University of Washington, Tacoma

TCSS 478: Fundamentals of Bioinformatics

Course Logistics

Winter 2019 January 3, 2019

Course Description: Introduces basic concepts and techniques used in the analysis of
biological data, as well as applications of computational techniques in biological applications. No
background in biology is required. Students will learn biology concepts and vocabulary. The
programming language R primarily will be used.

Instructor:
Ka Yee Yeung
[email protected]
CP 232

Course web site: canvas.uw.edu

Class Time and Place: MW 8am-9:20pm ADMC GWP 216

Recorded lectures on Canvas Panopto

Office hours: 9:30am-10:30am Wednesdays @ CP232.

Communication: I don’t read my emails through canvas. Email me at [email protected] directly.

I will also send announcements via emails. For topics of general interest to the entire class,
please use the “Discussion” mechanism via canvas. You are expected to check your email,
canvas announcements and discussion board regularly.

Learning objectives: Upon successful completion of this course, students will be able to:
• Discuss the contribution of computational methods to solve biological problems.
• Understand fundamental concepts of bioinformatics.
• Acquire hands-on experience using R for data analyses.
• Discuss various types of big data in biology.
• Acquire hands-on experience using bioinformatics resources, including PubMed for
literature search and downloading biomedical data from various databases.

Prerequisite: TCSS 343.

Textbook: An Introduction to Statistical Learning with Applications in R, by James, Witten,

Hastie and Tibshirani. The pdf of this textbook is available for free from http://www-
bcf.usc.edu/~gareth/ISL/.

What you can expect from this class. This is a project-oriented class. There will be no final
exam. Instead, there will be one quiz, group assignments, group final project, class
presentations and project reports. I will provide links to additional reading materials consisting
mostly of journal papers.

Grading:
Group assignments (3 * 10%) 30%
Quiz 20%
Mid quarter group project: presentations 10%
Final group project: reports and presentations 40%

The following table will be used; it shows the minimum decimal grades for the specified
percentage scores. Decimal grades may be adjusted upward from these minimum grades.

Grade Score Grade Score Grade Score Grade Score

4.0 98-100 3.4 89 2.4 79 1.4 69

3.9 95-97 3.3 88 2.3 78 1.3 68

3.8 93-94 3.2 87 2.2 77 1.2 67

3.7 92 3.1 86 2.1 76 1.1 66

3.6 91 3.0 85 2.0 75 1.0 65

3.5 90 2.9 84 1.9 74 0.9 64

2.8 83 1.8 73 0.8 62-63

2.7 82 1.7 72 0.7 61

2.6 81 1.6 71 0.0 0-60

2.5 80 1.5 70

Late homework/assignments/project (up to 24-hour late) will be accepted with a 20% penalty.
All homework/assignments/projects will be distributed and submitted through canvas.

Collaboration: assignments and projects. You are allowed to work in groups of 1-3 for the
assignments and final project. If you would like to work individually, it is ok. However, you are
strongly encouraged to work in groups, and the workload assumes that each team has more
than one student. You are expected to manage personnel issues within your own group.
We expect a steep learning curve to master the R programming language in the first couple of
weeks of the course. Working in groups enables students to help each other in learning R.

You are allowed to change your groups during the course.

In your reports and presentations, you are expected to document the division of labor (i.e. who
does what, and the challenges tackled by each individual). All team members must consent to
the content of the report before submission. By default, all team members get the same grade.
But I reserve the right to adjust the grade of each individual based on the contribution.

Classroom Policy. You can expect to write R code during class. You are encouraged to use
your tablets and laptops during class as long as the sound and ringer are turned OFF.
However, you are expected to look away from your screen to participate in class discussion.
You can also bring food and covered beverages to class.

Cheating: Cheating, either on an exam or turning in work (including code) that is not your own,
will not be tolerated. Suspected cheating cases will be reported to the University Conduct
Officer, Ed Mirecki.

Grade Appeal Procedure: Except in case of error, I cannot change a grade that has been
submitted to the Registrar.

Plagiarism and academic honesty

A major part of your experience at UW Tacoma will be reading, synthesizing, and using the
knowledge and ideas of others. To plagiarize is to use the ideas––or unique phrasing of those
ideas––without acknowledging that they originate from someone or someplace other than you.
Attributing where you get your information builds your own authority to speak on that topic and
provides valuable backing to the arguments you make. Attribution also distinguishes your ideas
and words from those of others who came before you. At the University of Washington,
plagiarism is a violation of the student conduct code, and the consequences can be serious.
Though citing, quoting, and paraphrasing can be confusing at first, it is essential for your
success at UWT that you familiarize yourself with these important conventions of academic
writing. Additionally, plagiarism can be understood differently in various disciplines. For
instance, the ways in which one summarizes others’ ideas in texts, or attributes information from
texts in one’s own paper, are not the same in the sciences as they are in the humanities, or the
social sciences. This means it is vital that you understand the specific expectations and
guidelines for writing that will help you avoid plagiarizing in this class. If you have questions
about what amounts to plagiarism, you are strongly encouraged to seek guidance from faculty
and the Teaching and Learning Center as soon as possible.

Inclement Weather Procedure: Call 253-383-INFO or check the UW Tacoma homepage to

determine whether campus operations have been suspended or delayed. If not, but driving
conditions remain problematic, check your emails and announcements on the canvas
course page. The canvas page should provide information on whether a particular class will be
held or not, and/or the status of pending assignments. If there is no announcement on canvas
and the student is still unable to determine whether a class(es) will be held, call the program
office number for updated information.

Teaching and Learning Center: The Teaching and Learning Center (TLC) offers free
academic support for students at all levels. We offer one-on-one consultations and group
workshops in writing, math, statistics, science, and Spanish. We also work with students on
questions about English grammar & vocabulary, reading, and learning strategies. We are
located in Snoqualmie 260 and online. Our schedules for appointments and drop-in visits are
posted on our website at www.tacoma.uw.edu/tlc . For special needs or subject tutoring
requests, please email [email protected] or call (253) 692-4417.

Student Counseling Center: The Student Counseling Center is an on-campus resource that
provides counseling to the students at UW Tacoma. There is no fee charged for Student
Counseling Center services for all enrolled UW Tacoma students. For more information, see
http://www.tacoma.washington.edu/studentaffairs/shw/scc_about.cfm

Disability Resources for Students (Office of Student Success):

The University of Washington Tacoma is committed to making physical facilities and
instructional programs accessible to students with disabilities. Disability Resources for Students
(DRS), located in MAT 354, functions as the focal point for coordination of services for students
with disabilities. If you have a physical, emotional, or mental disability that "substantially limits
one or more major life activities [including walking, seeing, hearing, speaking, breathing,
learning and working]," and will require accommodation in this class, please contact DRS at
253-692-4508, or email at [email protected] for assistance.

Campus Safety Information

Escort Service
Safety escorts are avaiable 24 hours a day, 7 days a week, there is no time limit. Call the main
office line at 253-692-4416.
In case of a fire alarm
During an emergency evacuation, take your valuables ONLY if it is safe to do so. You could put
yourself or someone else at risk by delaying your exit. Plan to return to class once the alarm has
stopped. Do not return until you have received an all-clear from somebody "official," the web or
email.
In case of an earthquake
DROP, COVER, and HOLD. Once the shaking stops, take your valuables and leave the
building. Do not plan to return for the rest of the day. Do not return to the building until you have
received an all-clear from somebody "official," the web or email.
For more information:
● Campus Safety's "What to do in an emergency" website .
● SafeCampus website

Emergency Aid -Life can be unpredictable. Unexpected costs and needs can cause significant
stress and impact student academic success and personal well being. That’s why the three
campuses of the University of Washington have Emergency Aid to support currently enrolled
UW students.

The Pantry - Providing supplemental, nutritional, and culturally relevant food as well as hygiene
items to all UWT students and their families. Stop by during weekly drop-in hours (DOUGAN
104) Monday-Friday, 9am-5pm.

Please also consult the syllabi service statements recommended by the UWT Faculty Assembly
regarding UWT resources, policies and expectations: https://www.tacoma.uw.edu/faculty-
assembly/syllabi-service-statements
TCSS 478 Lecture Schedule (dated 1/3/2019)

Subject to change! Check the canvas front page frequently for the latest schedule.

IMPORTANT: You are responsible for understanding all of the assigned reading material. The
reading refers to the textbook unless otherwise stated. I would specify the section number if
part of the chapter is not covered. Otherwise, I mean the entire chapter by default.
Date Lecture Topics Reading
Introduction to the course.
Textbook Ch. 2.3.
Week 1 Short introduction to molecular biology.
Larry Hunter's article: Molecular
1/7, 1/9, 1/11 Bioinformatics resources and tools on the
Biology for Computer Scientists.
web.
Jupyter notebooks.
Introduction to R.
Week 2
Review on probability and statistics. Textbook Ch. 3.
1/14, 1/16, 1/18
Data exploration and visualization.
Linear regression.
Week 3 Regression analyses.
Textbook Ch. 4.1, 4.2, 4.3.
1/23, 1/25 Using R to build regression models.
Big data in biology.
Next generation sequencing technology
Week 4
and applications.
1/28, 1/30, 2/1
Reproducibility of research. Creating and
sharing bioinformatics workflows.
Introduction to Bioconductor.
Week 5
Gene expression data and analysis.
2/4, 2/6, 2/8
Differential expression.
Week 6
Mid-quarter class presentations.
2/11, 2/13
Week 6 Personalized medicine: applications and
2/15 methods.
Tools for building predictive models.
Week 7 Logistic regression.
2/20, 2/22 Classification and feature selection. Model
selection.
Quiz.
Week 8
Sequence analysis.
2/25, 2/27, 3/1
Algorithms for sequence alignment.
Week 9 Graphs and networks.
3/ 4, 3/6, 3/8 Systems biology.
Week 10
Final project: Student presentations.
3/11, 3/13, 3/15