Homework 1

posted Jan 16, 2018, 5:48 AM by Xiaotong Li   [ updated Jan 16, 2018, 5:55 AM ]

Homework 0

posted Jan 16, 2018, 5:48 AM by Xiaotong Li   [ updated Jan 16, 2018, 2:49 PM ]

Welcome to the 21st iteration of "Biomedical Data Science: Mining and Modeling" course. Homework 0 is only meant for you to actively check-in to the class and get involved in a crowd-sourced activity.

HW 0 will be due on 1/24/2018. Please complete this assignment at your earliest convenience.

HW 0 consists of TWO parts, completing a poll to check you into the class and crowd-sourced comments and edits for "List of Study Topics in Bioinformatics" for both fun and educational purposes.

1. Please complete the following poll:
Assignment 0 poll 

2. First, please make sure you are logged onto Google with Yale email address. This will ensure us to track who made comments and edits. Once logged in, please make "comments and edits" for the following Google document:


posted Dec 14, 2017, 10:55 AM by William Meyerson   [ updated Feb 14, 2018, 12:08 PM ]

We expect to assign three to four homework assignments and a final project. They will be linked on this page.

To accommodate the diverse backgrounds and interests of the students, we offer students a choice of which style of assignments they wish to take. Students designate their track by selecting under which course number they wise to take the course. Quantitative track assignments involve more programming. Biology track assignments involve more writing. Some questions that are required on graduate track assignments will be counted as "extra credit challenge questions" for undergraduate students.
  • Undergraduate Biology Track 
  • Undergraduate Quantitative Track 
  • Graduate Biology Track 
  • Graduate Quantitative Track 
Listed below are tentative assignment topics and due dates, which will be finalized during the term.
  • HW 0: Survey; due Wednesday, January 24, 2018 
  • HW 1: Genomic variant calling; due Wednesday, February 28, 2018 [Likely due a bit later]
  • HW 2: Biomedical data mining; due Wednesday, March 7, 2018 [Likely due a bit later]
  • HW 3: Protein simulations; due Wednesday, April 18, 2018
  • Final Presentation; due April 25, 2018
The teaching fellows this year prefer for programming assignments to be written in R, which is the programming language they are most familiar with. The teaching fellows will also accept assignments in Python but will be less able to award partial credit and offer troubleshooting help in Python. 
The course wants to encourage students to learn to use Yale's High Performance Computing Cluster since and GitHub, since these are important tools in biomedical data science. 
Late homework assignments will be marked down 10% per day.
We expect that many students will find some of the assignments challenging due to the technical and conceptual demands of biomedical data science, but ample help will be offered to students who ask for it.
Students who are less familiar with R, HPC, and/or GitHub are especially encouraged to begin their assignments early so that they have time to get help from the teaching fellows.

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