Syllabus

Index
Objectives Course Materials
Academic Integrity Students with Special Needs
Assignments Grades
Course Schedule Important Dates

Course Objectives:

  • Analyze primary literature in the field of bioinformatics and computational biology
  • Design and implement advanced data structures for computational biology
  • Design and implement advanced algorithms for computational biology
  • Increase proficiency in object-oriented and scripting programming languages

Course Materials:

There is no specific text for this course. Rather, we will be using free online materials and the scientific literature. See Resources. Students must have access to a computer (Mac, Windows, or Linux operating system) with administrative rights, i.e. can install software. Computers must have a minimum of 8 GB of RAM and a reliable internet connection.

Academic Integrity:

Plagiarism and cheating will not be tolerated (see University Policy) and will be reported to the college. STUDENTS FOUND TO PRESENT SOMEONE ELSE’S WORK AS THEIR OWN WILL RECEIVE ZERO POINTS FOR THE ASSIGNMENT. ANY STUDENT WHO REPEATS SUCH AN ACTION WILL RECEIVE A FAILING GRADE (F) FOR THE COURSE.

The Unix, Python, and R programming assignments at the beginning of the semester will be done independently (although you can get help from each other in class). Cheating includes submitting as your own work something that has been written by another person (classmate, tutor, web site, etc.). You must comment your code in your own words to demonstrate that you understand it. You may be asked questions about how your code works and your comments will help you explain. Inability to explain how your code works will result in a reduced grade.

After the first half of the course, the rest of the course will be spent working on a group project. As part of a group, you are expected to contribute to the same degree as your teammates. “Coasting” or letting your teammates carry you is plagiarism; you are taking credit for contributions that you did not make. This is on-par with presenting in a paper someone else’s idea/work as your own without proper citation. Plagiarism and cheating of any form will not be tolerated. A student suspected of such behavior will be assessed on an individual basis and action taken per the instructor’s evaluation of the seriousness of the behavior. Repeat offenders will earn an F for the course. As a contributing member of a group, it is your responsibility to ensure that all members are contributing. Issues that cannot be resolved within the group should be reported to the instructor. (Anonymous reports are welcome.)

Students with Special Needs: 

Any student requesting accommodations related to a disability or other condition is required to register with Student Accessibility Center (SAC), located in Sullivan Center, Suite 117. Students will provide professors with an accommodation notification from SAC, preferably within the first two weeks of class. Students are encouraged to meet with their professor individually in order to discuss their accommodations. All information will remain confidential. For more information or further assistance, please call 773.508.3700 or visit https://www.luc.edu/sac/.

Assignments:

Your grade will comprise several assignments as listed below. Details can be found on the Assignments page. LATE ASSIGNMENTS WILL NOT BE ACCEPTED.

Grading:

Assignment Points
Unix Command Line Exercises 2
ROSALIND 1-5 3
ROSALIND 6-10 5
ROSALIND 11-13 5
ROSALIND 14-15 5
ROSALIND 16-21 5
R Plotting Exercises 5
Mini-Project 15
Initial Group Project Presentation 10
5-minute Group Progress Presentations (2.5 points each, 2 total) 5
GitHub Repo Checks (2 points each, 3 total) 6
Application Note Rough Draft 3
Final Presentation 10
Final Project (code) 15
Final Application Note 10

More than 100 points are available. Your final grade will simply be the sum of all of the points you have earned over the course of the semester. Course grades are assigned according to the following scale:

Grade Minimum Points
A 93
A- 90
B+ 87
B 83
B- 80
C+ 77
C 73
C- 70
D+ 67
D 63

Course Schedule:

Date Topics Exercises/Tools DUE
Jan 14 Course Introduction, Command Line and SSH LSA, compbio.cs.luc.edu  
Jan 16 Python and Biopython Review, Sequences as Strings ROSALIND UNIX Command Line Exercises
Jan 21 Splicing, k-Mers, Sets   ROSALIND 1-5
Jan 23 Dynamic Programming Review    
Jan 28 Genome Assembly Algorithms   ROSALIND 6-10
Jan 30 Genome Assembly and Mapping Software SRA, SPAdes, bowtie2  
Feb 4 Transcriptomics kallisto, sleuth ROSALIND 11-13
Feb 6 Programming BLAST NCBIWWW.qblast, BLAST+  
Feb 11 FASTQ and Assembly Quality   ROSALIND 14-15
Feb 13 Introduction to GitHub Introduce Mini-projects Start Mini-project Repo  
Feb 18 Data visualization in R ggplot2 tutorial ROSALIND 16-21
Feb 20 R/Mini-project Workday rank projects  
Feb 25 Group Project Introduction assign groups R Plotting Exercises
Feb 27 Mini-project Workday   Mini-project DUE 11:59PM
Mar 3 No class: SPRING BREAK    
Mar 5 No class: SPRING BREAK    
Mar 10 Initial Group Presentation Details Start Wiki on your Project Repo: define individual roles & set weekly benchmarks  
Mar 12 Group Work    
Mar 17 Group Work - open Zoom/slack office hours comp383483.slack.com  
Mar 19 Group Work - open Zoom/slack office hours    
Mar 24 Initial Group Presentations   Initial Group Presentation
Mar 26 Initial Group Presentations   Initial Group Presentation Repo Check #1
Mar 31 Group Work    
Apr 2 Group Work, 5-min Group Progress Presentations   5-min Group Progress Presentation
Apr 7 Group Work    
Apr 9 Group Work, 5-min Group Progress Presentations   5-min Group Progress Presentation, Repo Check #2
Apr 14 Group Work   Rough Draft App Note
Apr 16 Discuss Rough Draft    
Apr 21 Group Work    
Apr 23 Final Presentations   Final Presentation, Repo Check #3
Apr 30 Final Projects DUE   Project code, Final Application Note

Important Dates:

See the Loyola academic calendar for registration and withdrawal dates.


This syllabus is subject to change during the course at the discretion of the instructor.