CS6440: Introduction to Health Informatics — Fall 2021
The Fall 2021 semester of the CS6440 class will begin on August 23, 2021. This page provides information about the Georgia Tech CS6440 class on Health Informatics relevant only to the Fall 2021 semester. Note that this page is subject to change at any time. Below, you will find a basic form of the course’s calendar, grading criteria, and other information.
For more complete information about the course’s requirements and learning objectives, please see Course Description and Goals.
To help with navigation, here are some of the links you’ll be using frequently in this course:
Tools: Canvas | INGInious | Github | Ed | Slack
Class Pages: CS6440 Home | Fall 2021 Full Calendar | Reading List
Labs: Lab 1 | Lab 2 | Lab 3 | Lab 4 | Lab 5 | Lab 6
Mini Projects: Quiz #1 | Quiz #2 | Quiz #3 | Quiz #4 | Quiz #5
Individual / Team Project: Sprint #1 | Sprint #2 | Sprint #3 | Sprint #4 | Sprint #5 | Sprint #6 | Sprint #7 | Sprint #8 | Sprint #9 | Sprint #10
Course Feedback: Course Reflections | CIOS Survey
Course Calendar At-A-Glance
Below is a view of the calendar for the Fall 2021 CS6440 class that focuses on the graded deliverables. All of the assignment due dates are on Sundays at 11:59PM Anywhere on Earth time. We recommend changing your time zone in Canvas to show the due date in your local time. For the COMPLETE course calendar, please see the Full Course Calendar.
|Week #||Week Of||Lectures||Deliverable||Assignment Due Date|
|1||08/23/2021||1 & 2||Introductions, On-boarding Quiz, Course Projection||08/29/2021|
|2||08/30/2021||3 & 4||Quiz #1 – Lectures 1-4, Lab I – US Healthcare & Health Data, Ed Discussion||09/6/2021|
|3||09/6/2021||5 & 6||Quiz #2 – Lectures 5-6, Lab #2 – Health Standards, Ed Discussion||09/13/2021|
|4||09/13/2021||7 & 8||Practicum Sprint #1, Lab #3 – Health Interoperability, Ed Discussion||09/20/2021|
|5||09/20/2021||9 & 10||Quiz #3 – Lectures 7-9, Lab #4 – Health Applications, Ed Discussion, Course Reflection I||09/27/2021|
|6||09/27/2021||11 & 12||Quiz #4 – Lectures 10-12, Lab #5 – Data Modernization, Ed Discussion||10/4/2021|
|7||10/4/2021||13 & 14||Quiz #5 – Lectures 13-14, Lab #6 – Advanced Technologies, Ed Discussion||10/11/2021|
|8||10/11/2021||15||Practicum Sprint #2, Ed Discussion||10/18/2021|
|9||10/18/2021||16||Practicum Sprint #3, Ed Discussion, Course Reflection II||10/25/2021|
|10||10/25/2021||17||Practicum Sprint #4, Ed Discussion||11/1/2021|
|11||11/1/2021||18||Practicum Sprint #5, Ed Discussion||11/8/2021|
|12||11/8/2021||19||Practicum Sprint #6, Ed Discussion||11/15/2021|
|13||11/15/2021||20||Practicum Sprint #7, Ed Discussion, Course Reflection III||11/22/2021|
|14||11/22/2021||Practicum Sprint #8, Ed Discussion||11/29/2021|
|15||11/29/2021||Practicum Sprint #9, Ed Discussion||12/6/2021|
|16||12/6/2021||Practicum Sprint #10, Ed Discussion||12/13/2021|
|17||12/13/2021||Course Feedback, Mentor Evaluation, Team Member Evaluation, Individual Marks||12/15/2021|
Given above are the numeric labels for each Udacity lesson. For reference, here are those lessons’ titles:
- 1 Introduction to the Course
- 2 Primer on the US Healthcare System
- 3 Foundations in health Data: What are Health Data?
- 4 Foundations in health Data: How are Health Data Used
- 5 Electronic Medical Records
- 6 Foundations in health Data: Data Standards
- 7 Foundations in health Data: Data Interoperability Standards
- 8 FHIR Ecosystem (SMART and Beyond)
- 9 Foundations in health Data: Health Analytics
- 10 OMOP, OHDSI, and OMOP on FHIR
- 11 Data Modernization (Converters)
- 12 Data Modernization (Projects / IGs)
- 13 Applied Technology Tools (CQL, mHealth, Cloud)
- 14 Advanced Topics
- 15 Case Study / Guest Lecturer (Chronic Illness & Mortality Reporting)
- 16 Case Study / Guest Lecturer (Infectious Disease)
- 17 Case Study / Guest Lecturer (Data Surveillance)
- 18 Case Study / Guest Lecturer (Maternal / Fetal)
- 19 Case Study / Guest Lecturer (Everyday – Vaping)
- 20 Case Study / Guest Lecturer (Global Example)
Your grade in this class consists of four components: Quizzes, Labs, Practicum Sprints and Ed Discussion participation. These are weighted in the final grade calculation as explained below.
Final grades will be assigned as follows:
- Grades of 90pts or above will receive an A;
- Grades of 80pts to 90pts will receive a B;
- Grades of 70pts to 80pts will receive a C;
- Grades of 60pts to 70pts will receive a D;
- Grades below 60pts will receive an F.
There is no curve. Assignments and projects that are not submitted at all will be calculated as a 0.
Individual Assignments (65pts)
- Activities (65pts): Individual assignments consists of all quizzes, labs and Ed Discussion participation. These “hands on” activities enhance the material covered throughout the course. Each of the activities vary in weight (see the Assignments page for more details). The activities are auto-graded, with outcomes at or between 0% and 100%. 0% is given for wrong or incomplete solutions, 1%-99.99% is given for those partial solutions and 100% is given for fully correct solutions. These outcomes are then converted to points. There are 2 required practice activities that are worth a total of 0 points.
- FHIR Advanced Read Activity (worth 3 points) with a score of 50% would be converted into 1.5 pts towards the individual assignment grade (worth a total of 30 pts).
- FHIR Advanced Delete Activity (worth 2 points) with a score of 100% would be converted into 2 pts towards the individual assignment grade (worth a total of 30 pts).
Individual / Team Project (35pts)
There is only one project in this course: a team project or an individual project worth 35 points or 35% of your overall grade. For this project, you will select a healthcare technology problem, by a mentor or by your own research. At the conclusion, you will deliver a final project, graded out of 100 points, either as a team or individual that contains your final application solution. The application will be open sourced.
The Project is comprised of ten deliverables and an evaluation. Each of the deliverables vary in weight (see the Individual-Team Project page for more details). The deliverables are manually graded, with outcomes between 0-100%. The deliverable grades are based on the requirements, which also serves as the rubric. These outcomes are then converted to points.
- Sprint 1 (worth 5 points) with a score of 95% would be converted into 4.75 pts towards the project grade (worth a total of 30 pts).
- Sprint 2 (worth 5 points) with a score of 100% would be converted into 5.00 pts towards the team project grade (worth a total of 30 pts).
These assignments vary by semester in offering and in value. Please check out the Stretch Assignment page for more information.
The following policies are binding for this course.
Official Course Communication
You are responsible for knowing the following information:
- Anything posted to this syllabus (including the pages linked from here).
- Anything posted to the general course landing page.
- Anything posted to Canvas
- Anything emailed directly to you by the teaching team (including announcements via Ed), 24 hours after receiving such an email.
Because Piazza announcements are emailed to you as well, you need only to check your Georgia Tech email once every 24 hours to remain up-to-date on new information during the semester. Georgia Tech generally recommends students to check their Georgia Tech email once every 24 hours. So, if an announcement or message is time sensitive, you will not be responsible for the contents of the announcement until 24 hours after it has been sent.
We generally prefer to handle communication via Piazza to help with collaboration among the teaching team, but we understand Piazza is not ideal for having information “pushed” to you. We may contact you via a private Piazza post instead of an email, but if we do so, we will choose to send email notifications immediately, bypassing your individual settings, in order to ensure you’re alerted.
Note that in four years as a Georgia Tech OMSCS instructor, I’ve encountered exactly one instance of a time-sensitive email; so, the 24-hour rule likely won’t ever be relevant. As with other things, however, we believe it’s better to be clear at the beginning rather than write policies later.
Note that this means you won’t be responsible for knowing information communicated in several other methods we’ll be using. You aren’t responsible for knowing anything posted to Piazza that isn’t linked from an official announcement. You aren’t responsible for anything said in Slack, or other third-party sites we may sometimes use to communicate with students. You don’t need to worry about missing critical information so long as you keep up with your email and understand the documents on this web site.
This semester, we’ll be using Slack for office hours. If you are unaware, Slack is a popular team communication chat tool that allows conversations in public rooms, private rooms, and private messages. Slack office hours are times when the instructor and/or one or more teaching assistants will be available on the dedicated CS6440 student Slack community. You can sign up for the student Slack community at omscs6440.slack.com.
During Slack office hours, the instructor and/or teaching assistants in attendance will be available for conversations in the public #office-hours channel, or in private one-on-one channels. You are also encouraged to use the Slack community for discussions, project work, or anything else. The instructors and/or TAs will be available during office hours, but they may also be available at other times as well.
To find when office hours for OMS CS6440 are being held, check the office hours calendar or the weekly announcements. Changes to any given office hours session on the calendar will always be made at least 24 hours in advance; if late changes are needed, they’ll be announced with a Piazza announcement. If you are not comfortable signing up for Slack to participate in Slack office hours, you may also feel free to email or post privately on Piazza to set up a chat via an alternate technology at the same time. If you would like to participate in office hours but are unable to make the given times, feel free to email or post privately on Piazza and we’ll try our best to accommodate you.
Running such a large class involves a detailed workflow for assigning assignments to graders, grading those assignments, and returning those grades. As such, work that does not enter into that workflow presents a major delay. Thus, we cannot accept any late work in this class. All assignments must be submitted by the posted deadlines. If you have technical difficulties submitting the assignment to Canvas, post privately to Piazza immediately and attach your submission.
If you have an emergency and absolutely cannot submit an assignment by the posted deadlines, we ask you to go through the Dean of Students’ office regarding class absences with in 48 hours of the cause or incident. The Dean of Students is equipped to address emergencies that we lack the resources to address. Additionally, the Dean of Students office can coordinate with you and alert all your classes together instead of requiring you to contact each professor individually. You may find information on contacting the Dean of Students with regard to personal emergencies here: https://gatech-advocate.symplicity.com/care_report/
The Dean of Students is there to be an advocate and partner for you when you’re in a crisis; we wholeheartedly recommend taking advantage of this resource if you are in need. Justifiable excuses here would involve any major unforeseen disruption to your classwork, such as illnesses, injuries, deaths, and births, all for either you or your family. If you find that you will miss a significant portion of the course due to any one of theses excuses, we highly advise dropping the course if you will not be able to catch up. Note that for foreseen but unavoidable conflicts, like weddings, business trips, and conferences, you should complete your work in advance; this is why we have made sure to provide all assignment and project resources in advance. If you have such a conflict specifically with the tests, let us know and we’ll try to work with you. Unfortunately, team projects are hard to make up so if your TA mentor finds that there isn’t much you could do to make up aiding in a project, we will work to assign you an “Incomplete” for the course.
(also See “Stretch Assignments” above)
In general, we strongly encourage collaboration in this class. You are encouraged to discuss the course material, the activities, the written assignments, and project with your classmates, both before and after assignments and projects are due. Similarly, we will be posting the best assignments for public viewing so you may learn from the success of others’ designs.
However, we draw a firm line regarding what copying is permissible in your assignments. Specifically, you must adhere to the following rules:
- Any content that is copied or barely paraphrased from existing literature in healthcare or health informatics must be cited, both in the references at the conclusion of your assignment and in-line where the borrowed material appears. Failing to provide in-line citations for borrowed material will be regarded as plagiarism even if the source is provided in the references. This applies to figures as well as text, including those figures that are part of this course’s material. Any cited content greater than two sentences need to be properly cited and rewritten in your own words.
- Do not copy any content from other students in current or previous semesters of Introduction to Health Informatics or Health Informatics in the Cloud, even if cited.
- Each Essay and Programming Assignment will be reviewed with applicable plagiarism tools.
In all written work, sources should be cited in APA style, both in-line and at the end of the document. Please consult the Purdue OWL for information on when and how to cite sources in research. When in doubt, don’t hesitate to ask!
Welcome to CS6440: Introduction to Health Informatics!
Welcome! This is the landing page for Georgia Tech’s CS6440 Introduction to Health Informatics course. This page provides general information about the course. Specific information about a given semester’s assignments, grading, or scheduling can be found under that semester’s page and the Calendar page.
What is Health Informatics?
Health informatics seeks to integrate medical domain knowledge, information technology, and data to the enhance the delivery of care to patients and improve our understanding of health and disease.
About This Course
This is an introductory course on health informatics designed for a range of student backgrounds including computer science, engineering, human-computer interaction, biomedical sciences, and related domains. It touches on most of the key domains within health informatics to help students determine if they wish to pursue it further and, if they do, which of many possible directions they might take.
Conceptually the course is in three sections:
- Section 1: Healthcare Systems and Data (Lessons 1-5) provides background on the structure of the US healthcare system, its key challenges and the efforts the federal government and others have made to spur the use of digital records and data standards to help overcome those challenges. It also provides a snapshot of the current state of the key informatics tools for providers, patients and data sharing among them.
- Section 2: Healthcare Interoperability (Lessons 6-9) covers the key interoperability standards that are the ‘digital plumbing’ that support virtually all healthcare systems and tools. The course emphasizes the Fast Healthcare Interoperability Resource (FHIR) standard that supports data sharing and creates a ‘universal health app platform’ supporting innovative ways for providers and patients to use health data.
- Section 3: Future Facing Health Informatics Technologies (Lessons 10-12) introduces three of the current cutting-edge areas of health informatics: mHealth, public/population health and big data/analytics as well as a deep dive into application development.
Learning Goals and Outcomes
The goals of this course are to:
- Equip students with a working knowledge of the unique structure and problems of the US healthcare system.
- Provide students with a basic understanding of current informatics tools and systems and their limitations.
- Introduce students to the data and interoperability standards used to support those systems and tools with an emphasis on the new FHIR standard and an appreciation of the SMART on FHIR app platform built upon it.
- Provide students with a unique opportunity to work on an actual SMART on FHIR app under the guidance of a healthcare domain expert.
By the end of this course, students should:
- Be familiar with health data, how it is generated and used
- Be able to build an interoperable health application
- Be aware that health is a strong career path for students with CS and other technical backgrounds
Elements of the Course Grade
Course grades are based on:
- Successful completion of a set of structured activities, programming exercises, and case studies
- Results of their team’s FHIR-based application development project
- Scores on 2 content assessments
- Class Participation as measured by individual contributions to team projects, survey completion and Piazza.
Students should have at least a basic computer science background, however NO previous knowledge of health informatics is assumed or required. Any Georgia Tech student who is willing to put in the necessary time for course work should be prepared to do well. In fact, the team FHIR app development projects, a major component of the course, benefit from students with diverse technical skills and backgrounds.
Technical requirements include:
- Browser and connection speed: An up-to-date version of Chrome or Firefox is strongly recommended. We also support IE9 and the desktop version of IE 10 and above (not the metro versions) – however not recommended. Internet speeds should be at least 2+ Mbps and at minimum 0.768 Mbps download speed.
- Operating Systems: PC: Windows 7 or higher with latest updates installed. Mac: OS X 10.6 or higher with latest updates installed. Linux: Any recent distribution that has the supported browsers installed. Chromebooks are acceptable as long as you can perform all required coursework.
The information on this page is general to the CS6440 class. Specific information for the Spring 2019 course is on that semester page.