Overview

Catalog Description

Introduce the broad frontiers of bioinformatics topics from fundamental algorithms to practical tools. The main objective of the course is to provide the student with a solid foundation for conducting further research in bioinformatics and computational biology.

Class Meeting Time/Location

Time: Tue, Thu 11 am - 12:15 pm
Where: Ritter Hall R323
Online lectures via Zoom at the same classtime will begin starting with Monday, March 23 by COVID-19: Join https://slu.zoom.us/j/583209984 or by phone (Meeting ID: 583 209 984)

  • Recorded lecture link will be posted at Blackboard, but attending streaming lecture is desired.

Instructor

Tae-Hyuk (Ted) Ahn, Ph.D.
Assistant Professor
Department of Computer Science
Program of Bioinformatics and Computational Biology
Email: taehyuk.ahn@slu.edu
Office: 305 Ritter Hall (Lab: 302 Ritter Hall)
Phone: (314) 977-3633
Office Hour: Mon 10 am - 12 pm, Tue 3 pm - 4 pm or appointment by email

Supplemental Instructor Lead

Angela Wu
Email: angela.wu.1@slu.edu
Weekly Meeting Time: TBD

Credits/Pre-requisites

Credits: 3 Credits
Pre-requisites: The official prerequisite is a C- or better in BCB5200

Topical Outline

Introduction to Bioinformatics I and II are designed to introduce senior/graduate students to the fundamental concepts, methods, and research topics in Bioinformatics for analyzing large and complex biological data. In the course, we will intensely study specific research topics including genome assembly, metagenomics, RNA-Seq analysis, network analysis, and modeling and simulation. In the Introduction to Bioinformatics II course, students will be divided into groups and work on their proposed projects.

  • Introduce new trends of tools and environments for Bioinformatics
  • Genome assembly and genome/gene annotation
  • Metagenomics
  • RNA-Seq Analysis
  • Biological Modeling and Simulation

Student Learning Outcomes

After successfully complete this course, students are expected to:

  • Know fundamental concepts of bioinformatics;
  • Understand underlying basic bioinformatics algorithms;
  • Run bioinformatics applications and tools to study diverse and complex omics data;
  • Recognize how to apply different bioinformatics tools;
  • Understand cutting edge bioinformatics research topics;
  • Write pipeline scripts to automate existing applications;
  • Increase the ability to propose new algorithms and implement software tools;
  • Able to evaluate peer’s research works and understand the importance of peer review process;
  • Study the knowledge including substantive findings, as well as theoretical and methodological contributions to a particular topic in a literature;
  • Practice and improve presentation skills including logical format of contents, ordered in clear manner, effective information, and so on;
  • Conduct a research as a project to answer or analysis of a biological problem as a group for obtaining a successful, high-quality, collaborative experience.

Course Materials and Resources

Textbook

No textbook is required for this course. Assigned materials will be posted on class website. Optional reference books are as below:

Course website

https://biohpc.github.io/BCB5250S20/ will be used to announce schedules, slides, assignments, and news.

Rosalind

Students can enroll in the class with this link: http://rosalind.info/classes/enroll/c023b4d3bf/. It is free to register it. We will use the Rosalind for solving some programming assignments.

GitHub

Please follow my GitHub https://github.com/BioHPC. Course repository is https://github.com/BioHPC/BCB5250S20 and Couse Webpage is https://biohpc.github.io/BCB5250S20/

Jupyter Notebook (Jupyter Lab)

Blackboard:

Blackboard could be only used for posting grading scores.

Email

Face-to-face contact in class and in office hours is most desirable. Yet email is a convenient form of communication as well. I try to respond to email promptly, including at least once each evening when possible. Email contact over the weekend will likely be more sporadic, although I will be sure to check at least once.

If your question involves your progress on a current programming assignment, my response will be more informative if you can point out the specific problem you have encountered, and if I am able to see all of your source code. Therefore I strongly suggest that you either attach all relevant files to the email or submit preliminary versions of such files through git system.

Computer and Cell Phone Policy

Computers (laptops) will be an integral part of this course, both inside and outside of class. However, out of courtesy to both the instructor and other students, please do not use the laptops or computers for non-class related activity. In particular, you do not need to be using a computer unless an exercise or in class activity requiring them is in progress.

You are unlikely to need cell phones during the course of lecture. Please ensure that your cell phone is set to vibrate or silent during lecture, and do not send text messages of any kind.

Grading

Graded Work

  • Lab and Homework Assignments (40%)
    • Programming homework will be assigned in Rosalind. (10%)
    • There will be labs and assignments in a variety of format such as (but not exclusively) in-class labs and take-home assignments. (30%)
    • I usually give you a week time frame to submit the homework. Check the due in the online system.
  • Project (35%)
    • Midterm Report (10%)
      • Project Idea, Background, Plan, and Preliminary Results
    • Final Project Presentation and Final Report (25%)
      • Group Presentation (Evenly split talk!) (10%)
      • Report should include below sections (15%)
        • Abstract
        • Introduction
        • Methods
        • Results
        • Discussion
        • References
        • Contribution
  • Literature Review and Presentation (20%)
    • Submit literature review report (one paragraph or less than 1 page) for each reference paper with your critiques. (13%)
    • Present assigned reference paper and Q&A. (7%)
  • Attendance and Class Activities (5%)
    • Course attendance is not mandatory, but please try to attend all lectures. If you could not attend the lecture, please inform me in advance. I will check the attendance in multiple random days to give scores. Your class activities will be also evaluated.

Percentages

Letter grades will be based on each students overall percentage of awarded points according to the following formula.

Student percentage above 90% will result in a grade of A or better.
Student percentage above 87% will result in a grade of A- or better.
Student percentage above 83% will result in a grade of B+ or better.
Student percentage above 80% will result in a grade of B or better.
Student percentage above 77% will result in a grade of B- or better.
Student percentage above 73% will result in a grade of C+ or better.
Student percentage above 70% will result in a grade of C or better.
Student percentage above 67% will result in a grade of C- or better.
Student percentage above 60% will result in a grade of D or better.
Student percentage below 60% will result in a grade of F.

There will be no opportunity for “extra credit” to improve grades that have already been earned. Bargaining for grades will not be tolerated.

Extra Credit

In general, extra credit will not be assigned in this class.

Upon occasion (and solely at the instructor’s discretion), some small extra credit activities may be included, either by announcement in class or as part of an assignment. Please keep in mind that the extra credit is unlikely to significantly affect your grade; if you are concerned about your final grade, it is much better to focus your energy on the regular assignments. Extra credit is solely designed to provide an opportunity to students who wish to explore the topics further.

Late Homework

Late homework will suffer a penalty of 10% for every day they are late. For example, homework which is submitted two days late is worth at most 80% of the total credit.

In unusual circumstances, such as extreme illness or injury (documented by a doctor’s note), family emergencies, etc., please contact the instructor as early as possible to arrange accomidations.

Regrade Requests

I am happy to regrade any assignmentss or exam problems which you think were unfair or incorrect. Please bring me the original assignment, plus a written explanation of your question or complaint, within two weeks of the time the paper in question is graded and returned to you.

Policies and Resources

Academic Integrity

In the context of this course, I encourage students to discuss general course material, which includes studying for exams, sharing notes if a student must miss class, and working on any practice problems which are assigned. You are also allowed to turn in homework assignments in pairs. I also encourage you to discuss problems with other students, but please be careful to write up all solutions separately and do not copy any material from another student. As a good rule of thumb, make sure to write your solutions without using any notes or papers written while talking to anyone other than your partner. Remember, you will be on your own in the exam, so it is in your own best interest to make sure that you really understand the material and can solve each problem on your own!

You are allowed to use outside sources of information in this class, including textbooks and webpages. If the complete and correct answer is on page 263 of the lecture notes, the best solution you can submit is “See page 263 of the lecture notes.” Period. However, if you find a solution from any other source, such as a web page, a journal paper, a different algorithms textbook, or your mom, you must rewrite the solution in your own words, and you must properly cite your sources. Assume the grader has access to all the official course material, but nothing else. While we strongly encourge you to use any outside source at your disposal, please remember that the homework is supposed to demonstrate that you understand of the material, not just how to use Google. (In particular, if you blindly copy an incorrect solution, don’t expect to get very many points for it!)

Students who violate academic integrity policies will be reported to the department, particularly in cases where relevant sources are not cited or in cases of direct copying of another student’s work. First time offenses on homework will result in a minimum of a failing grade on the assignment in question, with egregious or repeated offenses resulting in failure in the course. In addition, students may be referred to the College of Arts and Sciences for further disciplinary action.

A statement of minimum standards for student academic integrity at Saint Louis University is described here; I expect full compliance with the policies described.

Attendance

Our course follows university level attendance policy.

Title IX

Saint Louis University and its faculty are committed to supporting our students and seeking an environment that is free of bias, discrimination and harassment. If you have encountered any form of sexual misconduct (e.g. sexual assault, sexual harassment, stalking, domestic or dating violence), we encourage you to report this to the University. If you speak with a faculty member about an incident of misconduct, that faculty member must notify SLU’s Title IX coordinator, Anna R. Kratky (DuBourg Hall, room 36; anna.kratky@slu.edu; 314-977-3886) and share the basic facts of your experience with her. The Title IX coordinator will then be available to assist you in understanding all of your options and in connecting you with all possible resources on and off campus.

If you wish to speak with a confidential source, you may contact the counselors at the University Counseling Center at 314-977-TALK. To view SLU’s sexual misconduct policy and for resources, please visit the Office of the General Counsel.

Please see the College of Arts and Sciences Syllabi statements. I am more than happy to accomodate any requested accommodations; come see me or get in touch via email if you have any questions.

Disability Services

Students with a documented disability who wish to request academic accommodations must contact Disability Services to discuss accommodation requests and eligibility requirements. Once successfully registered, the student also must notify the course instructor that they wish to access accommodations in the course.

Please contact Disability Services, located within the Student Success Center, at Disability_services@slu.edu or 314-977-3484 to schedule an appointment. Confidentiality will be observed in all inquiries. Once approved, information about the student’s eligibility for academic accommodations will be shared with course instructors via email from Disability Services and viewed within Banner via the instructor’s course roster.

Note: Students who do not have a documented disability but who think they may have one are encouraged to contact Disability Services.

Student Success Center

In recognition that people learn in a variety of ways and that learning is influenced by multiple factors (e.g., prior experience, study skills, learning disability), resources to support student success are available on campus. The Student Success Center assists students with academic-related services and is located in the Busch Student Center (Suite, 331). Students can visit the Student Success Center to learn more about tutoring services, university writing services, disability services, and academic coaching.

University Writing Services

Students are encouraged to take advantage of University Writing Services in the Student Success Center; getting feedback benefits writers at all skill levels. Trained writing consultants can help with writing projects, multimedia projects, and oral presentations. University Writing Services offers one-on-one consultations that address everything from brainstorming and developing ideas to crafting strong sentences and documenting sources. For more information, visit the Student Success Center or call the Student Success Center at 314-977-3484.

Basic Needs Security

Students in personal or academic distress and/or who may be specifically experiencing challenges such as securing food or difficulty navigating campus resources, and who believe this may affect their performance in the course, are encouraged to contact the Dean of Students Office (deanofstudents@slu.edu or 314-977-9378) for support. Furthermore, please notify the instructor if you are comfortable in doing so, as this will enable them to assist you with finding the resources you may need.