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.

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 third 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 with special needs or difficulties in learning and completing course assignments is strongly encouraged to contact the instructor as soon as possible. Please refer to the Student Handbook for student rights and available resources pertaining to assistance with special needs or disabilities.

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 Python Village 2
ROSALIND Bioinformatics Stronghold 1 5
ROSALIND Bioinformatics Stronghold 2 6
ROSALIND Bioinformatics Armory 5
Python Parser 5
R Plotting Exercises 5
Initial Group Project Presentation 10
5-minute Group Progress Presentations (5 points each, 2 total) 10
GitHub Repo Checks (2.5 points each, 4 total) 10
Application Note Rough Draft 5
Final Presentation 10
Final Project (code) 15
Final Application Note 10
TOTAL 100

Course grades are assigned according to the following scale:

Grade Minimum Points
A 90
A- 87
B+ 84
B 80
B- 77
C+ 74
C 70
C- 67
D+ 64
D 60

Course Schedule:

Date Topics Exercises DUE
Jan 16 Course Introduction, Command Line and SSH Connect to compbio.cs.luc.edu via guacomole, Command Line Bootcamp  
Jan 18 Intro to Python & ROSALIND LSA, Anaconda distribution, ROSALIND Python Village (Num 1-6) UNIX Command Line Exercises
Jan 23 LSA Help, Sequences as Strings Num 7-10: GC, RNA, PROT, SUBS  
Jan 25 Graphs and Motifs Num 11-13: GRPH, LCSM, MPRT Hints ROSALIND Python Village (Num 1-6)
Jan 30 ORFs, Splicing, k-Mers, oh my! Num 14-17: ORF, SPLC, TRAN, KMER Hints ROSALIND Bioinformatics Stronghold 1 (Num 7-13)
Feb 1 Constructing a de Bruijn Graph The future? Num 18-19: SETO, DBRU  
Feb 6 Dynamic Programming Num 20-21: EDIT, EDTA (BONUS: Num 22-23 LONG, GASM)  
Feb 8 BioPython, FASTQ Seq Files Num 24-30: INI, GBK, TFSQ, PHRE, FILT, BPHR, BFIL Hints ROSALIND Bioinformatics Stronghold 2 (Num 14-21, BONUS: 22-23)
Feb 13 Parsing in Python parse VCF file  
Feb 15 Data visualization in R ggplot2 tutorial ROSALIND Bioinformatics Armory (Num 24-30)
Feb 20 Group Project Introduction, Assign Groups and Projects   Python Parser, R Plotting Exercises
Feb 22 Introduction to GitHub, Group Meetings Start Project Repo  
Feb 27 Initial Group Presentation Details, Group Meetings Start Wiki on your Project Repo: define individual roles & set weekly benchmarks, Group Resources  
Mar 1 Group Meetings assign presentation date Repo Check #1
Mar 6 No class: SPRING BREAK    
Mar 8 No class: SPRING BREAK    
Mar 13 Initial Group Presentations   Initial Group Presentation
Mar 15 Initial Group Presentations   Initial Group Presentation
Mar 20 Group Work    
Mar 22 Group Work   Repo Check #2
Mar 27 Group Work    
Mar 29 Group Work, 5-min Group Progress Presentations   5-min Group Progress Presentation
Apr 3 Group Work    
Apr 5 Cross-team hacking   Repo Check #3
Apr 10 Group Work   Rough Draft Application Note
Apr 12 Group Work, 5-min Group Progress Presentations   5-min Group Progress Presentation
Apr 17 Group Work Discuss Rough Draft (Check Sakai), Final Presentation Dates  
Apr 19 Group Work   Repo Check #4
Apr 24 Final Presentations    
Apr 26 Final Presentations   Final Presentation, 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.