCI)
      • Statistics (Analysis)
    • Informatics Can Apply to Multiple Domains:
      • Pharmacology, Nursing, Medicine, Biology, etc.
      • Business, Fine Arts, Humanities
    People Information Technology Informatics Adapted from Shortcliff textbook
  • 5. What is Biomedical Informatics (BMI)?
    • 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.)
      • Clinical Informatics, Pharmacy Informatics, Consumer Health Informatics, Nursing Informatics
  • 6. BMI & 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
    • Informatics Support via:
      • Simulations, Super & Grid Computing
      • Data Mining, Data Reduction, Data Analysis
      • Database Interoperability, GUIs
  • 7. BMI & Clinical Research (Trials)
    • Applying Clinical Research Results via Trials with Patients on Medication, Devices, Treatment Plans
    • Multi-Phased Process for Clinical Trials:
      • Phase I: First Stage – 20-80 Healthy Patients
      • Phase II: Second Stage – 20-300 Patients
      • Phase III: Multi-Center Trials – 300-3000
      • Phase IV: Monitoring of Drug After Approval
    • Informatics Support via:
      • Electronic Multi-Site IRB, Collaboration Tools
      • Clinical Trials Recruitment and Management
      • Multi-Site Clinical Research Data Repository
  • 8. BMI & T2 Research (Clinical  Community )
    • Translating “Successful” Clinical Trials into Practice and the Community
      • Improvements in Practice
      • New Evidence-Based Guidelines or Care Models
      • Phase III Success Translated to Health Providers
    • Informatics Support for:
      • Disseminating Education Materials to Providers & Patients to Track Acceptance, Collect Outcomes
      • Includes Tools from Clinical Research (Trials)
  • 9. BMI & Clinical Practice
    • 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
    • Informatics Support via:
      • Electronic Medical Record
      • Linking/Accessing Data Repositories
      • Collaborative and Secure (HIPPA) Web Portals
  • 10. What is UConn Doing in this Area?
    • 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
      • 36+ Academic Medical Centers Awarded to Date see:
    • Under President Mike Hogan’s Leadership
      • UConn Submitted a CTSA Proposal in Oct 2008
      • Formed CICaTS: Connecticut Institute for Clinical and Translational Science (Sept. 29 th 09)
      • University Initiative with Partners
        • John Dempsey, St. Francis, Hartford Hospital, CCMC, Hospital for Central CT, Institute for Living, etc.
  • 11. CICATS
    • 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
  • 12. Increasing Biomedical Informatics Expertise
    • Grow “Our Own” Biomedical Informatics Faculty
      • Announced Provost Initiative in mid-July 2009
      • $100,000 Committed for Faculty Training Costs and Associated Release Time
    • Three On-Line Program Options:
      • AMIA 10x10 Health Informatics Program
      • MS Program in BMI (Oregon H&S, UIllinois, etc.)
      • Certificate Program in BMI
    • 8 UConn Faculty (7 UCHC/1 Storrs) took Course
  • 13. Eminent Faculty Search in BMI
    • Soon to be Approved (this week) Dual Campus Eminent Faculty Search for Biomedical Informatics
      • 7 to 9 total Faculty
      • Recruitment of “Leader” for BMI Center and Faculty at All Levels
    • Seeking Profiles that Include:
      • Clinical, Medical, and/or Health Informatics who are Medical Professions (MD Likely) with a Track Record in Informatics
      • Computing and/or Information Science PhDs with Medical, Clinical, or Health Background/Training
    • This year – Senior Leader (UCHC) and multiple Positions
  • 14. Biomedical Informatics in CICATS
  • 15. GAANN: Advanced Computing Graduate Assistants in Areas of National Need Proposal Funded by: US Dept. of Education PI: R. Ammar co-PIs: S. Demurjian, S. Rajasekaran, J.H. Cui, and S. Zhou Advanced Computing Spans: Biomedical Informatics (BMI) Underwater Sensor Networks (UWSN)
  • 16. Advanced Computing and its Focal Areas
  • 17. GAANN Funding
    • Support for Five Doctoral Students (each for 3 years) each of whom Must be US Citizen.
    • One Student will be Funded in the Areas of
      • BMI
        • Bio/Genome Informatics: Supercomputing
        • Medical Informatics: Warehouses and Mining
      • UWSN
        • Architecture and Protocols
        • Systems and Devices
      • 5 th student in Security and Networks will be in either BMI or UWSN
    • Educational Program for GAANN includes Research, Training in Teaching, etc., to Prepare Graduates to be Faculty Members
  • 18. Learn about New/Emerging Technology
    • Explore Smartphone Technologies and Applications
    • Four Smartphone Platforms
      • Android
      • Blackberry
      • iPhone
      • Microsoft
    • All with Differing APIs
      • Java
      • Java
      • Objective C
      • .NET
    • How do we Develop Applications?
    • How can we Link to Web and Existing BMI Apps?
  • 19. Learn about New/Emerging Technology
    • Personal Health Records (PHR) are Patient Controlled Repositories
      • Google Health ( )
        • Accessible via Java API
        • XML-Based Interface
      • Microsoft HealthVault ( )
        • Accessible via .Net Infrastructure
    • Electronic Medical Records (EMRs) are Health Provided Controlled Repositories
      • General Electric Centricity EMR
      • Version 9.2 – Secure Web Services
  • 20. Project Focus this Semester
    • Smartphone Applications that Interact with Google Health (or MS Health Vault) and GE Centricity
    • Focus on Observations for Daily Living (ODLs)
    • What are ODLs?
      • Patient Provided Information
      • Related to their Chronic Diseases or Health Goals
      • Augment Typical Information Provided at MD Visit
      • Continuous Input
      • Clinical Decision Support to Spot Problem Trends
      • Intervene Before Event Occurs
      • Monitor Progress Towards Goal (e.g., weigh loss)
  • 21. Two Types of ODLs
    • 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.
    • From Basic to Sophisticated!
    • All ODLs will have Help (Usability) and Education (Disease) Capability Built in.
  • 22. Overall Architecture
  • 23. Possible ODLs
    • Multi-Media Support Repository: It has been found in a number of settings, that people with chronic diseases may be able to cope with their pain, fatigue, etc., through the use of audio clips, video clips, or pictures that mean something too them. For example, for one person it may be pictures and clips of family and loved ones, for another person it may be popular music, for yet another inspirational speeches, and so on. The intent is to develop a Smartphone application that is capable of tracking a repository of audio, video, and pictures, categorized by Topic, Title, and/or Keywords. The system will track a complete historical record for each participant, noting the selections that are being utilized along with their date-time stamp and frequency. There will be the ability to have a favorites list of most frequently used selections, as well as for each participant to upload their own audio/videos for her own use. The intent is to also have a version of this application that could cache selections with the memory of the Smartphone to reduce download times, particularly for those selections chosen most frequently.
  • 24. Possible ODLs
    • Pedometer or Accelerometer : For either of these applications, you will need to have an actual Smartphone that has motion sensors. The idea would be that these applications would be initiated by a patient to collect information associated with walking (pedometer) or movement (accelerometer) for a fixed period of time.
  • 25. Possible ODLs
    • Discrete Measurement of Symptom/Condition: Historically, pain scales have been used extensively in medical settings (just to a Google Search on “pain scale” images). This type of scale can be generalized to collect information related to pain, fatigue, mobility, adherence to medication, and so on. Note that some of these ODLs may be regularly schedule (e.g., the smartphone beeps a reminder), triggered as the result of a contact to the patient (e.g., an automated call or email to the smartphone), or initiated by the user. The numerical values are tracked for each individual to capture all of the values entered. This would be a simplistic ODL based on a scale (1 to 10, Good to Bad, etc.) rather than any actual collection of medical/personal data.
  • 26. Possible ODLs
    • Discrete Measurement of Symptom/Condition: Historically, pain scales have been used extensively in medical settings (just to a Google Search on “pain scale” images). This type of scale can be generalized to collect information related to pain, fatigue, mobility, adherence to medication, and so on. Note that some of these ODLs may be regularly schedule (e.g., the smartphone beeps a reminder), triggered as the result of a contact to the patient (e.g., an automated call or email to the smartphone), or initiated by the user. The numerical values are tracked for each individual to capture all of the values entered. This would be a simplistic ODL based on a scale (1 to 10, Good to Bad, etc.) rather than any actual collection of medical/personal data.
  • 27. Possible ODLs
    • Synching Information with PHR/EMR: For this application, you need to consider the information that is stored in a PHR and/or EMR, and develop Smartphone applications that provide a means for patients to enter the information which can then be synchronized with the PHR/EMR. For example, Google Health lets a user maintain his/her prescriptions, but it is not set up to handle nutritional supplements and other home remedies. A application could support the data entry of this information, which would then be synchronized into Google Health, and if the user is also a patient with data in the EMR Centricity, a second step would synchronize to this repository using its secure web services. A different application could also be considered to handle side effects and reactions to medications, food, allergens.
  • 28. Possible ODLs
    • Scanning/Recognition: For this application, it may be possible to leverage the digital camera in a cell phone to take a “picture” of a medication and/or nutritional supplement label that can be then uploaded to the web into the PHR or EMR. The idea would be for the patient to be able to create a pictorial representation of medications/supplements, that would also be supplemented with their complete dosing information (size, frequency, etc.). This would involve being able to capture perhaps multiple images from the same medication/supplement and meld them together.
  • 29. Possible ODLs
    • Futuristic: Are you really Ambitious?
      • Link Commercial Glucose Meter to SmartPhone
      • Digital Camera on Smartphone to Scan Bar Codes on Supplements and/or Medications
        • May Involve OCR
      • Hooking up Sensors through Smartphones
        • Pulse, BP, etc.
        • Treadmill or Exercise Equipment
      • GPS and Smartphones? For Movement?
    • Many of these will need to store data in PHR/EMR
  • 30. Course Process and Overview
    • Identify Problem – by Thursday, 9am
    • Requirements Specification – by 3 rd Class
      • User-Interface Driven Design
      • Screen Shots and User Process
      • Chosen Technologies and Platforms
    • Interactions and Feedback
    • Explore Development Alternatives/Platforms
    • Detailed Development and Testing
    • Implementation and Integration
    • Team Interactions and Dynamics
    • Setting and Meeting Milestones
    • Evaluating Success/Failure
  • 31. Class Materials
    • CSE4904 Web Site at …
      • All Course Materials Available On-Line
      • Communication by Email
      • Available in Afternoons and by Appointment
    • Other Important Class Materials – Background on
      • Health Information Technology
      • Software Design, Java, Requirements Definition
      • Unified Modeling Language (UML)
  • 32. Milestones with Dates - Subject to Change
    • Project Proposal – 3 days after 1 st class
    • Presentation of Goals/Objectives/Focus – 2 nd Class
    • Requirements Specification – 3 rd Class
    • Revised Requirements Specification – 4 th class
    • Overall Design and Prototyping/Management Plan – 5 th class
    • Prototype Report 1/Presentation – 8 th class
    • Prototype Report 2/Presentation – 11 th class
    • Prototype Report 3/Presentation –13 th class
    • End of Semester (last day of classes)
      • Final Report/User Manual
      • Final Student Assessment
      • Solution/Materials in Source Code Repository
  • 33. Documentation Packages/Requirements
    • Development Environment/Source Code Control
      • Use of IDE (e.g., Visual Studio, Eclipse, etc.)
      • Source Code Control (Subversion)
      • Web Page for Each Team/Project?
    • All Project Specifications (Written Documents) Must be Done using: MS Word 03 or 07
    • All Project Presentations Must be Done Using Powerpoint (PPT)
      • Utilize Samples on Web Page for UML and CT Insurance Dept. Link for Guide
    • Submit Both Hard Copy and Electronic Versions
      • Hard Copy Produced on Laser Printer
      • Electronic as a Directory zipped
  • 34. Project/Team Web Page/Documentation
    • Should Each Team Develop a Web Page for their Project????
      • See Links for Former Projects as Examples
      • Use To Post On-Going Documents
    • Augment Web Page with Detailed Design Documents
      • Together CC Generates Documentation
      • Frame Based HTML Resembles Java Doc
      • Make Sure you Select “All” Diagrams
    • Documentation of Java with Java Doc
      • Utilize Together Architect
      • Utilize IDE
  • 35. Today’s Tasks
    • Individual or Teams?
    • Choosing Teams – At Most 2 Team Members
      • Self-Organized Teams
      • Instructor Sets Teams
    • Meet & Brainstorming
      • Remainder of Class
      • Exchange Email and Phone Numbers
    • First Project Due – 3 days after first class at 9am - Expect Feedback by End of Day
    • First Project Presentation – 2nd class
      • 5 to 10 minutes per team
      • Copy of Slides/Create & Post on Web Page