BMI 5007 Methods in Health Data Science

(web-based instruction and classroom instruction)
3 Semester Credits/meets part of the research informatics competencies
Prerequisites: Consent of instructor

Course Description:
The course introduces methods in health data science – defining the problem, accessing, and loading the data, formatting into data structures required for analysis. This course covers the basics of computational thinking to define a computational solution, methods to access healthcare data from variety of sources (EHR data, UMLS, Medline, etc.), and in different data formats. The students will apply methods for data wrangling and data quality assessments to structure the data for analysis. The students will be introduced to basics of design and evaluation of algorithms and application of data structures for healthcare data. The course will use Python programming language and basic python libraries for data sciences such as numpy, scipy, matplotlib and pandas.

Students should expect a good amount of programming exercises for each week. This course is not an introduction to programming, and not a course to improve programming skills. Students are expected to have some experience with introductory / beginner level Python programming.

Upon successful completion of the course, students will:

  • Abstract a business need for data analysis and define appropriate computational problem
  • Design and analysis (time complexity) of simple algorithms
  • List basic data structures and their characteristics, applications in biomedicine
  • Retrieve biomedical data from multiple sources formats – specifically flat files (text), tabular data (CSV), structured data (JSON, XML)
  • Implement Python programs to load data and apply basic data wrangling to structure output.

Pre-Requisite effective Fall 2017

Basic Python Programming: "Basic" python programming is defined as ability to working with 
a) Variables - define, access 
b) Use of appropriate operators 
c) Conditionals - if ... else
d) Lists, Dictionaries - creation, access, add or remove items
e) while and for loops 
f) function definition

There will be a 20-question closed book canvas quiz on the above-mentioned basics of python in the first week of course (or before signing up). A score of 80% and above is required to successfully complete the coursework. Contact the instructor for access to the quiz.

For student who do not have the per-requisites, they can obtain from any of the Massive Open Online Courses of their choice. Few recommendations are:

1) https://www.edx.org/course/introduction-computer-science-mitx-6-00-1x-10. Class materials are also archived here: https://ocw.mit.edu/courses/electrical-engineering-and-computer-science/6-0001-introduction-to-computer-science-and-programming-in-python-fall-2016/

OR

2) https://ocw.mit.edu/courses/electrical-engineering-and-computer-science/6-189-a-gentle-introduction-to-programming-using-python-january-iap-2011/

OR

3) https://developers.google.com/edu/python/